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Naghavi M, Mestrovic T, Gray A, Gershberg Hayoon A, Swetschinski LR, Robles Aguilar G, Davis Weaver N, Ikuta KS, Chung E, Wool EE, Han C, Araki DT, Albertson SB, Bender R, Bertolacci G, Browne AJ, Cooper BS, Cunningham MW, Dolecek C, Doxey M, Dunachie SJ, Ghoba S, Haines-Woodhouse G, Hay SI, Hsu RL, Iregbu KC, Kyu HH, Ledesma JR, Ma J, Moore CE, Mosser JF, Mougin V, Naghavi P, Novotney A, Rosenthal VD, Sartorius B, Stergachis A, Troeger C, Vongpradith A, Walters MK, Wunrow HY, Murray CJL. Global burden associated with 85 pathogens in 2019: a systematic analysis for the Global Burden of Disease Study 2019. Lancet Infect Dis 2024:S1473-3099(24)00158-0. [PMID: 38640940 DOI: 10.1016/s1473-3099(24)00158-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 04/21/2024]
Abstract
BACKGROUND Despite a global epidemiological transition towards increased burden of non-communicable diseases, communicable diseases continue to cause substantial morbidity and mortality worldwide. Understanding the burden of a wide range of infectious diseases, and its variation by geography and age, is pivotal to research priority setting and resource mobilisation globally. METHODS We estimated disability-adjusted life-years (DALYs) associated with 85 pathogens in 2019, globally, regionally, and for 204 countries and territories. The term pathogen included causative agents, pathogen groups, infectious conditions, and aggregate categories. We applied a novel methodological approach to account for underlying, immediate, and intermediate causes of death, which counted every death for which a pathogen had a role in the pathway to death. We refer to this measure as the burden associated with infection, which was estimated by combining different sources of information. To compare the burden among all pathogens, we used pathogen-specific ratios to incorporate the burden of immediate and intermediate causes of death for pathogens modelled previously by the GBD. We created the ratios by using multiple cause of death data, hospital discharge data, linkage data, and minimally invasive tissue sampling data to estimate the fraction of deaths coming from the pathway to death chain. We multiplied the pathogen-specific ratios by age-specific years of life lost (YLLs), calculated with GBD 2019 methods, and then added the adjusted YLLs to age-specific years lived with disability (YLDs) from GBD 2019 to produce adjusted DALYs to account for deaths in the chain. We used standard GBD methods to calculate 95% uncertainty intervals (UIs) for final estimates of DALYs by taking the 2·5th and 97·5th percentiles across 1000 posterior draws for each quantity of interest. We provided burden estimates pertaining to all ages and specifically to the under 5 years age group. FINDINGS Globally in 2019, an estimated 704 million (95% UI 610-820) DALYs were associated with 85 different pathogens, including 309 million (250-377; 43·9% of the burden) in children younger than 5 years. This burden accounted for 27·7% (and 65·5% in those younger than 5 years) of the previously reported total DALYs from all causes in 2019. Comparing super-regions, considerable differences were observed in the estimated pathogen-associated burdens in relation to DALYs from all causes, with the highest burden observed in sub-Saharan Africa (314 million [270-368] DALYs; 61·5% of total regional burden) and the lowest in the high-income super-region (31·8 million [25·4-40·1] DALYs; 9·8%). Three leading pathogens were responsible for more than 50 million DALYs each in 2019: tuberculosis (65·1 million [59·0-71·2]), malaria (53·6 million [27·0-91·3]), and HIV or AIDS (52·1 million [46·6-60·9]). Malaria was the leading pathogen for DALYs in children younger than 5 years (37·2 million [17·8-64·2]). We also observed substantial burden associated with previously less recognised pathogens, including Staphylococcus aureus and specific Gram-negative bacterial species (ie, Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, Acinetobacter baumannii, and Helicobacter pylori). Conversely, some pathogens had a burden that was smaller than anticipated. INTERPRETATION Our detailed breakdown of DALYs associated with a comprehensive list of pathogens on a global, regional, and country level has revealed the magnitude of the problem and helps to indicate where research funding mismatch might exist. Given the disproportionate impact of infection on low-income and middle-income countries, an essential next step is for countries and relevant stakeholders to address these gaps by making targeted investments. FUNDING Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Health and Social Care using UK aid funding managed by the Fleming Fund.
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Bender RG, Sirota SB, Swetschinski LR, Dominguez RMV, Novotney A, Wool EE, Ikuta KS, Vongpradith A, Rogowski ELB, Doxey M, Troeger CE, Albertson SB, Ma J, He J, Maass KL, A.F.Simões E, Abdoun M, Abdul Aziz JM, Abdulah DM, Abu Rumeileh S, Abualruz H, Aburuz S, Adepoju AV, Adha R, Adikusuma W, Adra S, Afraz A, Aghamiri S, Agodi A, Ahmadzade AM, Ahmed H, Ahmed A, Akinosoglou K, AL-Ahdal TMA, Al-amer RM, Albashtawy M, AlBataineh MT, Alemi H, Al-Gheethi AAS, Ali A, Ali SSS, Alqahtani JS, AlQudah M, Al-Tawfiq JA, Al-Worafi YM, Alzoubi KH, Amani R, Amegbor PM, Ameyaw EK, Amuasi JH, Anil A, Anyanwu PE, Arafat M, Areda D, Arefnezhad R, Atalell KA, Ayele F, Azzam AY, Babamohamadi H, Babin FX, Bahurupi Y, Baker S, Banik B, Barchitta M, Barqawi HJ, Basharat Z, Baskaran P, Batra K, Batra R, Bayileyegn NS, Beloukas A, Berkley JA, Beyene KA, Bhargava A, Bhattacharjee P, Bielicki JA, Bilalaga MM, Bitra VR, Brown CS, Burkart K, Bustanji Y, Carr S, Chahine Y, Chattu VK, Chichagi F, Chopra H, Chukwu IS, Chung E, Dadana S, Dai X, Dandona L, Dandona R, Darban I, Dash NR, Dashti M, Dashtkoohi M, Dekker DM, Delgado-Enciso I, Devanbu VGC, Dhama K, Diao N, Do THP, Dokova KG, Dolecek C, Dziedzic AM, Eckmanns T, Ed-Dra A, Efendi F, Eftekharimehrabad A, Eyre DW, Fahim A, Feizkhah A, Felton TW, Ferreira N, Flor LS, Gaihre S, Gebregergis MW, Gebrehiwot M, Geffers C, Gerema U, Ghaffari K, Goldust M, Goleij P, Guan SY, Gudeta MD, Guo C, Gupta VB, Gupta I, Habibzadeh F, Hadi NR, Haeuser E, Hailu WB, Hajibeygi R, Haj-Mirzaian A, Haller S, Hamiduzzaman M, Hanifi N, Hansel J, Hasnain MS, Haubold J, Hoan NQ, Huynh HH, Iregbu KC, Islam MR, Jafarzadeh A, Jairoun AA, Jalili M, Jomehzadeh N, Joshua CE, Kabir MA, Kamal Z, Kanmodi KK, Kantar RS, Karimi Behnagh A, Kaur N, Kaur H, Khamesipour F, Khan MN, Khan suheb MZ, Khanal V, Khatab K, Khatib MN, Kim G, Kim K, Kitila ATT, Komaki S, Krishan K, Krumkamp R, Kuddus MA, Kurniasari MD, Lahariya C, Latifinaibin K, Le NHH, Le TTT, Le TDT, Lee SW, LEPAPE A, Lerango TL, Li MC, Mahboobipour AA, Malhotra K, Mallhi TH, Manoharan A, Martinez-Guerra BA, Mathioudakis AG, Mattiello R, May J, McManigal B, McPhail SM, Mekene Meto T, Mendez-Lopez MAM, Meo SA, Merati M, Mestrovic T, Mhlanga L, Minh LHN, Misganaw A, Mishra V, Misra AK, Mohamed NS, Mohammadi E, Mohammed M, Mohammed M, Mokdad AH, Monasta L, Moore CE, Motappa R, Mougin V, Mousavi P, Mulita F, Mulu AA, Naghavi P, Naik GR, Nainu F, Nair TS, Nargus S, Negaresh M, Nguyen HTH, Nguyen DH, Nguyen VT, Nikolouzakis TK, Noman EA, Nri-Ezedi CA, Odetokun IA, Okwute PG, Olana MD, Olanipekun TO, Olasupo OO, Olivas-Martinez A, Ordak M, Ortiz-Brizuela E, Ouyahia A, Padubidri JR, Pak A, Pandey A, Pantazopoulos I, Parija PP, Parikh RR, Park S, Parthasarathi A, Pashaei A, Peprah P, Pham HT, Poddighe D, Pollard A, Ponce-De-Leon A, Prakash PY, Prates EJS, Quan NK, Raee P, Rahim F, Rahman M, Rahmati M, Ramasamy SK, Ranjan S, Rao IR, Rashid AM, Rattanavong S, Ravikumar N, Reddy MMRK, Redwan EMM, Reiner RC, Reyes LF, Roberts T, Rodrigues M, Rosenthal VD, Roy P, Runghien T, Saeed U, Saghazadeh A, Saheb Sharif-Askari N, Saheb Sharif-Askari F, Sahoo SS, Sahu M, Sakshaug JW, Salami AA, Saleh MA, Salehi omran H, Sallam M, Samadzadeh S, Samodra YL, Sanjeev RK, Sarasmita MA, Saravanan A, Sartorius B, Saulam J, Schumacher AE, Seyedi SA, Shafie M, Shahid S, Sham S, Shamim MA, Shamshirgaran MA, Shastry RP, Sherchan SP, Shiferaw D, Shittu A, Siddig EE, Sinto R, Sood A, Sorensen RJD, Stergachis A, Stoeva TZ, Swain CK, Szarpak L, Tamuzi JL, Temsah MH, Tessema MBT, Thangaraju P, Tran NM, Tran NH, Tumurkhuu M, Ty SS, Udoakang AJ, Ulhaq I, Umar TP, Umer AA, Vahabi SM, Vaithinathan AG, Van den Eynde J, Walson JL, Waqas M, Xing Y, Yadav MK, Yahya G, Yon DK, Zahedi Bialvaei A, Zakham F, Zeleke AM, Zhai C, Zhang Z, Zhang H, Zielińska M, Zheng P, Aravkin AY, Vos T, Hay SI, Mosser JF, Lim SS, Naghavi M, Murray CJL, Kyu HH. Global, regional, and national incidence and mortality burden of non-COVID-19 lower respiratory infections and aetiologies, 1990-2021: a systematic analysis from the Global Burden of Disease Study 2021. Lancet Infect Dis 2024:S1473-3099(24)00176-2. [PMID: 38636536 DOI: 10.1016/s1473-3099(24)00176-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/19/2024] [Accepted: 03/07/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Lower respiratory infections (LRIs) are a major global contributor to morbidity and mortality. In 2020-21, non-pharmaceutical interventions associated with the COVID-19 pandemic reduced not only the transmission of SARS-CoV-2, but also the transmission of other LRI pathogens. Tracking LRI incidence and mortality, as well as the pathogens responsible, can guide health-system responses and funding priorities to reduce future burden. We present estimates from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021 of the burden of non-COVID-19 LRIs and corresponding aetiologies from 1990 to 2021, inclusive of pandemic effects on the incidence and mortality of select respiratory viruses, globally, regionally, and for 204 countries and territories. METHODS We estimated mortality, incidence, and aetiology attribution for LRI, defined by the GBD as pneumonia or bronchiolitis, not inclusive of COVID-19. We analysed 26 259 site-years of mortality data using the Cause of Death Ensemble model to estimate LRI mortality rates. We analysed all available age-specific and sex-specific data sources, including published literature identified by a systematic review, as well as household surveys, hospital admissions, health insurance claims, and LRI mortality estimates, to generate internally consistent estimates of incidence and prevalence using DisMod-MR 2.1. For aetiology estimation, we analysed multiple causes of death, vital registration, hospital discharge, microbial laboratory, and literature data using a network analysis model to produce the proportion of LRI deaths and episodes attributable to the following pathogens: Acinetobacter baumannii, Chlamydia spp, Enterobacter spp, Escherichia coli, fungi, group B streptococcus, Haemophilus influenzae, influenza viruses, Klebsiella pneumoniae, Legionella spp, Mycoplasma spp, polymicrobial infections, Pseudomonas aeruginosa, respiratory syncytial virus (RSV), Staphylococcus aureus, Streptococcus pneumoniae, and other viruses (ie, the aggregate of all viruses studied except influenza and RSV), as well as a residual category of other bacterial pathogens. FINDINGS Globally, in 2021, we estimated 344 million (95% uncertainty interval [UI] 325-364) incident episodes of LRI, or 4350 episodes (4120-4610) per 100 000 population, and 2·18 million deaths (1·98-2·36), or 27·7 deaths (25·1-29·9) per 100 000. 502 000 deaths (406 000-611 000) were in children younger than 5 years, among which 254 000 deaths (197 000-320 000) occurred in countries with a low Socio-demographic Index. Of the 18 modelled pathogen categories in 2021, S pneumoniae was responsible for the highest proportions of LRI episodes and deaths, with an estimated 97·9 million (92·1-104·0) episodes and 505 000 deaths (454 000-555 000) globally. The pathogens responsible for the second and third highest episode counts globally were other viral aetiologies (46·4 million [43·6-49·3] episodes) and Mycoplasma spp (25·3 million [23·5-27·2]), while those responsible for the second and third highest death counts were S aureus (424 000 [380 000-459 000]) and K pneumoniae (176 000 [158 000-194 000]). From 1990 to 2019, the global all-age non-COVID-19 LRI mortality rate declined by 41·7% (35·9-46·9), from 56·5 deaths (51·3-61·9) to 32·9 deaths (29·9-35·4) per 100 000. From 2019 to 2021, during the COVID-19 pandemic and implementation of associated non-pharmaceutical interventions, we estimated a 16·0% (13·1-18·6) decline in the global all-age non-COVID-19 LRI mortality rate, largely accounted for by a 71·8% (63·8-78·9) decline in the number of influenza deaths and a 66·7% (56·6-75·3) decline in the number of RSV deaths. INTERPRETATION Substantial progress has been made in reducing LRI mortality, but the burden remains high, especially in low-income and middle-income countries. During the COVID-19 pandemic, with its associated non-pharmaceutical interventions, global incident LRI cases and mortality attributable to influenza and RSV declined substantially. Expanding access to health-care services and vaccines, including S pneumoniae, H influenzae type B, and novel RSV vaccines, along with new low-cost interventions against S aureus, could mitigate the LRI burden and prevent transmission of LRI-causing pathogens. FUNDING Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Health and Social Care (UK).
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Naghavi M, Ong KL, Aali A, Ababneh HS, Abate YH, Abbafati C, Abbasgholizadeh R, Abbasian M, Abbasi-Kangevari M, Abbastabar H, Abd ElHafeez S, Abdelmasseh M, Abd-Elsalam S, Abdelwahab A, Abdollahi M, Abdollahifar MA, Abdoun M, Abdulah DM, Abdullahi A, Abebe M, Abebe SS, Abedi A, Abegaz KH, Abhilash ES, Abidi H, Abiodun O, Aboagye RG, Abolhassani H, Abolmaali M, Abouzid M, Aboye GB, Abreu LG, Abrha WA, Abtahi D, Abu Rumeileh S, Abualruz H, Abubakar B, Abu-Gharbieh E, Abu-Rmeileh NME, Aburuz S, Abu-Zaid A, Accrombessi MMK, Adal TG, Adamu AA, Addo IY, Addolorato G, Adebiyi AO, Adekanmbi V, Adepoju AV, Adetunji CO, Adetunji JB, Adeyeoluwa TE, Adeyinka DA, Adeyomoye OI, Admass BAA, Adnani QES, Adra S, Afolabi AA, Afzal MS, Afzal S, Agampodi SB, Agasthi P, Aggarwal M, Aghamiri S, Agide FD, Agodi A, Agrawal A, Agyemang-Duah W, Ahinkorah BO, Ahmad A, Ahmad D, Ahmad F, Ahmad MM, Ahmad S, Ahmad S, Ahmad T, Ahmadi K, Ahmadzade AM, Ahmed A, Ahmed A, Ahmed H, Ahmed LA, Ahmed MS, Ahmed MS, Ahmed MB, Ahmed SA, Ajami M, Aji B, Akara EM, Akbarialiabad H, Akinosoglou K, Akinyemiju T, Akkaif MA, Akyirem S, Al Hamad H, Al Hasan SM, Alahdab F, Alalalmeh SO, Alalwan TA, Al-Aly Z, Alam K, Alam M, Alam N, Al-amer RM, Alanezi FM, Alanzi TM, Al-Azzam S, Albakri A, Albashtawy M, AlBataineh MT, Alcalde-Rabanal JE, Aldawsari KA, Aldhaleei WA, Aldridge RW, Alema HB, Alemayohu MA, Alemi S, Alemu YM, Al-Gheethi AAS, Alhabib KF, Alhalaiqa FAN, Al-Hanawi MK, Ali A, Ali A, Ali L, Ali MU, Ali R, Ali S, Ali SSS, Alicandro G, Alif SM, Alikhani R, Alimohamadi Y, Aliyi AA, Aljasir MAM, Aljunid SM, Alla F, Allebeck P, Al-Marwani S, Al-Maweri SAA, Almazan JU, Al-Mekhlafi HM, Almidani L, Almidani O, Alomari MA, Al-Omari B, Alonso J, Alqahtani JS, Alqalyoobi S, Alqutaibi AY, Al-Sabah SK, Altaany Z, Altaf A, Al-Tawfiq JA, Altirkawi KA, Aluh DO, Alvis-Guzman N, Alwafi H, Al-Worafi YM, Aly H, Aly S, Alzoubi KH, Amani R, Amare AT, Amegbor PM, Ameyaw EK, Amin TT, Amindarolzarbi A, Amiri S, Amirzade-Iranaq MH, Amu H, Amugsi DA, Amusa GA, Ancuceanu R, Anderlini D, Anderson DB, Andrade PP, Andrei CL, Andrei T, Angus C, Anil A, Anil S, Anoushiravani A, Ansari H, Ansariadi A, Ansari-Moghaddam A, Antony CM, Antriyandarti E, Anvari D, Anvari S, Anwar S, Anwar SL, Anwer R, Anyasodor AE, Aqeel M, Arab JP, Arabloo J, Arafat M, Aravkin AY, Areda D, Aremu A, Aremu O, Ariffin H, Arkew M, Armocida B, Arndt MB, Ärnlöv J, Arooj M, Artamonov AA, Arulappan J, Aruleba RT, Arumugam A, Asaad M, Asadi-Lari M, Asgedom AA, Asghariahmadabad M, Asghari-Jafarabadi M, Ashraf M, Aslani A, Astell-Burt T, Athar M, Athari SS, Atinafu BTT, Atlaw HW, Atorkey P, Atout MMW, Atreya A, Aujayeb A, Ausloos M, Avan A, Awedew AF, Aweke AM, Ayala Quintanilla BP, Ayatollahi H, Ayuso-Mateos JL, Ayyoubzadeh SM, Azadnajafabad S, Azevedo RMS, Azzam AY, B DB, Babu AS, Badar M, Badiye AD, Baghdadi S, Bagheri N, Bagherieh S, Bah S, Bahadorikhalili S, Bahmanziari N, Bai R, Baig AA, Baker JL, Bako AT, Bakshi RK, Balakrishnan S, Balasubramanian M, Baltatu OC, Bam K, Banach M, Bandyopadhyay S, Banik PC, Bansal H, Bansal K, Barbic F, Barchitta M, Bardhan M, Bardideh E, Barker-Collo SL, Bärnighausen TW, Barone-Adesi F, Barqawi HJ, Barrero LH, Barrow A, Barteit S, Barua L, Basharat Z, Bashiri A, Basiru A, Baskaran P, Basnyat B, Bassat Q, Basso JD, Basting AVL, Basu S, Batra K, Baune BT, Bayati M, Bayileyegn NS, Beaney T, Bedi N, Beghi M, Behboudi E, Behera P, Behnoush AH, Behzadifar M, Beiranvand M, Bejarano Ramirez DF, Béjot Y, Belay SA, Belete CM, Bell ML, Bello MB, Bello OO, Belo L, Beloukas A, Bender RG, Bensenor IM, Beran A, Berezvai Z, Berhie AY, Berice BN, Bernstein RS, Bertolacci GJ, Bettencourt PJG, Beyene KA, Bhagat DS, Bhagavathula AS, Bhala N, Bhalla A, Bhandari D, Bhangdia K, Bhardwaj N, Bhardwaj P, Bhardwaj PV, Bhargava A, Bhaskar S, Bhat V, Bhatti GK, Bhatti JS, Bhatti MS, Bhatti R, Bhutta ZA, Bikbov B, Bishai JD, Bisignano C, Bisulli F, Biswas A, Biswas B, Bitaraf S, Bitew BD, Bitra VR, Bjørge T, Boachie MK, Boampong MS, Bobirca AV, Bodolica V, Bodunrin AO, Bogale EK, Bogale KA, Bohlouli S, Bolarinwa OA, Boloor A, Bonakdar Hashemi M, Bonny A, Bora K, Bora Basara B, Borhany H, Borzutzky A, Bouaoud S, Boustany A, Boxe C, Boyko EJ, Brady OJ, Braithwaite D, Brant LC, Brauer M, Brazinova A, Brazo-Sayavera J, Breitborde NJK, Breitner S, Brenner H, Briko AN, Briko NI, Britton G, Brown J, Brugha T, Bulamu NB, Bulto LN, Buonsenso D, Burns RA, Busse R, Bustanji Y, Butt NS, Butt ZA, Caetano dos Santos FL, Calina D, Cámera LA, Campos LA, Campos-Nonato IR, Cao C, Cao Y, Capodici A, Cárdenas R, Carr S, Carreras G, Carrero JJ, Carugno A, Carvalheiro CG, Carvalho F, Carvalho M, Castaldelli-Maia JM, Castañeda-Orjuela CA, Castelpietra G, Catalá-López F, Catapano AL, Cattaruzza MS, Cederroth CR, Cegolon L, Cembranel F, Cenderadewi M, Cercy KM, Cerin E, Cevik M, Chadwick J, Chahine Y, Chakraborty C, Chakraborty PA, Chan JSK, Chan RNC, Chandika RM, Chandrasekar EK, Chang CK, Chang JC, Chanie GS, Charalampous P, Chattu VK, Chaturvedi P, Chatzimavridou-Grigoriadou V, Chaurasia A, Chen AW, Chen AT, Chen CS, Chen H, Chen MX, Chen S, Cheng CY, Cheng ETW, Cherbuin N, Cheru WA, Chien JH, Chimed-Ochir O, Chimoriya R, Ching PR, Chirinos-Caceres JL, Chitheer A, Cho WCS, Chong B, Chopra H, Choudhari SG, Chowdhury R, Christopher DJ, Chukwu IS, Chung E, Chung E, Chung E, Chung SC, Chutiyami M, Cindi Z, Cioffi I, Claassens MM, Claro RM, Coberly K, Cogen RM, Columbus A, Comfort H, Conde J, Cortese S, Cortesi PA, Costa VM, Costanzo S, Cousin E, Couto RAS, Cowden RG, Cramer KM, Criqui MH, Cruz-Martins N, Cuadra-Hernández SM, Culbreth GT, Cullen P, Cunningham M, Curado MP, Dadana S, Dadras O, Dai S, Dai X, Dai Z, Dalli LL, Damiani G, Darega Gela J, Das JK, Das S, Das S, Dascalu AM, Dash NR, Dashti M, Dastiridou A, Davey G, Dávila-Cervantes CA, Davis Weaver N, Davletov K, De Leo D, de Luca K, Debele AT, Debopadhaya S, Degenhardt L, Dehghan A, Deitesfeld L, Del Bo' C, Delgado-Enciso I, Demessa BH, Demetriades AK, Deng K, Deng X, Denova-Gutiérrez E, Deravi N, Dereje N, Dervenis N, Dervišević E, Des Jarlais DC, Desai HD, Desai R, Devanbu VGC, Dewan SMR, Dhali A, Dhama K, Dhimal M, Dhingra S, Dhulipala VR, Dias da Silva D, Diaz D, Diaz MJ, Dima A, Ding DD, Ding H, Dinis-Oliveira RJ, Dirac MA, Djalalinia S, Do THP, do Prado CB, Doaei S, Dodangeh M, Dodangeh M, Dohare S, Dokova KG, Dolecek C, Dominguez RMV, Dong W, Dongarwar D, D'Oria M, Dorostkar F, Dorsey ER, dos Santos WM, Doshi R, Doshmangir L, Dowou RK, Driscoll TR, Dsouza HL, Dsouza V, Du M, Dube J, Duncan BB, Duraes AR, Duraisamy S, Durojaiye OC, Dwyer-Lindgren L, Dzianach PA, Dziedzic AM, E'mar AR, Eboreime E, Ebrahimi A, Echieh CP, Edinur HA, Edvardsson D, Edvardsson K, Efendi D, Efendi F, Effendi DE, Eikemo TA, Eini E, Ekholuenetale M, Ekundayo TC, El Sayed I, Elbarazi I, Elema TB, Elemam NM, Elgar FJ, Elgendy IY, ElGohary GMT, Elhabashy HR, Elhadi M, El-Huneidi W, Elilo LT, Elmeligy OAA, Elmonem MA, Elshaer M, Elsohaby I, Emeto TI, Engelbert Bain L, Erkhembayar R, Esezobor CI, Eshrati B, Eskandarieh S, Espinosa-Montero J, Esubalew H, Etaee F, Fabin N, Fadaka AO, Fagbamigbe AF, Fahim A, Fahimi S, Fakhri-Demeshghieh A, Falzone L, Fareed M, Farinha CSES, Faris MEM, Faris PS, Faro A, Fasanmi AO, Fatehizadeh A, Fattahi H, Fauk NK, Fazeli P, Feigin VL, Feizkhah A, Fekadu G, Feng X, Fereshtehnejad SM, Feroze AH, Ferrante D, Ferrari AJ, Ferreira N, Fetensa G, Feyisa BR, Filip I, Fischer F, Flavel J, Flood D, Florin BT, Foigt NA, Folayan MO, Fomenkov AA, Foroutan B, Foroutan M, Forthun I, Fortuna D, Foschi M, Fowobaje KR, Francis KL, Franklin RC, Freitas A, Friedman J, Friedman SD, Fukumoto T, Fuller JE, Fux B, Gaal PA, Gadanya MA, Gaidhane AM, Gaihre S, Gakidou E, Galali Y, Galles NC, Gallus S, Ganbat M, Gandhi AP, Ganesan B, Ganiyani MA, Garcia-Gordillo MA, Gardner WM, Garg J, Garg N, Gautam RK, Gbadamosi SO, Gebi TG, Gebregergis MW, Gebrehiwot M, Gebremeskel TG, Georgescu SR, Getachew T, Gething PW, Getie M, Ghadiri K, Ghahramani S, Ghailan KY, Ghasemi MR, Ghasempour Dabaghi G, Ghasemzadeh A, Ghashghaee A, Ghassemi F, Ghazy RM, Ghimire A, Ghoba S, Gholamalizadeh M, Gholamian A, Gholamrezanezhad A, Gholizadeh N, Ghorbani M, Ghorbani Vajargah P, Ghoshal AG, Gill PS, Gill TK, Gillum RF, Ginindza TG, Girmay A, Glasbey JC, Gnedovskaya EV, Göbölös L, Godinho MA, Goel A, Golchin A, Goldust M, Golechha M, Goleij P, Gomes NGM, Gona PN, Gopalani SV, Gorini G, Goudarzi H, Goulart AC, Goulart BNG, Goyal A, Grada A, Graham SM, Grivna M, Grosso G, Guan SY, Guarducci G, Gubari MIM, Gudeta MD, Guha A, Guicciardi S, Guimarães RA, Gulati S, Gunawardane DA, Gunturu S, Guo C, Gupta AK, Gupta B, Gupta MK, Gupta M, Gupta RD, Gupta R, Gupta S, Gupta VB, Gupta VK, Gupta VK, Gurmessa L, Gutiérrez RA, Habibzadeh F, Habibzadeh P, Haddadi R, Hadei M, Hadi NR, Haep N, Hafezi-Nejad N, Hailu A, Haj-Mirzaian A, Halboub ES, Hall BJ, Haller S, Halwani R, Hamadeh RR, Hameed S, Hamidi S, Hamilton EB, Han C, Han Q, Hanif A, Hanifi N, 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Global burden of 288 causes of death and life expectancy decomposition in 204 countries and territories and 811 subnational locations, 1990-2021: a systematic analysis for the Global Burden of Disease Study 2021. Lancet 2024:S0140-6736(24)00367-2. [PMID: 38582094 DOI: 10.1016/s0140-6736(24)00367-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/15/2024] [Accepted: 02/22/2024] [Indexed: 04/08/2024]
Abstract
BACKGROUND Regular, detailed reporting on population health by underlying cause of death is fundamental for public health decision making. Cause-specific estimates of mortality and the subsequent effects on life expectancy worldwide are valuable metrics to gauge progress in reducing mortality rates. These estimates are particularly important following large-scale mortality spikes, such as the COVID-19 pandemic. When systematically analysed, mortality rates and life expectancy allow comparisons of the consequences of causes of death globally and over time, providing a nuanced understanding of the effect of these causes on global populations. METHODS The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021 cause-of-death analysis estimated mortality and years of life lost (YLLs) from 288 causes of death by age-sex-location-year in 204 countries and territories and 811 subnational locations for each year from 1990 until 2021. The analysis used 56 604 data sources, including data from vital registration and verbal autopsy as well as surveys, censuses, surveillance systems, and cancer registries, among others. As with previous GBD rounds, cause-specific death rates for most causes were estimated using the Cause of Death Ensemble model-a modelling tool developed for GBD to assess the out-of-sample predictive validity of different statistical models and covariate permutations and combine those results to produce cause-specific mortality estimates-with alternative strategies adapted to model causes with insufficient data, substantial changes in reporting over the study period, or unusual epidemiology. YLLs were computed as the product of the number of deaths for each cause-age-sex-location-year and the standard life expectancy at each age. As part of the modelling process, uncertainty intervals (UIs) were generated using the 2·5th and 97·5th percentiles from a 1000-draw distribution for each metric. We decomposed life expectancy by cause of death, location, and year to show cause-specific effects on life expectancy from 1990 to 2021. We also used the coefficient of variation and the fraction of population affected by 90% of deaths to highlight concentrations of mortality. Findings are reported in counts and age-standardised rates. Methodological improvements for cause-of-death estimates in GBD 2021 include the expansion of under-5-years age group to include four new age groups, enhanced methods to account for stochastic variation of sparse data, and the inclusion of COVID-19 and other pandemic-related mortality-which includes excess mortality associated with the pandemic, excluding COVID-19, lower respiratory infections, measles, malaria, and pertussis. For this analysis, 199 new country-years of vital registration cause-of-death data, 5 country-years of surveillance data, 21 country-years of verbal autopsy data, and 94 country-years of other data types were added to those used in previous GBD rounds. FINDINGS The leading causes of age-standardised deaths globally were the same in 2019 as they were in 1990; in descending order, these were, ischaemic heart disease, stroke, chronic obstructive pulmonary disease, and lower respiratory infections. In 2021, however, COVID-19 replaced stroke as the second-leading age-standardised cause of death, with 94·0 deaths (95% UI 89·2-100·0) per 100 000 population. The COVID-19 pandemic shifted the rankings of the leading five causes, lowering stroke to the third-leading and chronic obstructive pulmonary disease to the fourth-leading position. In 2021, the highest age-standardised death rates from COVID-19 occurred in sub-Saharan Africa (271·0 deaths [250·1-290·7] per 100 000 population) and Latin America and the Caribbean (195·4 deaths [182·1-211·4] per 100 000 population). The lowest age-standardised death rates from COVID-19 were in the high-income super-region (48·1 deaths [47·4-48·8] per 100 000 population) and southeast Asia, east Asia, and Oceania (23·2 deaths [16·3-37·2] per 100 000 population). Globally, life expectancy steadily improved between 1990 and 2019 for 18 of the 22 investigated causes. Decomposition of global and regional life expectancy showed the positive effect that reductions in deaths from enteric infections, lower respiratory infections, stroke, and neonatal deaths, among others have contributed to improved survival over the study period. However, a net reduction of 1·6 years occurred in global life expectancy between 2019 and 2021, primarily due to increased death rates from COVID-19 and other pandemic-related mortality. Life expectancy was highly variable between super-regions over the study period, with southeast Asia, east Asia, and Oceania gaining 8·3 years (6·7-9·9) overall, while having the smallest reduction in life expectancy due to COVID-19 (0·4 years). The largest reduction in life expectancy due to COVID-19 occurred in Latin America and the Caribbean (3·6 years). Additionally, 53 of the 288 causes of death were highly concentrated in locations with less than 50% of the global population as of 2021, and these causes of death became progressively more concentrated since 1990, when only 44 causes showed this pattern. The concentration phenomenon is discussed heuristically with respect to enteric and lower respiratory infections, malaria, HIV/AIDS, neonatal disorders, tuberculosis, and measles. INTERPRETATION Long-standing gains in life expectancy and reductions in many of the leading causes of death have been disrupted by the COVID-19 pandemic, the adverse effects of which were spread unevenly among populations. Despite the pandemic, there has been continued progress in combatting several notable causes of death, leading to improved global life expectancy over the study period. Each of the seven GBD super-regions showed an overall improvement from 1990 and 2021, obscuring the negative effect in the years of the pandemic. Additionally, our findings regarding regional variation in causes of death driving increases in life expectancy hold clear policy utility. Analyses of shifting mortality trends reveal that several causes, once widespread globally, are now increasingly concentrated geographically. These changes in mortality concentration, alongside further investigation of changing risks, interventions, and relevant policy, present an important opportunity to deepen our understanding of mortality-reduction strategies. Examining patterns in mortality concentration might reveal areas where successful public health interventions have been implemented. Translating these successes to locations where certain causes of death remain entrenched can inform policies that work to improve life expectancy for people everywhere. FUNDING Bill & Melinda Gates Foundation.
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Parthasarathi A, Pashaei A, Pasupula DK, Patel JR, Patel SK, Pathan AR, Patil A, Patil S, Patoulias D, Patthipati VS, Paudel U, Pawar S, Pazoki Toroudi H, Pease SA, Peden AE, Pedersini P, Peng M, Pensato U, Pepito VCF, Peprah EK, Pereira G, Pereira J, Pereira M, Peres MFP, Perianayagam A, Perico N, Petcu IR, Petermann-Rocha FE, Pezzani R, Pham HT, Phillips MR, Pierannunzio D, Pigeolet M, Pigott DM, Pilgrim T, Pinheiro M, Piradov MA, Plakkal N, Plotnikov E, Poddighe D, Pollner P, Poluru R, Pond CD, Postma MJ, Poudel GR, Poudel L, Pourali G, Pourtaheri N, Prada SI, Pradhan PMS, Prajapati VK, Prakash V, Prasad CP, Prasad M, Prashant A, Prates EJS, Purnobasuki H, Purohit BM, Puvvula J, Qaisar R, Qasim NH, Qattea I, Qian G, Quan NK, Radfar A, Radhakrishnan V, Raee P, Raeisi Shahraki H, Rafiei Alavi SN, Rafique I, Raggi A, Rahim F, Rahman MM, Rahman M, Rahman MA, Rahman T, Rahmani AM, Rahmani S, Rahnavard N, Rai P, Rajaa S, Rajabpour-Sanati A, Rajput P, Ram P, Ramadan H, Ramasamy SK, Ramazanu S, Rana J, Rana K, Ranabhat CL, Rancic N, Rani S, Ranjan S, Rao CR, Rao IR, Rao M, Rao SJ, Rasali DP, Rasella D, Rashedi S, Rashedi V, Rashid AM, Rasouli-Saravani A, Rastogi P, Rasul A, Ravangard R, Ravikumar N, Rawaf DL, Rawaf S, Rawassizadeh R, Razeghian-Jahromi I, Reddy MMRK, Redwan EMM, Rehman FU, Reiner Jr RC, Remuzzi G, Reshmi B, Resnikoff S, Reyes LF, Rezaee M, Rezaei N, Rezaei N, Rezaeian M, Riaz MA, Ribeiro AI, Ribeiro DC, Rickard J, Rios-Blancas MJ, Robinson-Oden HE, Rodrigues M, Rodriguez JAB, Roever L, Rohilla R, Rohloff P, Romadlon DS, Ronfani L, Roshandel G, Roshanzamir S, Rostamian M, Roy B, Roy P, Rubagotti E, Rumisha SF, Rwegerera GM, Rynkiewicz A, S M, S N C, S Sunnerhagen K, Saad AMA, Sabbatucci M, Saber K, Saber-Ayad MM, Sacco S, Saddik B, Saddler A, Sadee BA, Sadeghi E, Sadeghi M, Sadeghian S, Saeed U, Saeedi M, Safi S, Sagar R, Saghazadeh A, Saheb Sharif-Askari N, Sahoo SS, Sahraian MA, Sajedi SA, Sajid MR, Sakshaug JW, Salahi S, Salahi S, Salamati P, Salami AA, Salaroli LB, Saleh MA, Salehi S, Salem MR, Salem MZY, Salimi S, Samadi Kafil H, Samadzadeh S, Samara KA, Samargandy S, Samodra YL, Samuel VP, Samy AM, Sanabria J, Sanadgol N, Sanganyado E, Sanjeev RK, Sanmarchi F, Sanna F, Santri IN, Santric-Milicevic MM, Sarasmita MA, Saravanan A, Saravi B, Sarikhani Y, Sarkar C, Sarmiento-Suárez R, Sarode GS, Sarode SC, Sarveazad A, Sathian B, Sathish T, Sattin D, Saulam J, Sawyer SM, Saxena S, Saya GK, Sayadi Y, Sayeed A, Sayeed MA, Saylan M, Scarmeas N, Schaarschmidt BM, Schlee W, Schmidt MI, Schuermans A, Schwebel DC, Schwendicke F, Šekerija M, Selvaraj S, Semreen MH, Senapati S, Sengupta P, Senthilkumaran S, Sepanlou SG, Serban D, Sertsu A, Sethi Y, SeyedAlinaghi S, Seyedi SA, Shafaat A, Shafaat O, Shafie M, Shafiee A, Shah NS, Shah PA, Shahabi S, Shahbandi A, Shahid I, Shahid S, Shahid W, Shahwan MJ, Shaikh MA, Shakeri A, Shakil H, Sham S, Shamim MA, Shams-Beyranvand M, Shamshad H, Shamshirgaran MA, Shamsi MA, Shanawaz M, Shankar A, Sharfaei S, Sharifan A, Shariff M, Sharifi-Rad J, Sharma M, Sharma R, Sharma S, Sharma V, Shastry RP, Shavandi A, Shaw DH, Shayan AM, Shehabeldine AME, Sheikh A, Sheikhi RA, Shen J, Shenoy MM, Shetty BSK, Shetty RS, Shey RA, Shiani A, Shibuya K, Shiferaw D, Shigematsu M, Shin JI, Shin MJ, Shiri R, Shirkoohi R, Shittu A, Shiue I, Shivakumar KM, Shivarov V, Shool S, Shrestha S, Shuja KH, Shuval K, Si Y, Sibhat MM, Siddig EE, Sigfusdottir ID, Silva JP, Silva LMLR, Silva S, Simões JP, Simpson CR, Singal A, Singh A, Singh A, Singh A, Singh BB, Singh B, Singh M, Singh M, Singh NP, Singh P, Singh S, Siraj MS, Sitas F, Sivakumar S, Skryabin VY, Skryabina AA, Sleet DA, Slepak ELN, Sohrabi H, Soleimani H, Soliman SSM, Solmi M, Solomon Y, Song Y, Sorensen RJD, Soriano JB, Soyiri IN, Spartalis M, Sreeramareddy CT, Starnes JR, Starodubov VI, Starodubova AV, Stefan SC, Stein DJ, Steinbeis F, Steiropoulos P, Stockfelt L, Stokes MA, Stortecky S, Stranges S, Stroumpoulis K, Suleman M, Suliankatchi Abdulkader R, Sultana A, Sun J, Sunkersing D, Susanty S, Swain CK, Sykes BL, Szarpak L, Szeto MD, Szócska M, Tabaee Damavandi P, Tabatabaei Malazy O, Tabatabaeizadeh SA, Tabatabai S, Tabb KM, Tabish M, Taborda-Barata LM, Tabuchi T, Tadesse BT, Taheri A, Taheri Abkenar Y, Taheri Soodejani M, Taherkhani A, Taiba J, Tajbakhsh A, Talaat IM, Talukder A, Tamuzi JL, Tan KK, Tang H, Tang HK, Tat NY, Tat VY, Tavakoli Oliaee R, Tavangar SM, Taveira N, Tebeje TM, Tefera YM, Teimoori M, Temsah MH, Temsah RMH, Teramoto M, Tesfaye SH, Thangaraju P, Thankappan KR, Thapa R, Thapar R, Thomas N, Thrift AG, Thum CCC, Tian J, Tichopad A, Ticoalu JHV, Tiruye TY, Tohidast SA, Tonelli M, Touvier M, Tovani-Palone MR, Tram KH, Tran NM, Trico D, Trihandini I, Tromans SJ, Truong VT, Truyen TTTT, Tsermpini EE, Tumurkhuu M, Tung K, Tyrovolas S, Ubah CS, Udoakang AJ, Udoh A, Ulhaq I, Ullah S, Ullah S, Umair M, Umar TP, Umeokonkwo CD, Umesh A, Unim B, Unnikrishnan B, Upadhyay E, Urso D, Vacante M, Vahdani AM, Vaithinathan AG, Valadan Tahbaz S, Valizadeh R, Van den Eynde J, Varavikova E, Varga O, Varma SA, Vart P, Varthya SB, Vasankari TJ, Veerman LJ, Venketasubramanian N, Venugopal D, Verghese NA, Verma M, Verma P, Veroux M, Verras GI, Vervoort D, Vieira RJ, Villafañe JH, Villani L, Villanueva GI, Villeneuve PJ, Violante FS, Visontay R, Vlassov V, Vo B, Vollset SE, Volovat SR, Volovici V, Vongpradith A, Vos T, Vujcic IS, Vukovic R, Wado YD, Wafa HA, Waheed Y, Wamai RG, Wang C, Wang D, Wang F, Wang S, Wang S, Wang Y, Wang YP, Ward P, Watson S, Weaver MR, Weerakoon KG, Weiss DJ, Weldemariam AH, Wells KM, Wen YF, Werdecker A, Westerman R, Wickramasinghe DP, Wickramasinghe ND, Wijeratne T, Wilson S, Wojewodzic MW, Wool EE, Woolf AD, Wu D, Wulandari RD, Xiao H, Xu B, Xu X, Yadav L, Yaghoubi S, Yang L, Yano Y, Yao Y, Ye P, Yesera GE, Yesodharan R, Yesuf SA, Yiğit A, Yiğit V, Yip P, Yon DK, Yonemoto N, You Y, Younis MZ, Yu C, Zadey S, Zadnik V, Zafari N, Zahedi M, Zahid MN, Zahir M, Zakham F, Zaki N, Zakzuk J, Zamagni G, Zaman BA, Zaman SB, Zamora N, Zand R, Zandi M, Zandieh GGZ, Zanghì A, Zare I, Zastrozhin MS, Zeariya MGM, Zeng Y, Zhai C, Zhang C, Zhang H, Zhang H, Zhang Y, Zhang Z, Zhang Z, Zhao H, Zhao Y, Zhao Y, Zheng P, Zhong C, Zhou J, Zhu B, Zhu Z, Ziaeefar P, Zielińska M, Zou Z, Zumla A, Zweck E, Zyoud SH, Lim SS, Murray CJL. Global age-sex-specific mortality, life expectancy, and population estimates in 204 countries and territories and 811 subnational locations, 1950-2021, and the impact of the COVID-19 pandemic: a comprehensive demographic analysis for the Global Burden of Disease Study 2021. Lancet 2024:S0140-6736(24)00476-8. [PMID: 38484753 DOI: 10.1016/s0140-6736(24)00476-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/08/2023] [Accepted: 03/06/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND Estimates of demographic metrics are crucial to assess levels and trends of population health outcomes. The profound impact of the COVID-19 pandemic on populations worldwide has underscored the need for timely estimates to understand this unprecedented event within the context of long-term population health trends. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021 provides new demographic estimates for 204 countries and territories and 811 additional subnational locations from 1950 to 2021, with a particular emphasis on changes in mortality and life expectancy that occurred during the 2020-21 COVID-19 pandemic period. METHODS 22 223 data sources from vital registration, sample registration, surveys, censuses, and other sources were used to estimate mortality, with a subset of these sources used exclusively to estimate excess mortality due to the COVID-19 pandemic. 2026 data sources were used for population estimation. Additional sources were used to estimate migration; the effects of the HIV epidemic; and demographic discontinuities due to conflicts, famines, natural disasters, and pandemics, which are used as inputs for estimating mortality and population. Spatiotemporal Gaussian process regression (ST-GPR) was used to generate under-5 mortality rates, which synthesised 30 763 location-years of vital registration and sample registration data, 1365 surveys and censuses, and 80 other sources. ST-GPR was also used to estimate adult mortality (between ages 15 and 59 years) based on information from 31 642 location-years of vital registration and sample registration data, 355 surveys and censuses, and 24 other sources. Estimates of child and adult mortality rates were then used to generate life tables with a relational model life table system. For countries with large HIV epidemics, life tables were adjusted using independent estimates of HIV-specific mortality generated via an epidemiological analysis of HIV prevalence surveys, antenatal clinic serosurveillance, and other data sources. Excess mortality due to the COVID-19 pandemic in 2020 and 2021 was determined by subtracting observed all-cause mortality (adjusted for late registration and mortality anomalies) from the mortality expected in the absence of the pandemic. Expected mortality was calculated based on historical trends using an ensemble of models. In location-years where all-cause mortality data were unavailable, we estimated excess mortality rates using a regression model with covariates pertaining to the pandemic. Population size was computed using a Bayesian hierarchical cohort component model. Life expectancy was calculated using age-specific mortality rates and standard demographic methods. Uncertainty intervals (UIs) were calculated for every metric using the 25th and 975th ordered values from a 1000-draw posterior distribution. FINDINGS Global all-cause mortality followed two distinct patterns over the study period: age-standardised mortality rates declined between 1950 and 2019 (a 62·8% [95% UI 60·5-65·1] decline), and increased during the COVID-19 pandemic period (2020-21; 5·1% [0·9-9·6] increase). In contrast with the overall reverse in mortality trends during the pandemic period, child mortality continued to decline, with 4·66 million (3·98-5·50) global deaths in children younger than 5 years in 2021 compared with 5·21 million (4·50-6·01) in 2019. An estimated 131 million (126-137) people died globally from all causes in 2020 and 2021 combined, of which 15·9 million (14·7-17·2) were due to the COVID-19 pandemic (measured by excess mortality, which includes deaths directly due to SARS-CoV-2 infection and those indirectly due to other social, economic, or behavioural changes associated with the pandemic). Excess mortality rates exceeded 150 deaths per 100 000 population during at least one year of the pandemic in 80 countries and territories, whereas 20 nations had a negative excess mortality rate in 2020 or 2021, indicating that all-cause mortality in these countries was lower during the pandemic than expected based on historical trends. Between 1950 and 2021, global life expectancy at birth increased by 22·7 years (20·8-24·8), from 49·0 years (46·7-51·3) to 71·7 years (70·9-72·5). Global life expectancy at birth declined by 1·6 years (1·0-2·2) between 2019 and 2021, reversing historical trends. An increase in life expectancy was only observed in 32 (15·7%) of 204 countries and territories between 2019 and 2021. The global population reached 7·89 billion (7·67-8·13) people in 2021, by which time 56 of 204 countries and territories had peaked and subsequently populations have declined. The largest proportion of population growth between 2020 and 2021 was in sub-Saharan Africa (39·5% [28·4-52·7]) and south Asia (26·3% [9·0-44·7]). From 2000 to 2021, the ratio of the population aged 65 years and older to the population aged younger than 15 years increased in 188 (92·2%) of 204 nations. INTERPRETATION Global adult mortality rates markedly increased during the COVID-19 pandemic in 2020 and 2021, reversing past decreasing trends, while child mortality rates continued to decline, albeit more slowly than in earlier years. Although COVID-19 had a substantial impact on many demographic indicators during the first 2 years of the pandemic, overall global health progress over the 72 years evaluated has been profound, with considerable improvements in mortality and life expectancy. Additionally, we observed a deceleration of global population growth since 2017, despite steady or increasing growth in lower-income countries, combined with a continued global shift of population age structures towards older ages. These demographic changes will likely present future challenges to health systems, economies, and societies. The comprehensive demographic estimates reported here will enable researchers, policy makers, health practitioners, and other key stakeholders to better understand and address the profound changes that have occurred in the global health landscape following the first 2 years of the COVID-19 pandemic, and longer-term trends beyond the pandemic. FUNDING Bill & Melinda Gates Foundation.
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Browne AJ, Chipeta MG, Fell FJ, Haines-Woodhouse G, Kashef Hamadani BH, Kumaran EAP, Robles Aguilar G, McManigal B, Andrews JR, Ashley EA, Audi A, Baker S, Banda HC, Basnyat B, Bigogo G, Ngoun C, Chansamouth V, Chunga A, Clemens JD, Davong V, Dougan G, Dunachie SJ, Feasey NA, Garrett DO, Gordon MA, Hasan R, Haselbeck AH, Henry NJ, Heyderman RS, Holm M, Jeon HJ, Karkey A, Khanam F, Luby SP, Malik FR, Marks F, Mayxay M, Meiring JE, Moore CE, Munywoki PK, Musicha P, Newton PN, Pak G, Phommasone K, Pokharel S, Pollard AJ, Qadri F, Qamar FN, Rattanavong S, Reiner B, Roberts T, Saha S, Saha S, Shakoor S, Shakya M, Simpson AJ, Stanaway J, Turner C, Turner P, Verani JR, Vongsouvath M, Day NPJ, Naghavi M, Hay SI, Sartorius B, Dolecek C. Estimating the subnational prevalence of antimicrobial resistant Salmonella enterica serovars Typhi and Paratyphi A infections in 75 endemic countries, 1990-2019: a modelling study. Lancet Glob Health 2024; 12:e406-e418. [PMID: 38365414 PMCID: PMC10882211 DOI: 10.1016/s2214-109x(23)00585-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 11/19/2023] [Accepted: 12/04/2023] [Indexed: 02/18/2024]
Abstract
BACKGROUND Enteric fever, a systemic infection caused by Salmonella enterica serovars Typhi and Paratyphi A, remains a major cause of morbidity and mortality in low-income and middle-income countries. Enteric fever is preventable through the provision of clean water and adequate sanitation and can be successfully treated with antibiotics. However, high levels of antimicrobial resistance (AMR) compromise the effectiveness of treatment. We provide estimates of the prevalence of AMR S Typhi and S Paratyphi A in 75 endemic countries, including 30 locations without data. METHODS We used a Bayesian spatiotemporal modelling framework to estimate the percentage of multidrug resistance (MDR), fluoroquinolone non-susceptibility (FQNS), and third-generation cephalosporin resistance in S Typhi and S Paratyphi A infections for 1403 administrative level one districts in 75 endemic countries from 1990 to 2019. We incorporated data from a comprehensive systematic review, public health surveillance networks, and large multicountry studies on enteric fever. Estimates of the prevalence of AMR and the number of AMR infections (based on enteric fever incidence estimates by the Global Burden of Diseases study) were produced at the country, super-region, and total endemic area level for each year of the study. FINDINGS We collated data from 601 sources, comprising 184 225 isolates of S Typhi and S Paratyphi A, covering 45 countries over 30 years. We identified a decline of MDR S Typhi in south Asia and southeast Asia, whereas in sub-Saharan Africa, the overall prevalence increased from 6·0% (95% uncertainty interval 4·3-8·0) in 1990 to 72·7% (67·7-77·3) in 2019. Starting from low levels in 1990, the prevalence of FQNS S Typhi increased rapidly, reaching 95·2% (91·4-97·7) in south Asia in 2019. This corresponded to 2·5 million (1·5-3·8) MDR S Typhi infections and 7·4 million (4·7-11·3) FQNS S Typhi infections in endemic countries in 2019. The prevalence of third-generation cephalosporin-resistant S Typhi remained low across the whole endemic area over the study period, except for Pakistan where prevalence of third-generation cephalosporin resistance in S Typhi reached 61·0% (58·0-63·8) in 2019. For S Paratyphi A, we estimated low prevalence of MDR and third-generation cephalosporin resistance in all endemic countries, but a drastic increase of FQNS, which reached 95·0% (93·7-96·1; 3·5 million [2·2-5·6] infections) in 2019. INTERPRETATION This study provides a comprehensive and detailed analysis of the prevalence of MDR, FQNS, and third-generation cephalosporin resistance in S Typhi and S Paratyphi A infections in endemic countries, spanning the last 30 years. Our analysis highlights the increasing levels of AMR in this preventable infection and serves as a resource to guide urgently needed public health interventions, such as improvements in water, sanitation, and hygiene and typhoid fever vaccination campaigns. FUNDING Fleming Fund, UK Department of Health and Social Care; Wellcome Trust; and Bill and Melinda Gates Foundation.
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Sartorius B, Gray AP, Davis Weaver N, Robles Aguilar G, Swetschinski LR, Ikuta KS, Mestrovic T, Chung E, Wool EE, Han C, Gershberg Hayoon A, Araki DT, Abd-Elsalam S, Aboagye RG, Adamu LH, Adepoju AV, Ahmed A, Akalu GT, Akande-Sholabi W, Amuasi JH, Amusa GA, Argaw AM, Aruleba RT, Awoke T, Ayalew MK, Azzam AY, Babin FX, Banerjee I, Basiru A, Bayileyegn NS, Belete MA, Berkley JA, Bielicki JA, Dekker D, Demeke D, Demsie DG, Dessie AM, Dunachie SJ, Ed-Dra A, Ekholuenetale M, Ekundayo TC, El Sayed I, Elhadi M, Elsohaby I, Eyre D, Fagbamigbe AF, Feasey NA, Fekadu G, Fell F, Forrest KM, Gebrehiwot M, Gezae KE, Ghazy RM, Hailegiyorgis TT, Haines-Woodhouse G, Hasaballah AI, Haselbeck AH, Hsia Y, Iradukunda A, Iregbu KC, Iwu CCD, Iwu-Jaja CJ, Iyasu AN, Jaiteh F, Jeon H, Joshua CE, Kassa GG, Katoto PDMC, Krumkamp R, Kumaran EAP, Kyu HH, Manilal A, Marks F, May J, McLaughlin SA, McManigal B, Melese A, Misgina KH, Mohamed NS, Mohammed M, Mohammed S, Mohammed S, Mokdad AH, Moore CE, Mougin V, Mturi N, Mulugeta T, Musaigwa F, Musicha P, Musila LA, Muthupandian S, Naghavi P, Negash H, Nuckchady DC, Obiero CW, Odetokun IA, Ogundijo OA, Okidi L, Okonji OC, Olagunju AT, Olufadewa II, Pak GD, Perovic O, Pollard A, Raad M, Rafaï C, Ramadan H, Redwan EMM, Roca A, Rosenthal VD, Saleh MA, Samy AM, Sharland M, Shittu A, Siddig EE, Sisay EA, Stergachis A, Tesfamariam WB, Tigoi C, Tincho MB, Tiruye TY, Umeokonkwo CD, Walsh T, Walson JL, Yusuf H, Zeru NG, Hay SI, Dolecek C, Murray CJL, Naghavi M. The burden of bacterial antimicrobial resistance in the WHO African region in 2019: a cross-country systematic analysis. Lancet Glob Health 2024; 12:e201-e216. [PMID: 38134946 PMCID: PMC10805005 DOI: 10.1016/s2214-109x(23)00539-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/18/2023] [Accepted: 11/07/2023] [Indexed: 12/24/2023]
Abstract
BACKGROUND A critical and persistent challenge to global health and modern health care is the threat of antimicrobial resistance (AMR). Previous studies have reported a disproportionate burden of AMR in low-income and middle-income countries, but there remains an urgent need for more in-depth analyses across Africa. This study presents one of the most comprehensive sets of regional and country-level estimates of bacterial AMR burden in the WHO African region to date. METHODS We estimated deaths and disability-adjusted life-years (DALYs) attributable to and associated with AMR for 23 bacterial pathogens and 88 pathogen-drug combinations for countries in the WHO African region in 2019. Our methodological approach consisted of five broad components: the number of deaths in which infection had a role, the proportion of infectious deaths attributable to a given infectious syndrome, the proportion of infectious syndrome deaths attributable to a given pathogen, the percentage of a given pathogen resistant to an antimicrobial drug of interest, and the excess risk of mortality (or duration of an infection) associated with this resistance. These components were then used to estimate the disease burden by using two counterfactual scenarios: deaths attributable to AMR (considering an alternative scenario where infections with resistant pathogens are replaced with susceptible ones) and deaths associated with AMR (considering an alternative scenario where drug-resistant infections would not occur at all). We obtained data from research hospitals, surveillance networks, and infection databases maintained by private laboratories and medical technology companies. We generated 95% uncertainty intervals (UIs) for final estimates as the 25th and 975th ordered values across 1000 posterior draws, and models were cross-validated for out-of-sample predictive validity. FINDINGS In the WHO African region in 2019, there were an estimated 1·05 million deaths (95% UI 829 000-1 316 000) associated with bacterial AMR and 250 000 deaths (192 000-325 000) attributable to bacterial AMR. The largest fatal AMR burden was attributed to lower respiratory and thorax infections (119 000 deaths [92 000-151 000], or 48% of all estimated bacterial pathogen AMR deaths), bloodstream infections (56 000 deaths [37 000-82 000], or 22%), intra-abdominal infections (26 000 deaths [17 000-39 000], or 10%), and tuberculosis (18 000 deaths [3850-39 000], or 7%). Seven leading pathogens were collectively responsible for 821 000 deaths (636 000-1 051 000) associated with resistance in this region, with four pathogens exceeding 100 000 deaths each: Streptococcus pneumoniae, Klebsiella pneumoniae, Escherichia coli, and Staphylococcus aureus. Third-generation cephalosporin-resistant K pneumoniae and meticillin-resistant S aureus were shown to be the leading pathogen-drug combinations in 25 and 16 countries, respectively (53% and 34% of the whole region, comprising 47 countries) for deaths attributable to AMR. INTERPRETATION This study reveals a high level of AMR burden for several bacterial pathogens and pathogen-drug combinations in the WHO African region. The high mortality rates associated with these pathogens demonstrate an urgent need to address the burden of AMR in Africa. These estimates also show that quality and access to health care and safe water and sanitation are correlated with AMR mortality, with a higher fatal burden found in lower resource settings. Our cross-country analyses within this region can help local governments to leverage domestic and global funding to create stewardship policies that target the leading pathogen-drug combinations. FUNDING Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Health and Social Care using UK aid funding managed by the Fleming Fund.
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Kim JH, Choi J, Kim C, Pak GD, Parajulee P, Haselbeck A, Park SE, Mogasale V, Jeon HJ, Browne AJ, Owusu-Dabo E, Rakotozandrindrainy R, Bassiahi AS, Teferi M, Lunguya-Metila O, Dolecek C, Pitzer VE, Crump JA, Hay SI, Marks F. Mapping the incidence rate of typhoid fever in sub-Saharan Africa. PLoS Negl Trop Dis 2024; 18:e0011902. [PMID: 38408128 DOI: 10.1371/journal.pntd.0011902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 03/26/2024] [Accepted: 01/04/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND With more than 1.2 million illnesses and 29,000 deaths in sub-Saharan Africa in 2017, typhoid fever continues to be a major public health problem. Effective control of the disease would benefit from an understanding of the subnational geospatial distribution of the disease incidence. METHOD We collated records of the incidence rate of typhoid fever confirmed by culture of blood in Africa from 2000 to 2022. We estimated the typhoid incidence rate for sub-Saharan Africa on 20 km × 20 km grids by exploring the association with geospatial covariates representing access to improved water and sanitation, health conditions of the population, and environmental conditions. RESULTS We identified six published articles and one pre-print representing incidence rate estimates in 22 sites in 2000-2022. Estimated incidence rates showed geospatial variation at sub-national, national, and regional levels. The incidence rate was high in Western and Eastern African subregions followed by Southern and Middle African subregions. By age, the incidence rate was highest among 5-14 yo followed by 2-4 yo, > 14 yo, and 0-1 yo. When aggregated across all age classes and grids that comprise each country, predicted incidence rates ranged from 43.7 (95% confidence interval: 0.6 to 591.2) in Zimbabwe to 2,957.8 (95% CI: 20.8 to 4,245.2) in South Sudan per 100,000 person-years. Sub-national heterogeneity was evident with the coefficient of variation at the 20 km × 20 km grid-level ranging from 0.7 to 3.3 and was generally lower in high-incidence countries and widely varying in low-incidence countries. CONCLUSION Our study provides estimates of 20 km × 20 km incidence rate of typhoid fever across sub-Saharan Africa based on data collected from 2000 through 2020. Increased understanding of the subnational geospatial variation of typhoid fever in Africa may inform more effective intervention programs by better targeting resources to heterogeneously disturbed disease risk.
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Affiliation(s)
- Jong-Hoon Kim
- International Vaccine Institute, Seoul, Republic of Korea
| | - Jungsoon Choi
- Department of Mathematics, Hanyang University, Seoul, Republic of Korea
| | - Chaelin Kim
- International Vaccine Institute, Seoul, Republic of Korea
| | - Gi Deok Pak
- International Vaccine Institute, Seoul, Republic of Korea
| | | | | | - Se Eun Park
- International Vaccine Institute, Seoul, Republic of Korea
- Graduate School of Public Health, Yonsei University, Seoul, Republic of Korea
| | | | - Hyon Jin Jeon
- International Vaccine Institute, Seoul, Republic of Korea
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
| | - Annie J Browne
- Malaria Atlas Project, Telethon Kids Institute, Perth, Australia
| | - Ellis Owusu-Dabo
- Malaria Atlas Project, Telethon Kids Institute, Perth, Australia
| | - Raphaël Rakotozandrindrainy
- School of Public Health, Kwame Nkrumah University of Science and Technology, Laing Building Complex J.W. Acheampong CI, Kumasi, Ghana
| | | | - Mekonnen Teferi
- Armauer Hansen Research Institute, ALERT Compound Zenebework, Addis Ababa, Ethiopia
| | - Octavie Lunguya-Metila
- Department of Microbiology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
- Department of Medical Biology, Microbiology Service, University Teaching Hospital, Ave De L'hopital, Kinshasa, Democratic Republic of the Congo
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, New Haven, Connecticut, United States of America
- Yale Institute for Global Health, New Haven, Connecticut, United States of America
| | - John A Crump
- Centre for International Health, Division of Health Sciences, University of Otago, Dunedin, New Zealand
| | - Simon I Hay
- Institute for Health Metrics and Evaluation (IHME), University of Washington, Seattle, Washington, United States of America
- Department of Health Metrics Sciences, University of Washington, Seattle, Washington, United States of America
| | - Florian Marks
- International Vaccine Institute, Seoul, Republic of Korea
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- School of Public Health, Kwame Nkrumah University of Science and Technology, Laing Building Complex J.W. Acheampong CI, Kumasi, Ghana
- Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
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8
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Cavany S, Nanyonga S, Hauk C, Lim C, Tarning J, Sartorius B, Dolecek C, Caillet C, Newton PN, Cooper BS. The uncertain role of substandard and falsified medicines in the emergence and spread of antimicrobial resistance. Nat Commun 2023; 14:6153. [PMID: 37788991 PMCID: PMC10547756 DOI: 10.1038/s41467-023-41542-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/07/2023] [Indexed: 10/05/2023] Open
Abstract
Approximately 10% of antimicrobials used by humans in low- and middle-income countries are estimated to be substandard or falsified. In addition to their negative impact on morbidity and mortality, they may also be important drivers of antimicrobial resistance. Despite such concerns, our understanding of this relationship remains rudimentary. Substandard and falsified medicines have the potential to either increase or decrease levels of resistance, and here we discuss a range of mechanisms that could drive these changes. Understanding these effects and their relative importance will require an improved understanding of how different drug exposures affect the emergence and spread of resistance and of how the percentage of active pharmaceutical ingredients in substandard and falsified medicines is temporally and spatially distributed.
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Affiliation(s)
- Sean Cavany
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Stella Nanyonga
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Medicine Quality Research Group, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Infectious Diseases Data Observatory, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Cathrin Hauk
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Medicine Quality Research Group, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Infectious Diseases Data Observatory, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Cherry Lim
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Joel Tarning
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Infectious Diseases Data Observatory, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Benn Sartorius
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- School of Public Health, Faculty of Medicine, The University of Queensland, St Lucia, Australia
| | - Christiane Dolecek
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Céline Caillet
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Medicine Quality Research Group, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Infectious Diseases Data Observatory, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Paul N Newton
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Medicine Quality Research Group, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Infectious Diseases Data Observatory, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Ben S Cooper
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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9
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Carey ME, Dyson ZA, Ingle DJ, Amir A, Aworh MK, Chattaway MA, Chew KL, Crump JA, Feasey NA, Howden BP, Keddy KH, Maes M, Parry CM, Van Puyvelde S, Webb HE, Afolayan AO, Alexander AP, Anandan S, Andrews JR, Ashton PM, Basnyat B, Bavdekar A, Bogoch II, Clemens JD, da Silva KE, De A, de Ligt J, Diaz Guevara PL, Dolecek C, Dutta S, Ehlers MM, Francois Watkins L, Garrett DO, Godbole G, Gordon MA, Greenhill AR, Griffin C, Gupta M, Hendriksen RS, Heyderman RS, Hooda Y, Hormazabal JC, Ikhimiukor OO, Iqbal J, Jacob JJ, Jenkins C, Jinka DR, John J, Kang G, Kanteh A, Kapil A, Karkey A, Kariuki S, Kingsley RA, Koshy RM, Lauer AC, Levine MM, Lingegowda RK, Luby SP, Mackenzie GA, Mashe T, Msefula C, Mutreja A, Nagaraj G, Nagaraj S, Nair S, Naseri TK, Nimarota-Brown S, Njamkepo E, Okeke IN, Perumal SPB, Pollard AJ, Pragasam AK, Qadri F, Qamar FN, Rahman SIA, Rambocus SD, Rasko DA, Ray P, Robins-Browne R, Rongsen-Chandola T, Rutanga JP, Saha SK, Saha S, Saigal K, Sajib MSI, Seidman JC, Shakya J, Shamanna V, Shastri J, Shrestha R, Sia S, Sikorski MJ, Singh A, Smith AM, Tagg KA, Tamrakar D, Tanmoy AM, Thomas M, Thomas MS, Thomsen R, Thomson NR, Tupua S, Vaidya K, Valcanis M, Veeraraghavan B, Weill FX, Wright J, Dougan G, Argimón S, Keane JA, Aanensen DM, Baker S, Holt KE. Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes. eLife 2023; 12:e85867. [PMID: 37697804 PMCID: PMC10506625 DOI: 10.7554/elife.85867] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 08/02/2023] [Indexed: 09/13/2023] Open
Abstract
Background The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). Methods This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. Results Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. Conclusions The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. Funding No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]).
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Affiliation(s)
- Megan E Carey
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- IAVI, Chelsea & Westminster HospitalLondonUnited Kingdom
| | - Zoe A Dyson
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash UniversityMelbourneAustralia
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Danielle J Ingle
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of MelbourneMelbourneAustralia
| | | | - Mabel K Aworh
- Nigeria Field Epidemiology and Laboratory Training ProgrammeAbujaNigeria
- College of Veterinary Medicine, North Carolina State UniversityRaleighUnited States
| | | | - Ka Lip Chew
- National University HospitalSingaporeSingapore
| | - John A Crump
- Centre for International Health, University of OtagoDunedinNew Zealand
| | - Nicholas A Feasey
- Department of Clinical Sciences, Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
- Malawi-Liverpool Wellcome Programme, Kamuzu University of Health SciencesBlantyreMalawi
| | - Benjamin P Howden
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, University of Melbourne at Doherty Institute for Infection and ImmunityMelbourneAustralia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Christopher M Parry
- Department of Clinical Sciences, Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
| | - Sandra Van Puyvelde
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- University of AntwerpAntwerpBelgium
| | - Hattie E Webb
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Ayorinde Oluwatobiloba Afolayan
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | - Shalini Anandan
- Department of Clinical Microbiology, Christian Medical CollegeVelloreIndia
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Philip M Ashton
- Malawi-Liverpool Wellcome ProgrammeBlantyreMalawi
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Buddha Basnyat
- Oxford University Clinical Research Unit NepalKathmanduNepal
| | | | - Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of TorontoTorontoCanada
| | - John D Clemens
- International Vaccine InstituteSeoulRepublic of Korea
- International Centre for Diarrhoeal Disease ResearchDhakaBangladesh
- UCLA Fielding School of Public HealthLos AngelesUnited States
- Korea UniversitySeoulRepublic of Korea
| | - Kesia Esther da Silva
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Anuradha De
- Topiwala National Medical CollegeMumbaiIndia
| | - Joep de Ligt
- ESR, Institute of Environmental Science and Research Ltd., PoriruaWellingtonNew Zealand
| | | | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Shanta Dutta
- ICMR - National Institute of Cholera & Enteric DiseasesKolkataIndia
| | - Marthie M Ehlers
- Department of Medical Microbiology, Faculty of Health Sciences, University of PretoriaPretoriaSouth Africa
- Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory ServicePretoriaSouth Africa
| | | | | | - Gauri Godbole
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | - Melita A Gordon
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Andrew R Greenhill
- Federation University AustraliaChurchillAustralia
- Papua New Guinea Institute of Medical ResearchGorokaPapua New Guinea
| | - Chelsey Griffin
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Madhu Gupta
- Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | | | - Robert S Heyderman
- Research Department of Infection, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | | | - Juan Carlos Hormazabal
- Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomedico, Instituto de Salud Publica de Chile (ISP)SantiagoChile
| | - Odion O Ikhimiukor
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | - Junaid Iqbal
- Department of Pediatrics and Child Health, Aga Khan UniversityKarachiPakistan
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical CollegeVelloreIndia
| | - Claire Jenkins
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | | | - Jacob John
- Department of Community Health, Christian Medical CollegeVelloreIndia
| | - Gagandeep Kang
- Department of Community Health, Christian Medical CollegeVelloreIndia
| | - Abdoulie Kanteh
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical MedicineFajaraGambia
| | - Arti Kapil
- All India Institute of Medical SciencesDelhiIndia
| | | | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research InstituteNairobiKenya
| | | | | | - AC Lauer
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Myron M Levine
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USABaltimoreUnited States
| | | | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Grant Austin Mackenzie
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical MedicineFajaraGambia
| | - Tapfumanei Mashe
- National Microbiology Reference LaboratoryHarareZimbabwe
- World Health OrganizationHarareZimbabwe
| | | | - Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical SciencesBengaluruIndia
| | | | - Satheesh Nair
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | | | | | | | - Iruka N Okeke
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of OxfordOxfordUnited Kingdom
- The NIHR Oxford Biomedical Research CentreOxfordUnited Kingdom
| | | | - Firdausi Qadri
- International Centre for Diarrhoeal Disease ResearchDhakaBangladesh
| | - Farah N Qamar
- Department of Pediatrics and Child Health, Aga Khan UniversityKarachiPakistan
| | | | - Savitra Devi Rambocus
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - David A Rasko
- Department of Microbiology and Immunology, University of Maryland School of MedicineBaltimoreUnited States
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimoreUnited States
| | - Pallab Ray
- Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | - Roy Robins-Browne
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of MelbourneMelbourneAustralia
- Murdoch Children’s Research Institute, Royal Children’s HospitalParkvilleAustralia
| | | | | | | | | | | | - Mohammad Saiful Islam Sajib
- Child Health Research FoundationDhakaBangladesh
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of GlasgowGlasgowUnited Kingdom
| | | | - Jivan Shakya
- Dhulikhel HospitalDhulikhelNepal
- Institute for Research in Science and TechnologyKathmanduNepal
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical SciencesBengaluruIndia
| | - Jayanthi Shastri
- Topiwala National Medical CollegeMumbaiIndia
- Kasturba Hospital for Infectious DiseasesMumbaiIndia
| | - Rajeev Shrestha
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University HospitalDhulikhelNepal
| | - Sonia Sia
- Research Institute for Tropical Medicine, Department of HealthMuntinlupa CityPhilippines
| | - Michael J Sikorski
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USABaltimoreUnited States
- Department of Microbiology and Immunology, University of Maryland School of MedicineBaltimoreUnited States
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimoreUnited States
| | | | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable DiseasesJohannesburgSouth Africa
| | - Kaitlin A Tagg
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Dipesh Tamrakar
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University HospitalDhulikhelNepal
| | | | - Maria Thomas
- Christian Medical College, LudhianaLudhianaIndia
| | | | | | | | - Siaosi Tupua
- Ministry of Health, Government of SamoaApiaSamoa
| | | | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | | | - Jackie Wright
- ESR, Institute of Environmental Science and Research Ltd., PoriruaWellingtonNew Zealand
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Jacqueline A Keane
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- IAVI, Chelsea & Westminster HospitalLondonUnited Kingdom
| | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash UniversityMelbourneAustralia
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10
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Aguilar GR, Swetschinski LR, Weaver ND, Ikuta KS, Mestrovic T, Gray AP, Chung E, Wool EE, Han C, Hayoon AG, Araki DT, Abdollahi A, Abu-Zaid A, Adnan M, Agarwal R, Dehkordi JA, Aravkin AY, Areda D, Azzam AY, Berezin EN, Bhagavathula AS, Bhutta ZA, Bhuyan SS, Browne AJ, Castañeda-Orjuela CA, Chandrasekar EK, Ching PR, Dai X, Darmstadt GL, De la Hoz FP, Diao N, Diaz D, Mombaque dos Santos W, Eyre D, Garcia C, Haines-Woodhouse G, Hassen MB, Henry NJ, Hopkins S, Hossain MM, Iregbu KC, Iwu CC, Jacobs JA, Janko MM, Jones R, Karaye IM, Khalil IA, Khan IA, Khan T, Khubchandani J, Khusuwan S, Kisa A, Koyaweda GW, Krapp F, Kumaran EA, Kyu HH, Lim SS, Liu X, Luby S, Maharaj SB, Maronga C, Martorell M, May J, McManigal B, Mokdad AH, Moore CE, Mostafavi E, Murillo-Zamora E, Mussi-Pinhata MM, Nanavati R, Nassereldine H, Natto ZS, Qamar FN, Nuñez-Samudio V, Ochoa TJ, Ojo-Akosile TR, Olagunju AT, Olivas-Martinez A, Ortiz-Brizuela E, Ounchanum P, Paredes JL, Patthipati VS, Pawar S, Pereira M, Pollard A, Ponce-De-Leon A, Sady Prates EJ, Qattea I, Reyes LF, Roilides E, Rosenthal VD, Rudd KE, Sangchan W, Seekaew S, Seylani A, Shababi N, Sham S, Sifuentes-Osornio J, Singh H, Stergachis A, Tasak N, Tat NY, Thaiprakong A, Valdez PR, Yada DY, Yunusa I, Zastrozhin MS, Hay SI, Dolecek C, Sartorius B, Murray CJ, Naghavi M. The burden of antimicrobial resistance in the Americas in 2019: a cross-country systematic analysis. Lancet Reg Health Am 2023; 25:100561. [PMID: 37727594 PMCID: PMC10505822 DOI: 10.1016/j.lana.2023.100561] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/22/2023] [Accepted: 07/10/2023] [Indexed: 09/21/2023]
Abstract
Background Antimicrobial resistance (AMR) is an urgent global health challenge and a critical threat to modern health care. Quantifying its burden in the WHO Region of the Americas has been elusive-despite the region's long history of resistance surveillance. This study provides comprehensive estimates of AMR burden in the Americas to assess this growing health threat. Methods We estimated deaths and disability-adjusted life-years (DALYs) attributable to and associated with AMR for 23 bacterial pathogens and 88 pathogen-drug combinations for countries in the WHO Region of the Americas in 2019. We obtained data from mortality registries, surveillance systems, hospital systems, systematic literature reviews, and other sources, and applied predictive statistical modelling to produce estimates of AMR burden for all countries in the Americas. Five broad components were the backbone of our approach: the number of deaths where infection had a role, the proportion of infectious deaths attributable to a given infectious syndrome, the proportion of infectious syndrome deaths attributable to a given pathogen, the percentage of pathogens resistant to an antibiotic class, and the excess risk of mortality (or duration of an infection) associated with this resistance. We then used these components to estimate the disease burden by applying two counterfactual scenarios: deaths attributable to AMR (compared to an alternative scenario where resistant infections are replaced with susceptible ones), and deaths associated with AMR (compared to an alternative scenario where resistant infections would not occur at all). We generated 95% uncertainty intervals (UIs) for final estimates as the 25th and 975th ordered values across 1000 posterior draws, and models were cross-validated for out-of-sample predictive validity. Findings We estimated 569,000 deaths (95% UI 406,000-771,000) associated with bacterial AMR and 141,000 deaths (99,900-196,000) attributable to bacterial AMR among the 35 countries in the WHO Region of the Americas in 2019. Lower respiratory and thorax infections, as a syndrome, were responsible for the largest fatal burden of AMR in the region, with 189,000 deaths (149,000-241,000) associated with resistance, followed by bloodstream infections (169,000 deaths [94,200-278,000]) and peritoneal/intra-abdominal infections (118,000 deaths [78,600-168,000]). The six leading pathogens (by order of number of deaths associated with resistance) were Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Streptococcus pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. Together, these pathogens were responsible for 452,000 deaths (326,000-608,000) associated with AMR. Methicillin-resistant S. aureus predominated as the leading pathogen-drug combination in 34 countries for deaths attributable to AMR, while aminopenicillin-resistant E. coli was the leading pathogen-drug combination in 15 countries for deaths associated with AMR. Interpretation Given the burden across different countries, infectious syndromes, and pathogen-drug combinations, AMR represents a substantial health threat in the Americas. Countries with low access to antibiotics and basic health-care services often face the largest age-standardised mortality rates associated with and attributable to AMR in the region, implicating specific policy interventions. Evidence from this study can guide mitigation efforts that are tailored to the needs of each country in the region while informing decisions regarding funding and resource allocation. Multisectoral and joint cooperative efforts among countries will be a key to success in tackling AMR in the Americas. Funding Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Health and Social Care using UK aid funding managed by the Fleming Fund.
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11
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Fachrul M, Karkey A, Shakya M, Judd LM, Harshegyi T, Sim KS, Tonks S, Dongol S, Shrestha R, Salim A, Baker S, Pollard AJ, Khor CC, Dolecek C, Basnyat B, Dunstan SJ, Holt KE, Inouye M. Direct inference and control of genetic population structure from RNA sequencing data. Commun Biol 2023; 6:804. [PMID: 37532769 PMCID: PMC10397182 DOI: 10.1038/s42003-023-05171-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 07/24/2023] [Indexed: 08/04/2023] Open
Abstract
RNAseq data can be used to infer genetic variants, yet its use for estimating genetic population structure remains underexplored. Here, we construct a freely available computational tool (RGStraP) to estimate RNAseq-based genetic principal components (RG-PCs) and assess whether RG-PCs can be used to control for population structure in gene expression analyses. Using whole blood samples from understudied Nepalese populations and the Geuvadis study, we show that RG-PCs had comparable results to paired array-based genotypes, with high genotype concordance and high correlations of genetic principal components, capturing subpopulations within the dataset. In differential gene expression analysis, we found that inclusion of RG-PCs as covariates reduced test statistic inflation. Our paper demonstrates that genetic population structure can be directly inferred and controlled for using RNAseq data, thus facilitating improved retrospective and future analyses of transcriptomic data.
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Affiliation(s)
- Muhamad Fachrul
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia.
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia.
| | - Abhilasha Karkey
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
- Patan Academy of Health Sciences, Patan Hospital, Lalitpur, Nepal
| | - Mila Shakya
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
- Patan Academy of Health Sciences, Patan Hospital, Lalitpur, Nepal
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Taylor Harshegyi
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Kar Seng Sim
- Genome Institute of Singapore, Singapore, Singapore
| | - Susan Tonks
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Sabina Dongol
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
- Patan Academy of Health Sciences, Patan Hospital, Lalitpur, Nepal
| | | | - Agus Salim
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, Australia
- Department of Population Health, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Stephen Baker
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | | | - Christiane Dolecek
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Sarah J Dunstan
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia.
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK.
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
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Abdel Hamid MM, Abdelraheem MH, Acheampong DO, Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amenga-Etego L, Andagalu B, Anderson T, Andrianaranjaka V, Aniebo I, Aninagyei E, Ansah F, Ansah PO, Apinjoh T, Arnaldo P, Ashley E, Auburn S, Awandare GA, Ba H, Baraka V, Barry A, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Bouyou-Akotet M, Branch O, Bull PC, Cheah H, Chindavongsa K, Chookajorn T, Chotivanich K, Claessens A, Conway DJ, Corredor V, Courtier E, Craig A, D'Alessandro U, Dama S, Day N, Denis B, Dhorda M, Diakite M, Djimde A, Dolecek C, Dondorp A, Doumbia S, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Enosse SMM, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fleharty M, Forbes M, Fukuda M, Gamboa D, Ghansah A, Golassa L, Goncalves S, Harrison GLA, Healy SA, Hendry JA, Hernandez-Koutoucheva A, Hien TT, Hill CA, Hombhanje F, Hott A, Htut Y, Hussein M, Imwong M, Ishengoma D, Jackson SA, Jacob CG, Jeans J, Johnson KJ, Kamaliddin C, Kamau E, Keatley J, Kochakarn T, Konate DS, Konaté A, Kone A, Kwiatkowski DP, Kyaw MP, Kyle D, Lawniczak M, Lee SK, Lemnge M, Lim P, Lon C, Loua KM, Mandara CI, Marfurt J, Marsh K, Maude RJ, Mayxay M, Maïga-Ascofaré O, Miotto O, Mita T, Mobegi V, Mohamed AO, Mokuolu OA, Montgomery J, Morang’a CM, Mueller I, Murie K, Newton PN, Ngo Duc T, Nguyen T, Nguyen TN, Nguyen Thi Kim T, Nguyen Van H, Noedl H, Nosten F, Noviyanti R, Ntui VNN, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Oyibo WA, Pearson R, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Quang HH, Randrianarivelojosia M, Rayner JC, Ringwald P, Rosanas-Urgell A, Rovira-Vallbona E, Ruano-Rubio V, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Sissoko MS, Smith C, Su XZ, Sutherland C, Takala-Harrison S, Talman A, Tavul L, Thanh NV, Thathy V, Thu AM, Toure M, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Whitton G, Yavo W, van der Pluijm RW. Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples. Wellcome Open Res 2023; 8:22. [PMID: 36864926 PMCID: PMC9971654 DOI: 10.12688/wellcomeopenres.18681.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2022] [Indexed: 01/18/2023] Open
Abstract
We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations. We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent. We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines. Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.
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Affiliation(s)
| | | | - Mohamed Hassan Abdelraheem
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
- Nuclear Applications In Biological Sciences, Sudan Atomic Energy Commission, Khartoum, Sudan
| | - Desmond Omane Acheampong
- Department of Biomedical Sciences, School of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Ambroise Ahouidi
- Health Research Epidemiological Surveillance and Training Institute (IRESSEF), Université Cheikh Anta Diop, Dakar, Senegal
| | - Mozam Ali
- Wellcome Sanger Institute, Hinxton, UK
| | | | - Alfred Amambua-Ngwa
- Wellcome Sanger Institute, Hinxton, UK
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Ben Andagalu
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya
| | - Tim Anderson
- Texas Biomedical Research Institute, San Antonio, USA
| | | | | | - Enoch Aninagyei
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health & Allied Sciences, Ho, Ghana
| | - Felix Ansah
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
| | - Patrick O Ansah
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | | | - Paulo Arnaldo
- Instituto Nacional de Saúde (INS), Maputo, Mozambique
| | - Elizabeth Ashley
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Sarah Auburn
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Nuffield Department of Medicine, University of Oxford, UK
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
| | - Hampate Ba
- Institut National de Recherche en Santé Publique, Nouakchott, Mauritania
| | - Vito Baraka
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
- Department of Epidemiology, International Health Unit, Universiteit Antwerpen, Antwerp, Belgium
| | - Alyssa Barry
- Walter and Eliza Hall Institute, Melbourne, Australia
- Deakin University, Geelong, Australia
- Burnet Institute, Melbourne, Australia
| | - Philip Bejon
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Maciej F Boni
- Nuffield Department of Medicine, University of Oxford, UK
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Steffen Borrmann
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Teun Bousema
- London School of Hygiene and Tropical Medicine, London, UK
- Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marielle Bouyou-Akotet
- Department of Parasitology-Mycology, Université des Sciences de la Santé, Libreville, Gabon
| | - Oralee Branch
- NYU School of Medicine Langone Medical Center, New York, USA
| | - Peter C Bull
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Huch Cheah
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
| | | | | | | | - Antoine Claessens
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
- LPHI, MIVEGEC, INSERM, CNRS, IRD, University of Montpellier, Montpellier, France
| | - David J Conway
- London School of Hygiene and Tropical Medicine, London, UK
| | | | | | - Alister Craig
- Liverpool School of Tropical Medicine, Liverpool, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Program, Blantyre, Malawi
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Souleymane Dama
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nicholas Day
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research Program, Blantyre, Malawi
| | - Mehul Dhorda
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- WorldWide Antimalarial Resistance Network – Asia Regional Centre, Bangkok, Thailand
| | - Mahamadou Diakite
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center (UCRC), Bamako, Mali
| | - Abdoulaye Djimde
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Arjen Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Seydou Doumbia
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center (UCRC), Bamako, Mali
| | - Chris Drakeley
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Patrick Duffy
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | - Diego F Echeverry
- Departamento de Microbiología, Universidad del Valle, Cali, Colombia
- Centro Internacional de Entrenamiento e Investigaciones Médicas - CIDEIM, Cali, Colombia
| | | | | | - Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Caterina A Fanello
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Mark Fleharty
- Broad Institute of Harvard and MIT and Harvard, Cambridge, MA, USA
| | | | - Mark Fukuda
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anita Ghansah
- Nogouchi Memorial Institute for Medical Research, Legon-Accra, Ghana
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Sara Anne Healy
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | - Jason A Hendry
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Tran Tinh Hien
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Catherine A Hill
- Department of Entomology, Purdue University, West Lafayette, USA
| | - Francis Hombhanje
- Centre for Health Research & Diagnostics, Divine Word University, Madang, Papua New Guinea
| | | | - Ye Htut
- Department of Medical Research, Yangon, Myanmar
| | - Mazza Hussein
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | | | - Deus Ishengoma
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
- East African Consortium for Clinical Research (EACCR), Dar es Salaam, Tanzania
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | | | | | | | - Claire Kamaliddin
- Institute of Research for Development (IRD), Paris, France
- The University of Calgary, Calgary, Canada
| | - Edwin Kamau
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | | | - Drissa S Konate
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Aminatou Kone
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Myat P Kyaw
- Myanmar Oxford Clinical Research Unit, University of Oxford, Yangon, Myanmar
- University of Public Health, Yangon, Myanmar
| | - Dennis Kyle
- University of South Florida, Tampa, USA
- University of Georgia, Athens, USA
| | | | - Samuel K Lee
- Broad Institute of Harvard and MIT and Harvard, Cambridge, MA, USA
| | - Martha Lemnge
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
| | - Pharath Lim
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
- Medical Care Development International, Maryland, USA
| | - Chanthap Lon
- National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Kovana M Loua
- University Gamal Abdel Nasser of Conakry, Conakry, Guinea
- Institut National de Santé Publique, Conakry, Guinea
| | - Celine I Mandara
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania
| | - Jutta Marfurt
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Kevin Marsh
- Nuffield Department of Medicine, University of Oxford, UK
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Richard James Maude
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Harvard TH Chan School of Public Health, Harvard University, Boston, USA
| | - Mayfong Mayxay
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao People's Democratic Republic
| | - Oumou Maïga-Ascofaré
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Research in Tropical Medicine, Kwame Nkrumah University of Sciences and Technology, Kumasi, Ghana
| | - Olivo Miotto
- Wellcome Sanger Institute, Hinxton, UK
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- MRC Centre for Genomics and Global Health, Big Data Institute, Oxford University, Oxford, UK
| | | | - Victor Mobegi
- Department of Biochemistry and Centre for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya
| | | | - Olugbenga A Mokuolu
- Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria
| | - Jaqui Montgomery
- Malawi-Liverpool-Wellcome Trust Clinical Research Program, Blantyre, Malawi
- World Mosquito Program, Monash University, Melbourne, Australia
| | - Collins Misita Morang’a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
| | | | - Paul N Newton
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Thang Ngo Duc
- National Institute of Malariology, Parasitology and Entomology (NIMPE), Hanoi, Vietnam
| | | | - Thuy-Nhien Nguyen
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | | | - Hong Nguyen Van
- National Institute of Malariology, Parasitology and Entomology (NIMPE), Hanoi, Vietnam
| | - Harald Noedl
- MARIB - Malaria Research Initiative Bandarban, Bandarban, Bangladesh
- Medical University of Vienna, Vienna, Austria
| | - Francois Nosten
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | | | | | - Alexis Nzila
- King Fahid University of Petroleum and Minerals (KFUMP), Dhahran, Saudi Arabia
| | | | - Harold Ocholla
- KEMRI Centres for Disease Control and Prevention (CDC) Research Program, Kisumu, Kenya
- Centre for Bioinformatics and Biotechnology, University of Nairobi, Nairobi, Kenya
| | - Abraham Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Irene Omedo
- Wellcome Sanger Institute, Hinxton, UK
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Marie A Onyamboko
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Congo, Democratic Republic
| | | | - Kolapo Oyebola
- Nigerian Institute of Medical Research, Lagos, Nigeria
- Parasitology and Bioinformatics Unit, Faculty of Science, University of Lagos, Lagos, Nigeria
| | | | | | - Norbert Peshu
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Aung P Phyo
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Shoklo Malaria Research Unit, Bangkok, Thailand
| | | | - Ric N Price
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | | | - Huynh Hong Quang
- Institute of Malariology, Parasitology, and Entomology (IMPE) Quy Nhon, Ministry of Health, Quy Nhon, Vietnam
| | - Milijaona Randrianarivelojosia
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Universités d'Antananarivo et de Mahajanga, Antananarivo, Madagascar
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | | | | | | | - Lastenia Ruiz
- Universidad Nacional de la Amazonia Peruana, Iquitos, Peru
| | - David Saunders
- Department of Medicine, Uniformed Services University, Bethesda, MD, USA
| | - Alex Shayo
- Nelson Mandela Institute of Science and Technology, Arusha, Tanzania
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | | | - Mahamadou S. Sissoko
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Xin-zhuan Su
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | | | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland, School of Medicine, Baltimore, MD, USA
| | - Arthur Talman
- MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Ngo Viet Thanh
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Vandana Thathy
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Aung Myint Thu
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Mahamoudou Toure
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | | | - Joseph Vinetz
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Yale School of Medicine, New Haven, CT, USA
| | - Thomas E Wellems
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
| | - Jason Wendler
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Maryland, USA
- Seattle Children’s Hospital, Seattle, USA
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | - William Yavo
- University Félix Houphouët-Boigny, Abidjan, Cote d'Ivoire
- Malaria Research and Control Center of the National Institute of Public Health, Abidjan, Cote d'Ivoire
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Dolecek C, Shakoor S, Basnyat B, Okwor T, Sartorius B. Drug-resistant bacterial infections: We need urgent action and investment that focus on the weakest link. PLoS Biol 2022; 20:e3001903. [PMID: 36383561 PMCID: PMC9710749 DOI: 10.1371/journal.pbio.3001903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/30/2022] [Indexed: 11/17/2022] Open
Abstract
Despite high mortality and morbidity, drug-resistant bacterial infections remain the forgotten pandemic. We argue for strengthening of diagnostics, WASH (water, sanitation, and hygiene) and infection prevention and control to reduce drug-resistant infections, as an integral part of sustainable high-quality health services, particularly in low- and middle-income countries.
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Affiliation(s)
- Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- * E-mail:
| | - Sadia Shakoor
- Department of Pathology and Laboratory Medicine; Department of Pediatrics and Child Health, Aga Khan University and Hospitals, Karachi, Pakistan
| | - Buddha Basnyat
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford University Clinical Research Unit—Nepal, Kathmandu, Nepal
- Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Tochi Okwor
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Benn Sartorius
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
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Mestrovic T, Robles Aguilar G, Swetschinski LR, Ikuta KS, Gray AP, Davis Weaver N, Han C, Wool EE, Gershberg Hayoon A, Hay SI, Dolecek C, Sartorius B, Murray CJL, Addo IY, Ahinkorah BO, Ahmed A, Aldeyab MA, Allel K, Ancuceanu R, Anyasodor AE, Ausloos M, Barra F, Bhagavathula AS, Bhandari D, Bhaskar S, Cruz-Martins N, Dastiridou A, Dokova K, Dubljanin E, Durojaiye OC, Fagbamigbe AF, Ferrero S, Gaal PA, Gupta VB, Gupta VK, Gupta VK, Herteliu C, Hussain S, Ilic IM, Ilic MD, Jamshidi E, Joo T, Karch A, Kisa A, Kisa S, Kostyanev T, Kyu HH, Lám J, Lopes G, Mathioudakis AG, Mentis AFA, Michalek IM, Moni MA, Moore CE, Mulita F, Negoi I, Negoi RI, Palicz T, Pana A, Perdigão J, Petcu IR, Rabiee N, Rawaf DL, Rawaf S, Shakhmardanov MZ, Sheikh A, Silva LMLR, Skryabin VY, Skryabina AA, Socea B, Stergachis A, Stoeva TZ, Sumi CD, Thiyagarajan A, Tovani-Palone MR, Yesiltepe M, Zaman SB, Naghavi M. The burden of bacterial antimicrobial resistance in the WHO European region in 2019: a cross-country systematic analysis. Lancet Public Health 2022; 7:e897-e913. [PMID: 36244350 PMCID: PMC9630253 DOI: 10.1016/s2468-2667(22)00225-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Antimicrobial resistance (AMR) represents one of the most crucial threats to public health and modern health care. Previous studies have identified challenges with estimating the magnitude of the problem and its downstream effect on human health and mortality. To our knowledge, this study presents the most comprehensive set of regional and country-level estimates of AMR burden in the WHO European region to date. METHODS We estimated deaths and disability-adjusted life-years attributable to and associated with AMR for 23 bacterial pathogens and 88 pathogen-drug combinations for the WHO European region and its countries in 2019. Our methodological approach consisted of five broad components: the number of deaths in which infection had a role, the proportion of infectious deaths attributable to a given infectious syndrome, the proportion of infectious syndrome deaths attributable to a given pathogen, the percentage of a given pathogen resistant to an antimicrobial drug of interest, and the excess risk of mortality (or duration of an infection) associated with this resistance. These components were then used to estimate the disease burden by using two counterfactual scenarios: deaths attributable to AMR (considering an alternative scenario where infections with resistant pathogens are replaced with susceptible ones) and deaths associated with AMR (considering an alternative scenario where drug-resistant infections would not occur at all). Data were solicited from a wide array of international stakeholders; these included research hospitals, surveillance networks, and infection databases maintained by private laboratories and medical technology companies. We generated 95% uncertainty intervals (UIs) for final estimates as the 25th and 975th ordered values across 1000 posterior draws, and models were cross-validated for out-of-sample predictive validity. FINDINGS We estimated 541 000 deaths (95% UI 370 000-763 000) associated with bacterial AMR and 133 000 deaths (90 100-188 000) attributable to bacterial AMR in the whole WHO European region in 2019. The largest fatal burden of AMR in the region came from bloodstream infections, with 195 000 deaths (104 000-333 000) associated with resistance, followed by intra-abdominal infections (127 000 deaths [81 900-185 000]) and respiratory infections (120 000 deaths [94 500-154 000]). Seven leading pathogens were responsible for about 457 000 deaths associated with resistance in 53 countries of this region; these pathogens were, in descending order of mortality, Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterococcus faecium, Streptococcus pneumoniae, and Acinetobacter baumannii. Methicillin-resistant S aureus was shown to be the leading pathogen-drug combination in 27 countries for deaths attributable to AMR, while aminopenicillin-resistant E coli predominated in 47 countries for deaths associated with AMR. INTERPRETATION The high levels of resistance for several important bacterial pathogens and pathogen-drug combinations, together with the high mortality rates associated with these pathogens, show that AMR is a serious threat to public health in the WHO European region. Our regional and cross-country analyses open the door for strategies that can be tailored to leading pathogen-drug combinations and the available resources in a specific location. These results underscore that the most effective way to tackle AMR in this region will require targeted efforts and investments in conjunction with continuous outcome-based research endeavours. FUNDING Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Health and Social Care using UK aid funding managed by the Fleming Fund.
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Chipeta MG, Kumaran EPA, Browne AJ, Hamadani BHK, Haines-Woodhouse G, Sartorius B, Reiner RC, Dolecek C, Hay SI, Moore CE. Mapping local variation in household overcrowding across Africa from 2000 to 2018: a modelling study. Lancet Planet Health 2022; 6:e670-e681. [PMID: 35932787 PMCID: PMC9364142 DOI: 10.1016/s2542-5196(22)00149-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 05/31/2022] [Accepted: 06/13/2022] [Indexed: 05/10/2023]
Abstract
BACKGROUND Household overcrowding is a serious public health threat associated with high morbidity and mortality. Rapid population growth and urbanisation contribute to overcrowding and poor sanitation in low-income and middle- income countries, and are risk factors for the spread of infectious diseases, including COVID-19, and antimicrobial resistance. Many countries do not have adequate surveillance capacity to monitor household overcrowding. Geostatistical models are therefore useful tools for estimating household overcrowding. In this study, we aimed to estimate household overcrowding in Africa between 2000 and 2018 by combining available household survey data, population censuses, and other country-specific household surveys within a geostatistical framework. METHODS We used data from household surveys and population censuses to generate a Bayesian geostatistical model of household overcrowding in Africa for the 19-year period between 2000 and 2018. Additional sociodemographic and health-related covariates informed the model, which covered 54 African countries. FINDINGS We analysed 287 surveys and population censuses, covering 78 695 991 households. Spatial and temporal variability arose in household overcrowding estimates over time. In 2018, the highest overcrowding estimates were observed in the Horn of Africa region (median proportion 62% [IQR 57-63]); the lowest regional median proportion was estimated for the north of Africa region (16% [14-19]). Overall, 474·4 million (95% uncertainty interval [UI] 250·1 million-740·7 million) people were estimated to be living in overcrowded conditions in Africa in 2018, a 62·7% increase from the estimated 291·5 million (180·8 million-417·3 million) people who lived in overcrowded conditions in the year 2000. 48·5% (229·9 million) of people living in overcrowded conditions came from six African countries (Nigeria, Ethiopia, Democratic Republic of the Congo, Sudan, Uganda, and Kenya), with a combined population of 538·3 million people. INTERPRETATION This study incorporated survey and population censuses data and used geostatistical modelling to estimate continent-wide overcrowding over a 19-year period. Our analysis identified countries and areas with high numbers of people living in overcrowded conditions, thereby providing a benchmark for policy planning and the implementation of interventions such as in infectious disease control. FUNDING UK Department of Health and Social Care, Wellcome Trust, Bill & Melinda Gates Foundation.
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Affiliation(s)
- Michael G Chipeta
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK; African Institute for Development Policy, Lilongwe, Malawi
| | - Emmanuelle P A Kumaran
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Annie J Browne
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Bahar H Kashef Hamadani
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Georgina Haines-Woodhouse
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Benn Sartorius
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA
| | - Robert C Reiner
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA; Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle, WA, USA
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Simon I Hay
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA; Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle, WA, USA
| | - Catrin E Moore
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK; Centre for Neonatal and Paediatric Infection, St George's, University of London, London, UK.
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Birger R, Antillón M, Bilcke J, Dolecek C, Dougan G, Pollard AJ, Neuzil KM, Frost I, Laxminarayan R, Pitzer VE. Estimating the effect of vaccination on antimicrobial-resistant typhoid fever in 73 countries supported by Gavi: a mathematical modelling study. The Lancet Infectious Diseases 2022; 22:679-691. [PMID: 35123673 PMCID: PMC9021026 DOI: 10.1016/s1473-3099(21)00627-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/20/2021] [Accepted: 09/23/2021] [Indexed: 11/24/2022]
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Murray CJL, Ikuta KS, Sharara F, Swetschinski L, Robles Aguilar G, Gray A, Han C, Bisignano C, Rao P, Wool E, Johnson SC, Browne AJ, Chipeta MG, Fell F, Hackett S, Haines-Woodhouse G, Kashef Hamadani BH, Kumaran EAP, McManigal B, Achalapong S, Agarwal R, Akech S, Albertson S, Amuasi J, Andrews J, Aravkin A, Ashley E, Babin FX, Bailey F, Baker S, Basnyat B, Bekker A, Bender R, Berkley JA, Bethou A, Bielicki J, Boonkasidecha S, Bukosia J, Carvalheiro C, Castañeda-Orjuela C, Chansamouth V, Chaurasia S, Chiurchiù S, Chowdhury F, Clotaire Donatien R, Cook AJ, Cooper B, Cressey TR, Criollo-Mora E, Cunningham M, Darboe S, Day NPJ, De Luca M, Dokova K, Dramowski A, Dunachie SJ, Duong Bich T, Eckmanns T, Eibach D, Emami A, Feasey N, Fisher-Pearson N, Forrest K, Garcia C, Garrett D, Gastmeier P, Giref AZ, Greer RC, Gupta V, Haller S, Haselbeck A, Hay SI, Holm M, Hopkins S, Hsia Y, Iregbu KC, Jacobs J, Jarovsky D, Javanmardi F, Jenney AWJ, Khorana M, Khusuwan S, Kissoon N, Kobeissi E, Kostyanev T, Krapp F, Krumkamp R, Kumar A, Kyu HH, Lim C, Lim K, Limmathurotsakul D, Loftus MJ, Lunn M, Ma J, Manoharan A, Marks F, May J, Mayxay M, Mturi N, Munera-Huertas T, Musicha P, Musila LA, Mussi-Pinhata MM, Naidu RN, Nakamura T, Nanavati R, Nangia S, Newton P, Ngoun C, Novotney A, Nwakanma D, Obiero CW, Ochoa TJ, Olivas-Martinez A, Olliaro P, Ooko E, Ortiz-Brizuela E, Ounchanum P, Pak GD, Paredes JL, Peleg AY, Perrone C, Phe T, Phommasone K, Plakkal N, Ponce-de-Leon A, Raad M, Ramdin T, Rattanavong S, Riddell A, Roberts T, Robotham JV, Roca A, Rosenthal VD, Rudd KE, Russell N, Sader HS, Saengchan W, Schnall J, Scott JAG, Seekaew S, Sharland M, Shivamallappa M, Sifuentes-Osornio J, Simpson AJ, Steenkeste N, Stewardson AJ, Stoeva T, Tasak N, Thaiprakong A, Thwaites G, Tigoi C, Turner C, Turner P, van Doorn HR, Velaphi S, Vongpradith A, Vongsouvath M, Vu H, Walsh T, Walson JL, Waner S, Wangrangsimakul T, Wannapinij P, Wozniak T, Young Sharma TEMW, Yu KC, Zheng P, Sartorius B, Lopez AD, Stergachis A, Moore C, Dolecek C, Naghavi M. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 2022; 399:629-655. [PMID: 35065702 PMCID: PMC8841637 DOI: 10.1016/s0140-6736(21)02724-0] [Citation(s) in RCA: 3800] [Impact Index Per Article: 1900.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/18/2021] [Accepted: 11/24/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND Antimicrobial resistance (AMR) poses a major threat to human health around the world. Previous publications have estimated the effect of AMR on incidence, deaths, hospital length of stay, and health-care costs for specific pathogen-drug combinations in select locations. To our knowledge, this study presents the most comprehensive estimates of AMR burden to date. METHODS We estimated deaths and disability-adjusted life-years (DALYs) attributable to and associated with bacterial AMR for 23 pathogens and 88 pathogen-drug combinations in 204 countries and territories in 2019. We obtained data from systematic literature reviews, hospital systems, surveillance systems, and other sources, covering 471 million individual records or isolates and 7585 study-location-years. We used predictive statistical modelling to produce estimates of AMR burden for all locations, including for locations with no data. Our approach can be divided into five broad components: number of deaths where infection played a role, proportion of infectious deaths attributable to a given infectious syndrome, proportion of infectious syndrome deaths attributable to a given pathogen, the percentage of a given pathogen resistant to an antibiotic of interest, and the excess risk of death or duration of an infection associated with this resistance. Using these components, we estimated disease burden based on two counterfactuals: deaths attributable to AMR (based on an alternative scenario in which all drug-resistant infections were replaced by drug-susceptible infections), and deaths associated with AMR (based on an alternative scenario in which all drug-resistant infections were replaced by no infection). We generated 95% uncertainty intervals (UIs) for final estimates as the 25th and 975th ordered values across 1000 posterior draws, and models were cross-validated for out-of-sample predictive validity. We present final estimates aggregated to the global and regional level. FINDINGS On the basis of our predictive statistical models, there were an estimated 4·95 million (3·62-6·57) deaths associated with bacterial AMR in 2019, including 1·27 million (95% UI 0·911-1·71) deaths attributable to bacterial AMR. At the regional level, we estimated the all-age death rate attributable to resistance to be highest in western sub-Saharan Africa, at 27·3 deaths per 100 000 (20·9-35·3), and lowest in Australasia, at 6·5 deaths (4·3-9·4) per 100 000. Lower respiratory infections accounted for more than 1·5 million deaths associated with resistance in 2019, making it the most burdensome infectious syndrome. The six leading pathogens for deaths associated with resistance (Escherichia coli, followed by Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa) were responsible for 929 000 (660 000-1 270 000) deaths attributable to AMR and 3·57 million (2·62-4·78) deaths associated with AMR in 2019. One pathogen-drug combination, meticillin-resistant S aureus, caused more than 100 000 deaths attributable to AMR in 2019, while six more each caused 50 000-100 000 deaths: multidrug-resistant excluding extensively drug-resistant tuberculosis, third-generation cephalosporin-resistant E coli, carbapenem-resistant A baumannii, fluoroquinolone-resistant E coli, carbapenem-resistant K pneumoniae, and third-generation cephalosporin-resistant K pneumoniae. INTERPRETATION To our knowledge, this study provides the first comprehensive assessment of the global burden of AMR, as well as an evaluation of the availability of data. AMR is a leading cause of death around the world, with the highest burdens in low-resource settings. Understanding the burden of AMR and the leading pathogen-drug combinations contributing to it is crucial to making informed and location-specific policy decisions, particularly about infection prevention and control programmes, access to essential antibiotics, and research and development of new vaccines and antibiotics. There are serious data gaps in many low-income settings, emphasising the need to expand microbiology laboratory capacity and data collection systems to improve our understanding of this important human health threat. FUNDING Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Health and Social Care using UK aid funding managed by the Fleming Fund.
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Meiring JE, Shakya M, Khanam F, Voysey M, Phillips MT, Tonks S, Thindwa D, Darton TC, Dongol S, Karkey A, Zaman K, Baker S, Dolecek C, Dunstan SJ, Dougan G, Holt KE, Heyderman RS, Qadri F, Pitzer VE, Basnyat B, Gordon MA, Clemens J, Pollard AJ. Burden of enteric fever at three urban sites in Africa and Asia: a multicentre population-based study. The Lancet Global Health 2021; 9:e1688-e1696. [PMID: 34798028 PMCID: PMC8609278 DOI: 10.1016/s2214-109x(21)00370-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 05/29/2021] [Accepted: 07/30/2021] [Indexed: 12/13/2022] Open
Abstract
Background Enteric fever is a serious public health concern in many low-income and middle-income countries. Numerous data gaps exist concerning the epidemiology of Salmonella enterica serotype Typhi (S Typhi) and Salmonella enterica serotype Paratyphi (S Paratyphi), which are the causative agents of enteric fever. We aimed to determine the burden of enteric fever in three urban sites in Africa and Asia. Methods In this multicentre population-based study, we did a demographic census at three urban sites in Africa (Blantyre, Malawi) and Asia (Kathmandu, Nepal and Dhaka, Bangladesh) between June 1, 2016, and Sept 25, 2018. Households were selected randomly from the demographic census. Participants from within the geographical census area presenting to study health-care facilities were approached for recruitment if they had a history of fever for 72 h or more (later changed to >48 h) or temperature of 38·0°C or higher. Facility-based passive surveillance was done between Nov 11, 2016, and Dec 31, 2018, with blood-culture collection for febrile illness. We also did a community-based serological survey to obtain data on Vi-antibody defined infections. We calculated crude incidence for blood-culture-confirmed S Typhi and S Paratyphi infection, and calculated adjusted incidence and seroincidence of S Typhi blood-culture-confirmed infection. Findings 423 618 individuals were included in the demographic census, contributing 626 219 person-years of observation for febrile illness surveillance. 624 S Typhi and 108 S Paratyphi A isolates were collected from the blood of 12 082 febrile patients. Multidrug resistance was observed in 44% S Typhi isolates and fluoroquinolone resistance in 61% of S Typhi isolates. In Blantyre, the overall crude incidence of blood-culture confirmed S Typhi was 58 cases per 100 000 person-years of observation (95% CI 48–70); the adjusted incidence was 444 cases per 100 000 person-years of observation (95% credible interval [CrI] 347–717). The corresponding rates were 74 (95% CI 62–87) and 1062 (95% CrI 683–1839) in Kathmandu, and 161 (95% CI 145–179) and 1135 (95% CrI 898–1480) in Dhaka. S Paratyphi was not found in Blantyre; overall crude incidence of blood-culture-confirmed S Paratyphi A infection was 6 cases per 100 000 person-years of observation (95% CI 3–11) in Kathmandu and 42 (95% CI 34–52) in Dhaka. Seroconversion rates for S Typhi infection per 100 000 person-years estimated from anti-Vi seroconversion episodes in serological surveillance were 2505 episodes (95% CI 1605–3727) in Blantyre, 7631 (95% CI 5913–9691) in Kathmandu, and 3256 (95% CI 2432–4270) in Dhaka. Interpretation High disease incidence and rates of antimicrobial resistance were observed across three different transmission settings and thus necessitate multiple intervention strategies to achieve global control of these pathogens. Funding Wellcome Trust and the Bill & Melinda Gates Foundation.
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Affiliation(s)
- James E Meiring
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK.
| | - Mila Shakya
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal; Patan Academy of Health Sciences, Patan Hospital, Lalitpur, Nepal
| | - Farhana Khanam
- International Centre for Diarrhoeal Diseases Research, Bangladesh, Dhaka, Bangladesh
| | - Merryn Voysey
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Maile T Phillips
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Susan Tonks
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Deus Thindwa
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; College of Medicine, University of Malawi, Blantyre, Malawi
| | - Thomas C Darton
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Sabina Dongol
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal; Patan Academy of Health Sciences, Patan Hospital, Lalitpur, Nepal
| | - Abilasha Karkey
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal; Patan Academy of Health Sciences, Patan Hospital, Lalitpur, Nepal
| | - K Zaman
- International Centre for Diarrhoeal Diseases Research, Bangladesh, Dhaka, Bangladesh
| | - Stephen Baker
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Christiane Dolecek
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK; Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Sarah J Dunstan
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia; Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Robert S Heyderman
- National Institute for Health Research Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Firdausi Qadri
- International Centre for Diarrhoeal Diseases Research, Bangladesh, Dhaka, Bangladesh
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal; Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Melita A Gordon
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; College of Medicine, University of Malawi, Blantyre, Malawi; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - John Clemens
- International Centre for Diarrhoeal Diseases Research, Bangladesh, Dhaka, Bangladesh
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
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Browne AJ, Chipeta MG, Haines-Woodhouse G, Kumaran EPA, Hamadani BHK, Zaraa S, Henry NJ, Deshpande A, Reiner RC, Day NPJ, Lopez AD, Dunachie S, Moore CE, Stergachis A, Hay SI, Dolecek C. Global antibiotic consumption and usage in humans, 2000-18: a spatial modelling study. Lancet Planet Health 2021; 5:e893-e904. [PMID: 34774223 PMCID: PMC8654683 DOI: 10.1016/s2542-5196(21)00280-1] [Citation(s) in RCA: 211] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a serious threat to global public health. WHO emphasises the need for countries to monitor antibiotic consumption to combat AMR. Many low-income and middle-income countries (LMICs) lack surveillance capacity; we aimed to use multiple data sources and statistical models to estimate global antibiotic consumption. METHODS In this spatial modelling study, we used individual-level data from household surveys to inform a Bayesian geostatistical model of antibiotic usage in children (aged <5 years) with lower respiratory tract infections in LMICs. Antibiotic consumption data were obtained from multiple sources, including IQVIA, WHO, and the European Surveillance of Antimicrobial Consumption Network (ESAC-Net). The estimates of the antibiotic usage model were used alongside sociodemographic and health covariates to inform a model of total antibiotic consumption in LMICs. This was combined with a single model of antibiotic consumption in high-income countries to produce estimates of antibiotic consumption covering 204 countries and 19 years. FINDINGS We analysed 209 surveys done between 2000 and 2018, covering 284 045 children with lower respiratory tract infections. We identified large national and subnational variations of antibiotic usage in LMICs, with the lowest levels estimated in sub-Saharan Africa and the highest in eastern Europe and central Asia. We estimated a global antibiotic consumption rate of 14·3 (95% uncertainty interval 13·2-15·6) defined daily doses (DDD) per 1000 population per day in 2018 (40·2 [37·2-43·7] billion DDD), an increase of 46% from 9·8 (9·2-10·5) DDD per 1000 per day in 2000. We identified large spatial disparities, with antibiotic consumption rates varying from 5·0 (4·8-5·3) DDD per 1000 per day in the Philippines to 45·9 DDD per 1000 per day in Greece in 2018. Additionally, we present trends in consumption of different classes of antibiotics for selected Global Burden of Disease study regions using the IQVIA, WHO, and ESAC-net input data. We identified large increases in the consumption of fluoroquinolones and third-generation cephalosporins in North Africa and Middle East, and south Asia. INTERPRETATION To our knowledge, this is the first study that incorporates antibiotic usage and consumption data and uses geostatistical modelling techniques to estimate antibiotic consumption for 204 countries from 2000 to 2018. Our analysis identifies both high rates of antibiotic consumption and a lack of access to antibiotics, providing a benchmark for future interventions. FUNDING Fleming Fund, UK Department of Health and Social Care; Wellcome Trust; and Bill & Melinda Gates Foundation.
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Affiliation(s)
- Annie J Browne
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Michael G Chipeta
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Georgina Haines-Woodhouse
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Emmanuelle P A Kumaran
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Bahar H Kashef Hamadani
- Oxford Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sabra Zaraa
- School of Pharmacy and School of Public Health, University of Washington, Seattle, WA, USA
| | - Nathaniel J Henry
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aniruddha Deshpande
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA
| | - Robert C Reiner
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA; Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle, WA, USA
| | - Nicholas P J Day
- Oxford Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Alan D Lopez
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA
| | - Susanna Dunachie
- Oxford Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Catrin E Moore
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andy Stergachis
- School of Pharmacy and School of Public Health, University of Washington, Seattle, WA, USA; Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA
| | - Simon I Hay
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA; Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle, WA, USA
| | - Christiane Dolecek
- Oxford Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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20
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Phillips MT, Meiring JE, Voysey M, Warren JL, Baker S, Basnyat B, Clemens JD, Dolecek C, Dunstan SJ, Dougan G, Gordon MA, Thindwa D, Heyderman RS, Holt KE, Qadri F, Pollard AJ, Pitzer VE. A Bayesian approach for estimating typhoid fever incidence from large-scale facility-based passive surveillance data. Stat Med 2021; 40:5853-5870. [PMID: 34428309 PMCID: PMC9291985 DOI: 10.1002/sim.9159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 12/04/2022]
Abstract
Decisions about typhoid fever prevention and control are based on estimates of typhoid incidence and their uncertainty. Lack of specific clinical diagnostic criteria, poorly sensitive diagnostic tests, and scarcity of accurate and complete datasets contribute to difficulties in calculating age‐specific population‐level typhoid incidence. Using data from the Strategic Typhoid Alliance across Africa and Asia program, we integrated demographic censuses, healthcare utilization surveys, facility‐based surveillance, and serological surveillance from Malawi, Nepal, and Bangladesh to account for under‐detection of cases. We developed a Bayesian approach that adjusts the count of reported blood‐culture‐positive cases for blood culture detection, blood culture collection, and healthcare seeking—and how these factors vary by age—while combining information from prior published studies. We validated the model using simulated data. The ratio of observed to adjusted incidence rates was 7.7 (95% credible interval [CrI]: 6.0‐12.4) in Malawi, 14.4 (95% CrI: 9.3‐24.9) in Nepal, and 7.0 (95% CrI: 5.6‐9.2) in Bangladesh. The probability of blood culture collection led to the largest adjustment in Malawi, while the probability of seeking healthcare contributed the most in Nepal and Bangladesh; adjustment factors varied by age. Adjusted incidence rates were within or below the seroincidence rate limits of typhoid infection. Estimates of blood‐culture‐confirmed typhoid fever without these adjustments results in considerable underestimation of the true incidence of typhoid fever. Our approach allows each phase of the reporting process to be synthesized to estimate the adjusted incidence of typhoid fever while correctly characterizing uncertainty, which can inform decision‐making for typhoid prevention and control.
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Affiliation(s)
- Maile T Phillips
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - James E Meiring
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.,National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK.,Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Merryn Voysey
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.,National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Stephen Baker
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - John D Clemens
- International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Sarah J Dunstan
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Melita A Gordon
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi.,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Deus Thindwa
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi.,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Robert S Heyderman
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi.,NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Department of Infection Biology, London School of Hygiene and Tropical Medicine, London
| | - Firdausi Qadri
- International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.,National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
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21
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Giri A, Karkey A, Dongol S, Arjyal A, Maharjan A, Veeraraghavan B, Paudyal B, Dolecek C, Gajurel D, Phuong DNT, Thanh DP, Qamar F, Kang G, Hien HV, John J, Lawson K, Wolbers M, Hossain MS, Sharifuzzaman M, Luangasanatip N, Maharjan N, Olliaro P, Rupali P, Shakya R, Shakoor S, Rijal S, Qureshi S, Baker S, Joshi S, Ahmed T, Darton T, Bao TN, Lubell Y, Kestelyn E, Thwaites G, Parry CM, Basnyat B. Azithromycin and cefixime combination versus azithromycin alone for the out-patient treatment of clinically suspected or confirmed uncomplicated typhoid fever in South Asia: a randomised controlled trial protocol. Wellcome Open Res 2021; 6:207. [PMID: 35097222 PMCID: PMC8772527 DOI: 10.12688/wellcomeopenres.16801.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2021] [Indexed: 12/03/2022] Open
Abstract
Background: Typhoid and paratyphoid fever (enteric fever) is a common cause of non-specific febrile infection in adults and children presenting to health care facilities in low resource settings such as the South Asia. A 7-day course of a single oral antimicrobial such as ciprofloxacin, cefixime, or azithromycin is commonly used for its treatment. Increasing antimicrobial resistance threatens the effectiveness of these treatment choices. We hypothesize that combined treatment with azithromycin (active mainly intracellularly) and cefixime (active mainly extracellularly) will be a better option for the treatment of clinically suspected and culture-confirmed typhoid fever in South Asia. Methods: This is a phase IV, international multi-center, multi-country, comparative participant-and observer-blind, 1:1 randomised clinical trial. Patients with suspected uncomplicated typhoid fever will be randomized to one of the two interventions: Arm A: azithromycin 20mg/kg/day oral dose once daily (maximum 1gm/day) and cefixime 20mg/kg/day oral dose in two divided doses (maximum 400mg bd) for 7 days, Arm B: azithromycin 20mg/kg/day oral dose once daily (max 1gm/day) for 7 days AND cefixime-matched placebo for 7 days. We will recruit 1500 patients across sites in Bangladesh, India, Nepal, and Pakistan. We will assess whether treatment outcomes are better with the combination after one week of treatment and at one- and three-months follow-up. Discussion: Combined treatment may limit the emergence of resistance if one of the components is active against resistant sub-populations not covered by the other antimicrobial activity. If the combined treatment is better than the single antimicrobial treatment, this will be an important result for patients across South Asia and other typhoid endemic areas. Clinicaltrials.gov registration: NCT04349826 (16/04/2020)
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Affiliation(s)
- Abhishek Giri
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
| | - Abhilasha Karkey
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sabina Dongol
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
| | - Amit Arjyal
- Patan Academy of Health Sciences, Lalitpur, Bagmati, 44700, Nepal
| | - Archana Maharjan
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
| | | | - Buddhi Paudyal
- Patan Academy of Health Sciences, Lalitpur, Bagmati, 44700, Nepal
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | - Duy Pham Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Farah Qamar
- Aga Khan University Hospital, Karachi, 74800, Pakistan
| | - Gagandeep Kang
- Christian Medical College, Vellore, Tamil Nadu, 632004, India
| | - Ho Van Hien
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Jacob John
- Christian Medical College, Vellore, Tamil Nadu, 632004, India
| | - Katrina Lawson
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Marcel Wolbers
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
| | - Md. Shabab Hossain
- International Centre for Diarrhoeal Disease Research (icddr, b), Dhaka, Bangladesh
| | - M Sharifuzzaman
- International Centre for Diarrhoeal Disease Research (icddr, b), Dhaka, Bangladesh
| | | | - Nhukesh Maharjan
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
| | - Piero Olliaro
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Ronas Shakya
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
| | - Sadia Shakoor
- Aga Khan University Hospital, Karachi, 74800, Pakistan
| | - Samita Rijal
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
| | - Sonia Qureshi
- Aga Khan University Hospital, Karachi, 74800, Pakistan
| | - Stephen Baker
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Subi Joshi
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research (icddr, b), Dhaka, Bangladesh
| | - Thomas Darton
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, South Yorkshire, UK
| | - Tran Nguyen Bao
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Yoel Lubell
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Bangkok, 10400, Thailand
| | - Evelyne Kestelyn
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Christopher M. Parry
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Buddha Basnyat
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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22
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Giri A, Karkey A, Dongol S, Arjyal A, Maharjan A, Veeraraghavan B, Paudyal B, Dolecek C, Gajurel D, Phuong DNT, Thanh DP, Qamar F, Kang G, Hien HV, John J, Lawson K, Wolbers M, Hossain MS, Sharifuzzaman M, Luangasanatip N, Maharjan N, Olliaro P, Rupali P, Shakya R, Shakoor S, Rijal S, Qureshi S, Baker S, Joshi S, Ahmed T, Darton T, Bao TN, Lubell Y, Kestelyn E, Thwaites G, Parry CM, Basnyat B. Azithromycin and cefixime combination versus azithromycin alone for the out-patient treatment of clinically suspected or confirmed uncomplicated typhoid fever in South Asia: a randomised controlled trial protocol. Wellcome Open Res 2021; 6:207. [PMID: 35097222 PMCID: PMC8772527 DOI: 10.12688/wellcomeopenres.16801.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2021] [Indexed: 12/27/2023] Open
Abstract
Background: Typhoid and paratyphoid fever (enteric fever) is a common cause of non-specific febrile infection in adults and children presenting to health care facilities in low resource settings such as the South Asia. A 7-day course of a single oral antimicrobial such as ciprofloxacin, cefixime, or azithromycin is commonly used for its treatment. Increasing antimicrobial resistance threatens the effectiveness of these treatment choices. We hypothesize that combined treatment with azithromycin (active mainly intracellularly) and cefixime (active mainly extracellularly) will be a better option for the treatment of clinically suspected and culture-confirmed typhoid fever in South Asia. Methods: This is a phase IV, international multi-center, multi-country, comparative participant-and observer-blind, 1:1 randomised clinical trial. Patients with suspected uncomplicated typhoid fever will be randomized to one of the two interventions: Arm A: azithromycin 20mg/kg/day oral dose once daily (maximum 1gm/day) and cefixime 20mg/kg/day oral dose in two divided doses (maximum 400mg bd) for 7 days, Arm B: azithromycin 20mg/kg/day oral dose once daily (max 1gm/day) for 7 days AND cefixime-matched placebo for 7 days. We will recruit 1500 patients across sites in Bangladesh, India, Nepal, and Pakistan. We will assess whether treatment outcomes are better with the combination after one week of treatment and at one- and three-months follow-up. Discussion: Combined treatment may limit the emergence of resistance if one of the components is active against resistant sub-populations not covered by the other antimicrobial activity. If the combined treatment is better than the single antimicrobial treatment, this will be an important result for patients across South Asia and other typhoid endemic areas. Clinicaltrials.gov registration: NCT04349826 (16/04/2020).
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Affiliation(s)
- Abhishek Giri
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
| | - Abhilasha Karkey
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sabina Dongol
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
| | - Amit Arjyal
- Patan Academy of Health Sciences, Lalitpur, Bagmati, 44700, Nepal
| | - Archana Maharjan
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
| | | | - Buddhi Paudyal
- Patan Academy of Health Sciences, Lalitpur, Bagmati, 44700, Nepal
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | - Duy Pham Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Farah Qamar
- Aga Khan University Hospital, Karachi, 74800, Pakistan
| | - Gagandeep Kang
- Christian Medical College, Vellore, Tamil Nadu, 632004, India
| | - Ho Van Hien
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Jacob John
- Christian Medical College, Vellore, Tamil Nadu, 632004, India
| | - Katrina Lawson
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Marcel Wolbers
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
| | - Md. Shabab Hossain
- International Centre for Diarrhoeal Disease Research (icddr, b), Dhaka, Bangladesh
| | - M Sharifuzzaman
- International Centre for Diarrhoeal Disease Research (icddr, b), Dhaka, Bangladesh
| | | | - Nhukesh Maharjan
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
| | - Piero Olliaro
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Ronas Shakya
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
| | - Sadia Shakoor
- Aga Khan University Hospital, Karachi, 74800, Pakistan
| | - Samita Rijal
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
| | - Sonia Qureshi
- Aga Khan University Hospital, Karachi, 74800, Pakistan
| | - Stephen Baker
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Subi Joshi
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research (icddr, b), Dhaka, Bangladesh
| | - Thomas Darton
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, South Yorkshire, UK
| | - Tran Nguyen Bao
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Yoel Lubell
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Bangkok, 10400, Thailand
| | - Evelyne Kestelyn
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Christopher M. Parry
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Buddha Basnyat
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Scineces, Lalitpur, Bagmati, 44700, Nepal
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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23
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Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley EA, Auburn S, Awandare GA, Ba H, Baraka V, Barry AE, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Branch O, Bull PC, Busby GBJ, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day NPJ, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp AM, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fukuda MM, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton WL, Harrison GLA, Hart L, Henrichs C, Hien TT, Hill CA, Hodgson A, Hubbart C, Imwong M, Ishengoma DS, Jackson SA, Jacob CG, Jeffery B, Jeffreys AE, Johnson KJ, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu OA, Montgomery J, Mueller I, Newton PN, Nguyen T, Nguyen TN, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Pearson RD, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Randrianarivelojosia M, Rayner JC, Ringwald P, Rockett KA, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Stalker J, Su XZ, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Wright I, Yavo W, Ye H. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Res 2021; 6:42. [PMID: 33824913 PMCID: PMC8008441 DOI: 10.12688/wellcomeopenres.16168.1] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2021] [Indexed: 02/02/2023] Open
Abstract
MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.
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Affiliation(s)
| | | | - Mozam Ali
- Wellcome Sanger Institute, Hinxton, UK
| | - Jacob Almagro-Garcia
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Alfred Amambua-Ngwa
- Wellcome Sanger Institute, Hinxton, UK,Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Roberto Amato
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Lucas Amenga-Etego
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana,West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Ben Andagalu
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya
| | | | | | | | | | - Elizabeth A Ashley
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Sarah Auburn
- Menzies School of Health Research, Darwin, Australia,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana,University of Ghana, Legon, Ghana
| | - Hampate Ba
- Institut National de Recherche en Santé Publique, Nouakchott, Mauritania
| | - Vito Baraka
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania,Department of Epidemiology, International Health Unit, University of Antwerp, Antwerp, Belgium
| | - Alyssa E. Barry
- Deakin University, Geelong, Australia,Burnet Institute, Melbourne, Australia,Walter and Eliza Hall Institute, Melbourne, Australia
| | - Philip Bejon
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Maciej F. Boni
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Steffen Borrmann
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Teun Bousema
- London School of Hygiene and Tropical Medicine, London, UK,Radboud University Medical Center, Nijmegen, The Netherlands
| | - Oralee Branch
- NYU School of Medicine Langone Medical Center, New York, USA
| | - Peter C. Bull
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya,Department of Pathology, University of Cambridge, Cambridge, UK
| | - George B. J. Busby
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | | | - Antoine Claessens
- Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia,LPHI, MIVEGEC, INSERM, CNRS, IRD, University of Montpellier, Montpellier, France
| | - David Conway
- London School of Hygiene and Tropical Medicine, London, UK
| | - Alister Craig
- Liverpool School of Tropical Medicine, Liverpool, UK,Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Souleymane Dama
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nicholas PJ Day
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi
| | - Mahamadou Diakite
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye Djimdé
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Chris Drakeley
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Patrick Duffy
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Diego F. Echeverry
- Centro Internacional de Entrenamiento e Investigaciones Médicas - CIDEIM, Cali, Colombia,Universidad Icesi, Cali, Colombia
| | | | - Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | | | - Mark M. Fukuda
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anita Ghansah
- Nogouchi Memorial Institute for Medical Research, Legon-Accra, Ghana
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - William L. Hamilton
- Wellcome Sanger Institute, Hinxton, UK,Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Lee Hart
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Christa Henrichs
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | | | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Deus S. Ishengoma
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania,East African Consortium for Clinical Research (EACCR), Dar es Salaam, Tanzania
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | | | - Ben Jeffery
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Anna E. Jeffreys
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kimberly J. Johnson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | | | - Edwin Kamau
- Walter Reed Army Institute of Research, U.S. Military HIV Research Program, Silver Spring, MD, USA
| | | | - Krzysztof Kluczynski
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Theerarat Kochakarn
- Wellcome Sanger Institute, Hinxton, UK,Mahidol University, Bangkok, Thailand
| | | | - Dominic P. Kwiatkowski
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Myat Phone Kyaw
- The Myanmar Oxford Clinical Research Unit, University of Oxford, Yangon, Myanmar,University of Public Health, Yangon, Myanmar
| | - Pharath Lim
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA,Medical Care Development International, Maryland, USA
| | - Chanthap Lon
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | | | - Oumou Maïga-Ascofaré
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany,Research in Tropical Medicine, Kwame Nkrumah University of Sciences and Technology, Kumasi, Ghana
| | | | | | - Jutta Marfurt
- Menzies School of Health Research, Darwin, Australia
| | - Kevin Marsh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,African Academy of Sciences, Nairobi, Kenya
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane, Lao People's Democratic Republic,Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao People's Democratic Republic
| | - Alistair Miles
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Olivo Miotto
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK,Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Victor Mobegi
- School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Olugbenga A. Mokuolu
- Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria
| | - Jacqui Montgomery
- Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, 3800, Australia
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Melbourne, Australia,Barcelona Centre for International Health Research, Barcelona, Spain
| | - Paul N. Newton
- Wellcome Trust-Mahosot Hospital-Oxford Tropical Medicine Research Collaboration, Vientiane, Lao People's Democratic Republic
| | | | - Thuy-Nhien Nguyen
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Harald Noedl
- MARIB - Malaria Research Initiative Bandarban, Bandarban, Bangladesh
| | - Francois Nosten
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Shoklo Malaria Research Unit, Bangkok, Thailand
| | | | - Alexis Nzila
- King Fahid University of Petroleum and Minerals (KFUMP), Dharhran, Saudi Arabia
| | | | - Harold Ocholla
- KEMRI - Centres for Disease Control and Prevention (CDC) Research Program, Kisumu, Kenya,Centre for Bioinformatics and Biotechnology, University of Nairobi, Nairobi, Kenya
| | - Abraham Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Irene Omedo
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Marie A. Onyamboko
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Congo, Democratic Republic
| | | | - Kolapo Oyebola
- Nigerian Institute of Medical Research, Lagos, Nigeria,Parasitology and Bioinformatics Unit, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Richard D. Pearson
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Norbert Peshu
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Aung Pyae Phyo
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand,Shoklo Malaria Research Unit, Bangkok, Thailand
| | - Chris V. Plowe
- School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Ric N. Price
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand,Menzies School of Health Research, Darwin, Australia,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | - Milijaona Randrianarivelojosia
- Institut Pasteur de Madagascar, Antananarivo, Madagascar,Universités d'Antananarivo et de Mahajanga, Antananarivo, Madagascar
| | | | | | - Kirk A. Rockett
- Wellcome Sanger Institute, Hinxton, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Lastenia Ruiz
- Universidad Nacional de la Amazonia Peruana, Iquitos, Peru
| | - David Saunders
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Alex Shayo
- Nelson Mandela Institute of Science and Technology, Arusha, Tanzania
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Victoria J. Simpson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | - Xin-zhuan Su
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | | | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland, School of Medicine, Baltimore, MD, USA
| | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Vandana Thathy
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya,Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | | | | | - Joseph Vinetz
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru,Yale School of Medicine, New Haven, CT, USA
| | - Thomas E. Wellems
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Jason Wendler
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Nicholas J. White
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Ian Wright
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - William Yavo
- University Félix Houphouët-Boigny, Abidjan, Cote d'Ivoire,Malaria Research and Control Center of the National Institute of Public Health, Abidjan, Cote d'Ivoire
| | - Htut Ye
- Department of Medical Research, Yangon, Myanmar
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24
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Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley EA, Auburn S, Awandare GA, Ba H, Baraka V, Barry AE, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Branch O, Bull PC, Busby GBJ, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day NPJ, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp AM, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fukuda MM, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton WL, Harrison GLA, Hart L, Henrichs C, Hien TT, Hill CA, Hodgson A, Hubbart C, Imwong M, Ishengoma DS, Jackson SA, Jacob CG, Jeffery B, Jeffreys AE, Johnson KJ, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu OA, Montgomery J, Mueller I, Newton PN, Nguyen T, Nguyen TN, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Pearson RD, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Randrianarivelojosia M, Rayner JC, Ringwald P, Rockett KA, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Stalker J, Su XZ, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Wright I, Yavo W, Ye H. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Res 2021; 6:42. [PMID: 33824913 PMCID: PMC8008441.2 DOI: 10.12688/wellcomeopenres.16168.2] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2021] [Indexed: 02/02/2023] Open
Abstract
MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.
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Affiliation(s)
| | | | - Mozam Ali
- Wellcome Sanger Institute, Hinxton, UK
| | - Jacob Almagro-Garcia
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Alfred Amambua-Ngwa
- Wellcome Sanger Institute, Hinxton, UK,Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Roberto Amato
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Lucas Amenga-Etego
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana,West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Ben Andagalu
- United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute/Walter Reed Project, Kisumu, Kenya
| | | | | | | | | | - Elizabeth A Ashley
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Sarah Auburn
- Menzies School of Health Research, Darwin, Australia,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana,University of Ghana, Legon, Ghana
| | - Hampate Ba
- Institut National de Recherche en Santé Publique, Nouakchott, Mauritania
| | - Vito Baraka
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania,Department of Epidemiology, International Health Unit, University of Antwerp, Antwerp, Belgium
| | - Alyssa E. Barry
- Deakin University, Geelong, Australia,Burnet Institute, Melbourne, Australia,Walter and Eliza Hall Institute, Melbourne, Australia
| | - Philip Bejon
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Maciej F. Boni
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Steffen Borrmann
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Teun Bousema
- London School of Hygiene and Tropical Medicine, London, UK,Radboud University Medical Center, Nijmegen, The Netherlands
| | - Oralee Branch
- NYU School of Medicine Langone Medical Center, New York, USA
| | - Peter C. Bull
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya,Department of Pathology, University of Cambridge, Cambridge, UK
| | - George B. J. Busby
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | | | - Antoine Claessens
- Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia,LPHI, MIVEGEC, INSERM, CNRS, IRD, University of Montpellier, Montpellier, France
| | - David Conway
- London School of Hygiene and Tropical Medicine, London, UK
| | - Alister Craig
- Liverpool School of Tropical Medicine, Liverpool, UK,Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia, at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Souleymane Dama
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nicholas PJ Day
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research, Blantyre, Malawi
| | - Mahamadou Diakite
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye Djimdé
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Chris Drakeley
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Patrick Duffy
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Diego F. Echeverry
- Centro Internacional de Entrenamiento e Investigaciones Médicas - CIDEIM, Cali, Colombia,Universidad Icesi, Cali, Colombia
| | | | - Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | | | - Mark M. Fukuda
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anita Ghansah
- Nogouchi Memorial Institute for Medical Research, Legon-Accra, Ghana
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - William L. Hamilton
- Wellcome Sanger Institute, Hinxton, UK,Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Lee Hart
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Christa Henrichs
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | | | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Deus S. Ishengoma
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania,East African Consortium for Clinical Research (EACCR), Dar es Salaam, Tanzania
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | | | - Ben Jeffery
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Anna E. Jeffreys
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kimberly J. Johnson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | | | - Edwin Kamau
- Walter Reed Army Institute of Research, U.S. Military HIV Research Program, Silver Spring, MD, USA
| | | | - Krzysztof Kluczynski
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Theerarat Kochakarn
- Wellcome Sanger Institute, Hinxton, UK,Mahidol University, Bangkok, Thailand
| | | | - Dominic P. Kwiatkowski
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Myat Phone Kyaw
- The Myanmar Oxford Clinical Research Unit, University of Oxford, Yangon, Myanmar,University of Public Health, Yangon, Myanmar
| | - Pharath Lim
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA,Medical Care Development International, Maryland, USA
| | - Chanthap Lon
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | | | - Oumou Maïga-Ascofaré
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany,Research in Tropical Medicine, Kwame Nkrumah University of Sciences and Technology, Kumasi, Ghana
| | | | | | - Jutta Marfurt
- Menzies School of Health Research, Darwin, Australia
| | - Kevin Marsh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,African Academy of Sciences, Nairobi, Kenya
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane, Lao People's Democratic Republic,Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao People's Democratic Republic
| | - Alistair Miles
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Olivo Miotto
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK,Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Victor Mobegi
- School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Olugbenga A. Mokuolu
- Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria
| | - Jacqui Montgomery
- Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, 3800, Australia
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Melbourne, Australia,Barcelona Centre for International Health Research, Barcelona, Spain
| | - Paul N. Newton
- Wellcome Trust-Mahosot Hospital-Oxford Tropical Medicine Research Collaboration, Vientiane, Lao People's Democratic Republic
| | | | - Thuy-Nhien Nguyen
- Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam
| | - Harald Noedl
- MARIB - Malaria Research Initiative Bandarban, Bandarban, Bangladesh
| | - Francois Nosten
- Nuffield Department of Medicine, University of Oxford, Oxford, UK,Shoklo Malaria Research Unit, Bangkok, Thailand
| | | | - Alexis Nzila
- King Fahid University of Petroleum and Minerals (KFUMP), Dharhran, Saudi Arabia
| | | | - Harold Ocholla
- KEMRI - Centres for Disease Control and Prevention (CDC) Research Program, Kisumu, Kenya,Centre for Bioinformatics and Biotechnology, University of Nairobi, Nairobi, Kenya
| | - Abraham Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Irene Omedo
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Marie A. Onyamboko
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Congo, Democratic Republic
| | | | - Kolapo Oyebola
- Nigerian Institute of Medical Research, Lagos, Nigeria,Parasitology and Bioinformatics Unit, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Richard D. Pearson
- Wellcome Sanger Institute, Hinxton, UK,MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Norbert Peshu
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Aung Pyae Phyo
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand,Shoklo Malaria Research Unit, Bangkok, Thailand
| | - Chris V. Plowe
- School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Ric N. Price
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand,Menzies School of Health Research, Darwin, Australia,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | - Milijaona Randrianarivelojosia
- Institut Pasteur de Madagascar, Antananarivo, Madagascar,Universités d'Antananarivo et de Mahajanga, Antananarivo, Madagascar
| | | | | | - Kirk A. Rockett
- Wellcome Sanger Institute, Hinxton, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Lastenia Ruiz
- Universidad Nacional de la Amazonia Peruana, Iquitos, Peru
| | - David Saunders
- Department of Immunology and Medicine, US Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Alex Shayo
- Nelson Mandela Institute of Science and Technology, Arusha, Tanzania
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Victoria J. Simpson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | | | - Xin-zhuan Su
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | | | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland, School of Medicine, Baltimore, MD, USA
| | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Vandana Thathy
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya,Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | | | | | - Joseph Vinetz
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru,Yale School of Medicine, New Haven, CT, USA
| | - Thomas E. Wellems
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Jason Wendler
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Nicholas J. White
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
| | - Ian Wright
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - William Yavo
- University Félix Houphouët-Boigny, Abidjan, Cote d'Ivoire,Malaria Research and Control Center of the National Institute of Public Health, Abidjan, Cote d'Ivoire
| | - Htut Ye
- Department of Medical Research, Yangon, Myanmar
| |
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25
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Carey ME, MacWright WR, Im J, Meiring JE, Gibani MM, Park SE, Longley A, Jeon HJ, Hemlock C, Yu AT, Soura A, Aiemjoy K, Owusu-Dabo E, Terferi M, Islam S, Lunguya O, Jacobs J, Gordon M, Dolecek C, Baker S, Pitzer VE, Yousafzai MT, Tonks S, Clemens JD, Date K, Qadri F, Heyderman RS, Saha SK, Basnyat B, Okeke IN, Qamar FN, Voysey M, Luby S, Kang G, Andrews J, Pollard AJ, John J, Garrett D, Marks F. The Surveillance for Enteric Fever in Asia Project (SEAP), Severe Typhoid Fever Surveillance in Africa (SETA), Surveillance of Enteric Fever in India (SEFI), and Strategic Typhoid Alliance Across Africa and Asia (STRATAA) Population-based Enteric Fever Studies: A Review of Methodological Similarities and Differences. Clin Infect Dis 2021; 71:S102-S110. [PMID: 32725221 PMCID: PMC7388711 DOI: 10.1093/cid/ciaa367] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Building on previous multicountry surveillance studies of typhoid and others salmonelloses such as the Diseases of the Most Impoverished program and the Typhoid Surveillance in Africa Project, several ongoing blood culture surveillance studies are generating important data about incidence, severity, transmission, and clinical features of invasive Salmonella infections in sub-Saharan Africa and South Asia. These studies are also characterizing drug resistance patterns in their respective study sites. Each study answers a different set of research questions and employs slightly different methodologies, and the geographies under surveillance differ in size, population density, physician practices, access to healthcare facilities, and access to microbiologically safe water and improved sanitation. These differences in part reflect the heterogeneity of the epidemiology of invasive salmonellosis globally, and thus enable generation of data that are useful to policymakers in decision-making for the introduction of typhoid conjugate vaccines (TCVs). Moreover, each study is evaluating the large-scale deployment of TCVs, and may ultimately be used to assess post-introduction vaccine impact. The data generated by these studies will also be used to refine global disease burden estimates. It is important to ensure that lessons learned from these studies not only inform vaccination policy, but also are incorporated into sustainable, low-cost, integrated vaccine-preventable disease surveillance systems.
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Affiliation(s)
- Megan E Carey
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Justin Im
- International Vaccine Institute, SNU Research Park, Seoul, Republic of Korea
| | - James E Meiring
- Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Malick M Gibani
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Se Eun Park
- International Vaccine Institute, SNU Research Park, Seoul, Republic of Korea
| | - Ashley Longley
- Global Immunization Division, Centers for Disease Control Foundation, Atlanta, Georgia, USA
| | - Hyon Jin Jeon
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom.,International Vaccine Institute, SNU Research Park, Seoul, Republic of Korea
| | - Caitlin Hemlock
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, California, USA
| | - Alexander T Yu
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, California, USA
| | - Abdramane Soura
- Institut Supérieur des Sciences de la Population, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Kristen Aiemjoy
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, California, USA
| | - Ellis Owusu-Dabo
- School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Sahidul Islam
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Octavie Lunguya
- Department of Microbiology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Melita Gordon
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Institute of Infection and Global Health, University of Liverpool, United Kingdom
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Stephen Baker
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut, USA
| | | | - Susan Tonks
- Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
| | - John D Clemens
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh.,Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California, USA
| | - Kashmira Date
- Global Immunization Division, Centers for Disease Control Foundation, Atlanta, Georgia, USA
| | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Robert S Heyderman
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Samir K Saha
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Buddha Basnyat
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Idaban, Nigeria
| | - Farah N Qamar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Merryn Voysey
- Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
| | - Stephen Luby
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, California, USA
| | | | - Jason Andrews
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, California, USA
| | - Andrew J Pollard
- Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
| | - Jacob John
- Christian Medical College, Vellore, India
| | - Denise Garrett
- Sabin Vaccine Institute, Washington, District of Columbia, USA
| | - Florian Marks
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom.,International Vaccine Institute, SNU Research Park, Seoul, Republic of Korea
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Browne A, Chipeta M, Kashef Hamadani B, Kumaran E, Moore C, Dolecek C, Hay S. Geospatial mapping of the global prevalence of antimicrobial resistant Salmonella Typhi and Paratyphi A isolates. Int J Infect Dis 2020. [DOI: 10.1016/j.ijid.2020.09.109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Browne A, Chipeta M, Haines-Woodhouse G, Kumaran E, Deshpande A, Zaraa S, Reiner R, Dunachie S, Moore C, Stergachis A, Dolecek C, Hay S. Global antibiotic consumption: A modelling study. Int J Infect Dis 2020. [DOI: 10.1016/j.ijid.2020.09.262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Dunachie SJ, Day NP, Dolecek C. The challenges of estimating the human global burden of disease of antimicrobial resistant bacteria. Curr Opin Microbiol 2020; 57:95-101. [PMID: 33147565 PMCID: PMC7763986 DOI: 10.1016/j.mib.2020.09.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 12/29/2022]
Abstract
Estimating the contribution of antimicrobial resistance (AMR) to global mortality and healthcare costs enables evaluation of interventions, informs policy decisions on resource allocation, and drives research priorities. However assembling the high quality, patient-level data required for global estimates is challenging. Capacity for accurate microbiology culture and antimicrobial susceptibility testing is woefully neglected in low and middle-income countries, and further surveillance and research on community antimicrobial usage, bias in blood culture sampling, and the contribution of co-morbidities such as diabetes is essential. International collaboration between governments, policy makers, academics, microbiologists, front-line clinicians, veterinarians, the food and agriculture industry and the public is critical to understand and tackle AMR.
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Affiliation(s)
- Susanna J Dunachie
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Nicholas Pj Day
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Deshpande A, Miller-Petrie MK, Lindstedt PA, Baumann MM, Johnson KB, Blacker BF, Abbastabar H, Abd-Allah F, Abdelalim A, Abdollahpour I, Abegaz KH, Abejie AN, Abreu LG, Abrigo MR, Abualhasan A, Accrombessi MMK, Adamu AA, Adebayo OM, Adedeji IA, Adedoyin RA, Adekanmbi V, Adetokunboh OO, Adhikari TB, Afarideh M, Agudelo-Botero M, Ahmadi M, Ahmadi K, Ahmed MB, Ahmed AE, Akalu TY, Akanda AS, Alahdab F, Al-Aly Z, Alam S, Alam N, Alamene GM, Alanzi TM, Albright J, Albujeer A, Alcalde-Rabanal JE, Alebel A, Alemu ZA, Ali M, Alijanzadeh M, Alipour V, Aljunid SM, Almasi A, Almasi-Hashiani A, Al-Mekhlafi HM, Altirkawi KA, Alvis-Guzman N, Alvis-Zakzuk NJ, Amini S, Amit AML, Amul GGH, Andrei CL, Anjomshoa M, Ansariadi A, Antonio CAT, Antony B, Antriyandarti E, Arabloo J, Aref HMA, Aremu O, Armoon B, Arora A, Aryal KK, Arzani A, Asadi-Aliabadi M, Asmelash D, Atalay HT, Athari SM, Athari SS, Atre SR, Ausloos M, Awasthi S, Awoke N, Ayala Quintanilla BP, Ayano G, Ayanore MA, Aynalem YA, Azari S, Azman AS, Babaee E, Badawi A, Bagherzadeh M, Bakkannavar SM, Balakrishnan S, Banach M, Banoub JAM, Barac A, Barboza MA, Bärnighausen TW, Basu S, Bay VD, Bayati M, Bedi N, Beheshti M, Behzadifar M, Behzadifar M, Bejarano Ramirez DF, Bell ML, Bennett DA, Benzian H, Berbada DA, Bernstein RS, Bhat AG, Bhattacharyya K, Bhaumik S, Bhutta ZA, Bijani A, Bikbov B, Bin Sayeed MS, Biswas RK, Bohlouli S, Boufous S, Brady OJ, Briko AN, Briko NI, Britton GB, Brown A, Burugina Nagaraja S, Butt ZA, Cámera LA, Campos-Nonato IR, Campuzano Rincon JC, Cano J, Car J, Cárdenas R, Carvalho F, Castañeda-Orjuela CA, Castro F, Cerin E, Chalise B, Chattu VK, Chin KL, Christopher DJ, Chu DT, Cormier NM, Costa VM, Cromwell EA, Dadi AFF, Dahiru T, Dahlawi SMA, Dandona R, Dandona L, Dang AK, Daoud F, Darwesh AM, Darwish AH, Daryani A, Das JK, Das Gupta R, Dash AP, Dávila-Cervantes CA, Davis Weaver N, De la Hoz FP, De Neve JW, Demissie DB, Demoz GT, Denova-Gutiérrez E, Deribe K, Desalew A, Dharmaratne SD, Dhillon P, Dhimal M, Dhungana GP, Diaz D, Dipeolu IO, Do HT, Dolecek C, Doyle KE, Dubljanin E, Duraes AR, Edinur HA, Effiong A, Eftekhari A, El Nahas N, El Sayed Zaki M, El Tantawi M, Elhabashy HR, El-Jaafary SI, El-Khatib Z, Elkout H, Elsharkawy A, Enany S, Endalew DA, Eshrati B, Eskandarieh S, Etemadi A, Ezekannagha O, Faraon EJA, Fareed M, Faro A, Farzadfar F, Fasil AF, Fazlzadeh M, Feigin VL, Fekadu W, Fentahun N, Fereshtehnejad SM, Fernandes E, Filip I, Fischer F, Flohr C, Foigt NA, Folayan MO, Foroutan M, Franklin RC, Frostad JJ, Fukumoto T, Gad MM, Garcia GM, Gatotoh AM, Gayesa RT, Gebremedhin KB, Geramo YCD, Gesesew HA, Gezae KE, Ghashghaee A, Ghazi Sherbaf F, Gill TK, Gill PS, Ginindza TG, Girmay A, Gizaw Z, Goodridge A, Gopalani SV, Goulart BNG, Goulart AC, Grada A, Green MS, Gubari MIM, Gugnani HC, Guido D, Guimarães RA, Guo Y, Gupta R, Gupta R, Ha GH, Haagsma JA, Hafezi-Nejad N, Haile DH, Haile MT, Hall BJ, Hamidi S, Handiso DW, Haririan H, Hariyani N, Hasaballah AI, Hasan MM, Hasanzadeh A, Hassen HY, Hayelom DH, Hegazy MI, Heibati B, Heidari B, Hendrie D, Henok A, Herteliu C, Heydarpour F, Hidru HDD, Hird TR, Hoang CL, Hollerich GI, Hoogar P, Hossain N, Hosseinzadeh M, Househ M, Hu G, Humayun A, Hussain SA, Hussen MAA, Ibitoye SE, Ilesanmi OS, Ilic MD, Imani-Nasab MH, Iqbal U, Irvani SSN, Islam SMS, Ivers RQ, Iwu CJ, Jahanmehr N, Jakovljevic M, Jalali A, Jayatilleke AU, Jenabi E, Jha RP, Jha V, Ji JS, Jonas JB, Jozwiak JJ, Kabir A, Kabir Z, Kanchan T, Karch A, Karki S, Kasaeian A, Kasahun GG, Kasaye HK, Kassa GG, Kassa GM, Kayode GA, Kebede MM, Keiyoro PN, Ketema DB, Khader YS, Khafaie MA, Khalid N, Khalilov R, Khan EA, Khan J, Khan MN, Khatab K, Khater MM, Khater AM, Khayamzadeh M, Khazaei M, Khosravi MH, Khubchandani J, Kiadaliri A, Kim YJ, Kimokoti RW, Kisa S, Kisa A, Kochhar S, Kolola T, Komaki H, Kosen S, Koul PA, Koyanagi A, Krishan K, Kuate Defo B, Kugbey N, Kumar P, Kumar GA, Kumar M, Kusuma D, La Vecchia C, Lacey B, Lal A, Lal DK, Lam H, Lami FH, Lansingh VC, Lasrado S, Lebedev G, Lee PH, LeGrand KE, Leili M, Lenjebo TL, Leshargie CT, Levine AJ, Lewycka S, Li S, Linn S, Liu S, Lopez JCF, Lopukhov PD, Magdy Abd El Razek M, Mahadeshwara Prasad D, Mahasha PW, Mahotra NB, Majeed A, Malekzadeh R, Malta DC, Mamun AA, Manafi N, Mansournia MA, Mapoma CC, Martinez G, Martini S, Martins-Melo FR, Mathur MR, Mayala BK, Mazidi M, McAlinden C, Meharie BG, Mehndiratta MM, Mehrabi Nasab E, Mehta KM, Mekonnen T, Mekonnen TC, Meles GG, Meles HG, Memiah PTN, Memish ZA, Mendoza W, Menezes RG, Mereta ST, Meretoja TJ, Mestrovic T, Metekiya WM, Metekiya WM, Miazgowski B, Miller TR, Mini GK, Mirrakhimov EM, Moazen B, Mohajer B, Mohammad Y, Mohammad DK, Mohammad Gholi Mezerji N, Mohammadibakhsh R, Mohammed S, Mohammed JA, Mohammed H, Mohebi F, Mokdad AH, Moodley Y, Moradi M, Moradi G, Moradi-Joo M, Moraga P, Morales L, Mosapour A, Mosser JF, Mouodi S, Mousavi SM, Mozaffor M, Munro SB, Muriithi MK, Murray CJL, Musa KI, Mustafa G, Muthupandian S, Naderi M, Nagarajan AJ, Naghavi M, Naik G, Nangia V, Nascimento BR, Nazari J, Ndwandwe DE, Negoi I, Netsere HB, Ngunjiri JW, Nguyen CT, Nguyen HLT, Nguyen QP, Nigatu SG, Ningrum DNA, Nnaji CA, Nojomi M, Norheim OF, Noubiap JJ, Oancea B, Ogbo FA, Oh IH, Olagunju AT, Olusanya JO, Olusanya BO, Onwujekwe OE, Ortega-Altamirano DV, Osarenotor O, Osei FB, Owolabi MO, P A M, Padubidri JR, Pakhale S, Pana A, Park EK, Patel SK, Pathak A, Patle A, Paulos K, Pepito VCF, Perico N, Pervaiz A, Pescarini JM, Pesudovs K, Pham HQ, Pigott DM, Pilgrim T, Pirsaheb M, Poljak M, Pollock I, Postma MJ, Pourmalek F, Pourshams A, Prada SI, Preotescu L, Quintana H, Rabiee N, Rabiee M, Radfar A, Rafiei A, Rahim F, Rahimi S, Rahimi-Movaghar V, Rahman MA, Rahman MHU, Rajati F, Ranabhat CL, Rao PC, Rasella D, Rath GK, Rawaf S, Rawal L, Rawasia WF, Remuzzi G, Renjith V, Renzaho AM, Resnikoff S, Riahi SM, Ribeiro AI, Rickard J, Roever L, Ronfani L, Rubagotti E, Rubino S, Saad AM, Sabour S, Sadeghi E, Saeedi Moghaddam S, Safari Y, Sagar R, Sahraian MA, Sajadi SM, Salahshoor MR, Salam N, Saleem A, Salem H, Salem MR, Salimi Y, Salimzadeh H, Samy AM, Sanabria J, Santos IS, Santric-Milicevic MM, Sao Jose BP, Saraswathy SYI, Sarrafzadegan N, Sartorius B, Sathian B, Sathish T, Satpathy M, Sawhney M, Sayyah M, Sbarra AN, Schaeffer LE, Schwebel DC, Senbeta AM, Senthilkumaran S, Sepanlou SG, Serván-Mori E, Shafieesabet A, Shaheen AA, Shahid I, Shaikh MA, Shalash AS, Shams-Beyranvand M, Shamsi M, Shamsizadeh M, Shannawaz M, Sharafi K, Sharma R, Sheikh A, Shetty BSK, Shiferaw WS, Shigematsu M, Shin JI, Shiri R, Shirkoohi R, Shivakumar KM, Si S, Siabani S, Siddiqi TJ, Silva DAS, Singh V, Singh NP, Singh BBS, Singh JA, Singh A, Sinha DN, Sisay MM, Skiadaresi E, Smith DL, Soares Filho AM, Sobhiyeh MR, Sokhan A, Soriano JB, Sorrie MB, Soyiri IN, Spurlock EE, Sreeramareddy CT, Sudaryanto A, Sufiyan MB, Suleria HAR, Sykes BL, Tabarés-Seisdedos R, Tabuchi T, Tadesse DB, Tarigan IU, Taye B, Tefera YM, Tehrani-Banihashemi A, Tekelemedhin SW, Tekle MG, Temsah MH, Tesfay BE, Tesfay FH, Tessema ZT, Thankappan KR, ThekkePurakkal AS, Thomas N, Thompson RL, Thomson AJ, Topor-Madry R, Tovani-Palone MR, Traini E, Tran BX, Tran KB, Ullah I, Unnikrishnan B, Usman MS, Uthman OA, Uzochukwu BSC, Valdez PR, Varughese S, Veisani Y, Violante FS, Vollmer S, W/hawariat FG, Waheed Y, Wallin MT, Wang YP, Wang Y, Wangdi K, Weiss DJ, Weldesamuel GT, Werkneh AA, Westerman R, Wiangkham T, Wiens KE, Wijeratne T, Wiysonge CS, Wolde HF, Wondafrash DZ, Wonde TE, Worku GT, Yadollahpour A, Yahyazadeh Jabbari SH, Yamada T, Yaseri M, Yatsuya H, Yeshaneh A, Yilma MT, Yip P, Yisma E, Yonemoto N, Younis MZ, Yousof HASA, Yu C, Yusefzadeh H, Zadey S, Zahirian Moghadam T, Zaidi Z, Zaman SB, Zamani M, Zandian H, Zar HJ, Zerfu TA, Zhang Y, Ziapour A, Zodpey S, Zuniga YMH, Hay SI, Reiner RC. Mapping geographical inequalities in access to drinking water and sanitation facilities in low-income and middle-income countries, 2000-17. Lancet Glob Health 2020; 8:e1162-e1185. [PMID: 32827479 PMCID: PMC7443708 DOI: 10.1016/s2214-109x(20)30278-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/01/2020] [Accepted: 06/04/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Universal access to safe drinking water and sanitation facilities is an essential human right, recognised in the Sustainable Development Goals as crucial for preventing disease and improving human wellbeing. Comprehensive, high-resolution estimates are important to inform progress towards achieving this goal. We aimed to produce high-resolution geospatial estimates of access to drinking water and sanitation facilities. METHODS We used a Bayesian geostatistical model and data from 600 sources across more than 88 low-income and middle-income countries (LMICs) to estimate access to drinking water and sanitation facilities on continuous continent-wide surfaces from 2000 to 2017, and aggregated results to policy-relevant administrative units. We estimated mutually exclusive and collectively exhaustive subcategories of facilities for drinking water (piped water on or off premises, other improved facilities, unimproved, and surface water) and sanitation facilities (septic or sewer sanitation, other improved, unimproved, and open defecation) with use of ordinal regression. We also estimated the number of diarrhoeal deaths in children younger than 5 years attributed to unsafe facilities and estimated deaths that were averted by increased access to safe facilities in 2017, and analysed geographical inequality in access within LMICs. FINDINGS Across LMICs, access to both piped water and improved water overall increased between 2000 and 2017, with progress varying spatially. For piped water, the safest water facility type, access increased from 40·0% (95% uncertainty interval [UI] 39·4-40·7) to 50·3% (50·0-50·5), but was lowest in sub-Saharan Africa, where access to piped water was mostly concentrated in urban centres. Access to both sewer or septic sanitation and improved sanitation overall also increased across all LMICs during the study period. For sewer or septic sanitation, access was 46·3% (95% UI 46·1-46·5) in 2017, compared with 28·7% (28·5-29·0) in 2000. Although some units improved access to the safest drinking water or sanitation facilities since 2000, a large absolute number of people continued to not have access in several units with high access to such facilities (>80%) in 2017. More than 253 000 people did not have access to sewer or septic sanitation facilities in the city of Harare, Zimbabwe, despite 88·6% (95% UI 87·2-89·7) access overall. Many units were able to transition from the least safe facilities in 2000 to safe facilities by 2017; for units in which populations primarily practised open defecation in 2000, 686 (95% UI 664-711) of the 1830 (1797-1863) units transitioned to the use of improved sanitation. Geographical disparities in access to improved water across units decreased in 76·1% (95% UI 71·6-80·7) of countries from 2000 to 2017, and in 53·9% (50·6-59·6) of countries for access to improved sanitation, but remained evident subnationally in most countries in 2017. INTERPRETATION Our estimates, combined with geospatial trends in diarrhoeal burden, identify where efforts to increase access to safe drinking water and sanitation facilities are most needed. By highlighting areas with successful approaches or in need of targeted interventions, our estimates can enable precision public health to effectively progress towards universal access to safe water and sanitation. FUNDING Bill & Melinda Gates Foundation.
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Reiner RC, Wiens KE, Deshpande A, Baumann MM, Lindstedt PA, Blacker BF, Troeger CE, Earl L, Munro SB, Abate D, Abbastabar H, Abd-Allah F, Abdelalim A, Abdollahpour I, Abdulkader RS, Abebe G, Abegaz KH, Abreu LG, Abrigo MRM, Accrombessi MMK, Acharya D, Adabi M, Adebayo OM, Adedoyin RA, Adekanmbi V, Adetokunboh OO, Adhena BM, Afarideh M, Ahmadi K, Ahmadi M, Ahmed AE, Ahmed MB, Ahmed R, Ajumobi O, Akal CG, Akalu TY, Akanda AS, Alamene GM, Alanzi TM, Albright JR, Alcalde Rabanal JE, Alemnew BT, Alemu ZA, Ali BA, Ali M, Alijanzadeh M, Alipour V, Aljunid SM, Almasi A, Almasi-Hashiani A, Al-Mekhlafi HM, Altirkawi K, Alvis-Guzman N, Alvis-Zakzuk NJ, Amare AT, Amini S, Amit AML, Andrei CL, Anegago MT, Anjomshoa M, Ansari F, Antonio CAT, Antriyandarti E, Appiah SCY, Arabloo J, Aremu O, Armoon B, Aryal KK, Arzani A, Asadi-Lari M, Ashagre AF, Atalay HT, Atique S, Atre SR, Ausloos M, Avila-Burgos L, Awasthi A, Awoke N, Ayala Quintanilla BP, Ayano G, Ayanore MA, Ayele AA, Aynalem YAA, Azari S, Babaee E, Badawi A, Bakkannavar SM, Balakrishnan S, Bali AG, Banach M, Barac A, Bärnighausen TW, Basaleem H, Bassat Q, Bayati M, Bedi N, Behzadifar M, Behzadifar M, Bekele YA, Bell ML, Bennett DA, Berbada DA, Beyranvand T, Bhat AG, Bhattacharyya K, Bhattarai S, Bhaumik S, Bijani A, Bikbov B, Biswas RK, Bogale KA, Bohlouli S, Brady OJ, Bragazzi NL, Briko NI, Briko AN, Burugina Nagaraja S, Butt ZA, Campos-Nonato IR, Campuzano Rincon JC, Cárdenas R, Carvalho F, Castro F, Chansa C, Chatterjee P, Chattu VK, Chauhan BG, Chin KL, Christopher DJ, Chu DT, Claro RM, Cormier NM, Costa VM, Damiani G, Daoud F, Dandona L, Dandona R, Darwish AH, Daryani A, Das JK, Das Gupta R, Dasa TT, Davila CA, Davis Weaver N, Davitoiu DV, De Neve JW, Demeke FM, Demis AB, Demoz GT, Denova-Gutiérrez E, Deribe K, Desalew A, Dessie GA, Dharmaratne SD, Dhillon P, Dhimal M, Dhungana GP, Diaz D, Ding EL, Diro HD, Djalalinia S, Do HP, Doku DT, Dolecek C, Dubey M, Dubljanin E, Duko Adema B, Dunachie SJ, Durães AR, Duraisamy S, Effiong A, Eftekhari A, El Sayed I, El Sayed Zaki M, El Tantawi M, Elemineh DA, El-Jaafary SI, Elkout H, Elsharkawy A, Enany S, Endalamfaw A, Endalew DA, Eskandarieh S, Esteghamati A, Etemadi A, Farag TH, Faraon EJA, Fareed M, Faridnia R, Farioli A, Faro A, Farzam H, Fazaeli AA, Fazlzadeh M, Fentahun N, Fereshtehnejad SM, Fernandes E, Filip I, Fischer F, Foroutan M, Francis JM, Franklin RC, Frostad JJ, Fukumoto T, Gayesa RT, Gebremariam KT, Gebremedhin KBB, Gebremeskel GG, Gedefaw GA, Geramo YCD, Geta B, Gezae KE, Ghashghaee A, Ghassemi F, Gill PS, Ginawi IA, Goli S, Gomes NGM, Gopalani SV, Goulart BNG, Grada A, Gugnani HC, Guido D, Guimares RA, Guo Y, Gupta R, Gupta R, Hafezi-Nejad N, Haile MT, Hailu GB, Haj-Mirzaian A, Haj-Mirzaian A, Hall BJ, Handiso DW, Haririan H, Hariyani N, Hasaballah AI, Hasan MM, Hasanzadeh A, Hassankhani H, Hassen HY, Hayelom DH, Heidari B, Henry NJ, Herteliu C, Heydarpour F, Hidru HDD, Hoang CL, Hoogar P, Hoseini-Ghahfarokhi M, Hossain N, Hosseini M, Hosseinzadeh M, Househ M, Hu G, Humayun A, Hussain SA, Ibitoye SE, Ilesanmi OS, Ilic MD, Inbaraj LR, Irvani SSN, Islam SMS, Iwu CJ, Jaca A, Jafari Balalami N, Jahanmehr N, Jakovljevic M, Jalali A, Jayatilleke AU, Jenabi E, Jha RP, Jha V, Ji JS, Jia P, Johnson KB, Jonas JB, Jozwiak JJ, Kabir A, Kabir Z, Kahsay A, Kalani H, Kanchan T, Karami Matin B, Karch A, Karki S, Kasaeian A, Kasahun GG, Kayode GA, Kazemi Karyani A, Keiyoro PN, Ketema DB, Khader YS, Khafaie MA, Khalid N, Khalil AT, Khalil I, Khalilov R, Khan MN, Khan EA, Khan G, Khan J, Khatab K, Khater A, Khater MM, Khatony A, Khayamzadeh M, Khazaei M, Khazaei S, Khodamoradi E, Khosravi MH, Khubchandani J, Kiadaliri AA, Kim YJ, Kimokoti RW, Kisa S, Kisa A, Kissoon N, Kondlahalli SKMKMM, Kosek MN, Koyanagi A, Kraemer MUG, Krishan K, Kugbey N, Kumar GA, Kumar M, Kumar P, Kusuma D, La Vecchia C, Lacey B, Lal A, Lal DK, Lami FH, Lansingh VC, Lasrado S, Lee PH, Leili M, Lenjebo TTLL, Levine AJ, Lewycka S, Li S, Linn S, Lodha R, Longbottom J, Lopukhov PD, Magdeldin S, Mahasha PW, Mahotra NB, Malta DC, Mamun AA, Manafi N, Manafi F, Manda AL, Mansournia MA, Mapoma CC, Marami D, Marczak LB, Martins-Melo FR, März W, Masaka A, Mathur MR, Maulik PK, Mayala BK, McAlinden C, Mehndiratta MM, Mehrotra R, Mehta KM, Meles GG, Melese A, Memish ZA, Mena AT, Menezes RG, Mengesha MM, Mengistu DT, Mengistu G, Meretoja TJ, Miazgowski B, Mihretie KMM, Miller-Petrie MK, Mills EJ, Mir SM, Mirabi P, Mirrakhimov EM, Mohamadi-Bolbanabad A, Mohammad KA, Mohammad Y, Mohammad DK, Mohammad Darwesh A, Mohammad Gholi Mezerji N, Mohammadifard N, Mohammed AS, Mohammed S, Mohammed JA, Mohebi F, Mokdad AH, Monasta L, Moodley Y, Moradi M, Moradi G, Moradi-Joo M, Moradi-Lakeh M, Moraga P, Mosapour A, Mouodi S, Mousavi SM, Mozaffor MMM, Muluneh AG, Muriithi MK, Murray CJL, Murthy GVS, Musa KI, Mustafa G, Muthupandian S, Naderi M, Nagarajan AJ, Naghavi M, Najafi F, Nangia V, Nazari J, Ndwandwe DE, Negoi I, Ngunjiri JW, Nguyen QP, Nguyen TH, Nguyen CT, Nigatu D, Ningrum DNA, Nnaji CA, Nojomi M, Noubiap JJ, Oh IH, Okpala O, Olagunju AT, Omar Bali A, Onwujekwe OE, Ortega-Altamirano DDV, Osarenotor O, Osei FB, Owolabi MO, P A M, Padubidri JR, Pana A, Pashaei T, Pati S, Patle A, Patton GC, Paulos K, Pepito VCF, Pereira A, Perico N, Pesudovs K, Pigott DM, Piroozi B, Platts-Mills JA, Poljak M, Postma MJ, Pourjafar H, Pourmalek F, Pourshams A, Poustchi H, Prada SI, Preotescu L, Quintana H, Rabiee N, Rabiee M, Radfar A, Rafiei A, Rahim F, Rahimi-Movaghar V, Rahman MA, Rajati F, Ramezanzadeh K, Rana SM, Ranabhat CL, Rasella D, Rawaf S, Rawaf DL, Rawal L, Remuzzi G, Renjith V, Renzaho AMN, Reta MA, Rezaei S, Ribeiro AI, Rickard J, Rios González CM, Rios-Blancas MJ, Roever L, Ronfani L, Roro EM, Rostami A, Rothenbacher D, Rubagotti E, Rubino S, Saad AM, Sabour S, Sadeghi E, Safari S, Safdarian M, Sagar R, Sahraian MA, Sajadi SM, Salahshoor MR, Salam N, Salehi F, Salehi Zahabi S, Salem MRR, Salem H, Salimi Y, Salimzadeh H, Sambala EZ, Samy AM, Sanabria J, Santos IS, Saraswathy SYI, Sarker AR, Sartorius B, Sathian B, Satpathy M, Sbarra AN, Schaeffer LE, Schwebel DC, Senbeta AM, Senthilkumaran S, Shabaninejad H, Shaheen AA, Shaikh MA, Shalash AS, Shallo SA, Shams-Beyranvand M, Shamsi M, Shamsizadeh M, Sharif M, Shey MS, Shibuya K, Shiferaw WSS, Shigematsu M, Shil A, Shin JI, Shiri R, Shirkoohi R, Si S, Siabani S, Singh JA, Singh NP, Sinha DN, Sisay MM, Skiadaresi E, Smith DL, Sobhiyeh MR, Sokhan A, Soofi M, Soriano JB, Sorrie MB, Soyiri IN, Sreeramareddy CT, Sudaryanto A, Sufiyan MB, Suleria HAR, Sykes BL, Tamirat KS, Tassew AA, Taveira N, Taye B, Tehrani-Banihashemi A, Temsah MH, Tesfay BE, Tesfay FH, Tessema ZT, Thankappan KR, Thirunavukkarasu S, Thomas N, Tlaye KG, Tlou B, Tovani-Palone MR, Traini E, Tran KB, Trihandini I, Ullah I, Unnikrishnan B, Valadan Tahbaz S, Valdez PR, Varughese S, Veisani Y, Violante FS, Vollmer S, Vos T, Wada FW, Waheed Y, Wang Y, Wang YP, Weldesamuel GT, Welgan CA, Westerman R, Wiangkham T, Wijeratne T, Wiysonge CSS, Wolde HF, Wondafrash DZ, Wonde TE, Wu AM, Xu G, Yadollahpour A, Yahyazadeh Jabbari SH, Yamada T, Yaseri M, Yenesew MA, Yeshaneh A, Yilma MT, Yimer EM, Yip P, Yirsaw BD, Yisma E, Yonemoto N, Younis MZ, Yousof HASA, Yu C, Yusefzadeh H, Zamani M, Zambrana-Torrelio C, Zandian H, Zeleke AJ, Zepro NB, Zewale TA, Zhang D, Zhang Y, Zhao XJ, Ziapour A, Zodpey S, Hay SI. Mapping geographical inequalities in childhood diarrhoeal morbidity and mortality in low-income and middle-income countries, 2000-17: analysis for the Global Burden of Disease Study 2017. Lancet 2020; 395:1779-1801. [PMID: 32513411 PMCID: PMC7314599 DOI: 10.1016/s0140-6736(20)30114-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 10/24/2019] [Accepted: 01/10/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Across low-income and middle-income countries (LMICs), one in ten deaths in children younger than 5 years is attributable to diarrhoea. The substantial between-country variation in both diarrhoea incidence and mortality is attributable to interventions that protect children, prevent infection, and treat disease. Identifying subnational regions with the highest burden and mapping associated risk factors can aid in reducing preventable childhood diarrhoea. METHODS We used Bayesian model-based geostatistics and a geolocated dataset comprising 15 072 746 children younger than 5 years from 466 surveys in 94 LMICs, in combination with findings of the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017, to estimate posterior distributions of diarrhoea prevalence, incidence, and mortality from 2000 to 2017. From these data, we estimated the burden of diarrhoea at varying subnational levels (termed units) by spatially aggregating draws, and we investigated the drivers of subnational patterns by creating aggregated risk factor estimates. FINDINGS The greatest declines in diarrhoeal mortality were seen in south and southeast Asia and South America, where 54·0% (95% uncertainty interval [UI] 38·1-65·8), 17·4% (7·7-28·4), and 59·5% (34·2-86·9) of units, respectively, recorded decreases in deaths from diarrhoea greater than 10%. Although children in much of Africa remain at high risk of death due to diarrhoea, regions with the most deaths were outside Africa, with the highest mortality units located in Pakistan. Indonesia showed the greatest within-country geographical inequality; some regions had mortality rates nearly four times the average country rate. Reductions in mortality were correlated to improvements in water, sanitation, and hygiene (WASH) or reductions in child growth failure (CGF). Similarly, most high-risk areas had poor WASH, high CGF, or low oral rehydration therapy coverage. INTERPRETATION By co-analysing geospatial trends in diarrhoeal burden and its key risk factors, we could assess candidate drivers of subnational death reduction. Further, by doing a counterfactual analysis of the remaining disease burden using key risk factors, we identified potential intervention strategies for vulnerable populations. In view of the demands for limited resources in LMICs, accurately quantifying the burden of diarrhoea and its drivers is important for precision public health. FUNDING Bill & Melinda Gates Foundation.
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Browne AJ, Kashef Hamadani BH, Kumaran EAP, Rao P, Longbottom J, Harriss E, Moore CE, Dunachie S, Basnyat B, Baker S, Lopez AD, Day NPJ, Hay SI, Dolecek C. Drug-resistant enteric fever worldwide, 1990 to 2018: a systematic review and meta-analysis. BMC Med 2020; 18:1. [PMID: 31898501 PMCID: PMC6941399 DOI: 10.1186/s12916-019-1443-1] [Citation(s) in RCA: 247] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/02/2019] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is an increasing threat to global health. There are > 14 million cases of enteric fever every year and > 135,000 deaths. The disease is primarily controlled by antimicrobial treatment, but this is becoming increasingly difficult due to AMR. Our objectives were to assess the prevalence and geographic distribution of AMR in Salmonella enterica serovars Typhi and Paratyphi A infections globally, to evaluate the extent of the problem, and to facilitate the creation of geospatial maps of AMR prevalence to help targeted public health intervention. METHODS We performed a systematic review of the literature by searching seven databases for studies published between 1990 and 2018. We recategorised isolates to allow the analysis of fluoroquinolone resistance trends over the study period. The prevalence of multidrug resistance (MDR) and fluoroquinolone non-susceptibility (FQNS) in individual studies was illustrated by forest plots, and a random effects meta-analysis was performed, stratified by Global Burden of Disease (GBD) region and 5-year time period. Heterogeneity was assessed using the I2 statistics. We present a descriptive analysis of ceftriaxone and azithromycin resistance. FINDINGS We identified 4557 articles, of which 384, comprising 124,347 isolates (94,616 S. Typhi and 29,731 S. Paratyphi A) met the pre-specified inclusion criteria. The majority (276/384; 72%) of studies were from South Asia; 40 (10%) articles were identified from Sub-Saharan Africa. With the exception of MDR S. Typhi in South Asia, which declined between 1990 and 2018, and MDR S. Paratyphi A, which remained at low levels, resistance trends worsened for all antimicrobials in all regions. We identified several data gaps in Africa and the Middle East. Incomplete reporting of antimicrobial susceptibility testing (AST) and lack of quality assurance were identified. INTERPRETATION Drug-resistant enteric fever is widespread in low- and middle-income countries, and the situation is worsening. It is essential that public health and clinical measures, which include improvements in water quality and sanitation, the deployment of S. Typhi vaccination, and an informed choice of treatment are implemented. However, there is no licenced vaccine for S. Paratyphi A. The standardised reporting of AST data and rollout of external quality control assessment are urgently needed to facilitate evidence-based policy and practice. TRIAL REGISTRATION PROSPERO CRD42018029432.
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Affiliation(s)
- Annie J Browne
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Bahar H Kashef Hamadani
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Emmanuelle A P Kumaran
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Puja Rao
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA
| | - Joshua Longbottom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Eli Harriss
- Bodleian Health Care Libraries, University of Oxford, Oxford, UK
| | - Catrin E Moore
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Susanna Dunachie
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Buddha Basnyat
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit Nepal, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Stephen Baker
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit Vietnam, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Alan D Lopez
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Nicholas P J Day
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Simon I Hay
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle, USA
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Limmathurotsakul D, Dunachie S, Fukuda K, Feasey NA, Okeke IN, Holmes AH, Moore CE, Dolecek C, van Doorn HR, Shetty N, Lopez AD, Peacock SJ. Improving the estimation of the global burden of antimicrobial resistant infections. Lancet Infect Dis 2019; 19:e392-e398. [PMID: 31427174 DOI: 10.1016/s1473-3099(19)30276-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 05/16/2019] [Accepted: 05/22/2019] [Indexed: 12/25/2022]
Abstract
Estimating the global burden of disease from infections caused by pathogens that have acquired antimicrobial resistance (AMR) is essential for resource allocation and to inform AMR action plans at national and global levels. However, the scarcity of robust and accepted methods to determine burden is widely acknowledged. In this Personal View, we discuss the underlying assumptions, characteristics, limitations, and comparability of the approaches used to quantify mortality from AMR bacterial infections. We show that the global burdens of AMR estimated in previous studies are not comparable because of their different methodological approaches, assumptions, and data used to generate the estimates. The analytical frameworks from previous studies are inadequate, and we conclude that a new approach to the estimation of deaths caused by AMR infection is needed. The innovation of a new approach will require the development of mechanisms to systematically collect a clinical dataset of substantial breadth and quality to support the accurate assessment of burden, combined with decision-making and resource allocation for interventions against AMR. We define key actions required and call for innovative thinking and solutions to address these problems.
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Affiliation(s)
- Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.
| | - Susanna Dunachie
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Keiji Fukuda
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Nicholas A Feasey
- The Malawi Liverpool School Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Alison H Holmes
- Department of Medicine, Faculty of Medicine, Imperial College London, London, UK
| | - Catrin E Moore
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Christiane Dolecek
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - H Rogier van Doorn
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK; Oxford University Clinical Research Unit, National Hospital for Tropical Diseases, Hanoi, VietNam
| | - Nandini Shetty
- National Infection Service, Public Health England, London, UK
| | - Alan D Lopez
- School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
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Stanaway JD, Reiner RC, Blacker BF, Goldberg EM, Khalil IA, Troeger CE, Andrews JR, Bhutta ZA, Crump JA, Im J, Marks F, Mintz E, Park SE, Zaidi AKM, Abebe Z, Abejie AN, Adedeji IA, Ali BA, Amare AT, Atalay HT, Avokpaho EFGA, Bacha U, Barac A, Bedi N, Berhane A, Browne AJ, Chirinos JL, Chitheer A, Dolecek C, El Sayed Zaki M, Eshrati B, Foreman KJ, Gemechu A, Gupta R, Hailu GB, Henok A, Hibstu DT, Hoang CL, Ilesanmi OS, Iyer VJ, Kahsay A, Kasaeian A, Kassa TD, Khan EA, Khang YH, Magdy Abd El Razek H, Melku M, Mengistu DT, Mohammad KA, Mohammed S, Mokdad AH, Nachega JB, Naheed A, Nguyen CT, Nguyen HLT, Nguyen LH, Nguyen NB, Nguyen TH, Nirayo YL, Pangestu T, Patton GC, Qorbani M, Rai RK, Rana SM, Ranabhat CL, Roba KT, Roberts NLS, Rubino S, Safiri S, Sartorius B, Sawhney M, Shiferaw MS, Smith DL, Sykes BL, Tran BX, Tran TT, Ukwaja KN, Vu GT, Vu LG, Weldegebreal F, Yenit MK, Murray CJL, Hay SI. The global burden of typhoid and paratyphoid fevers: a systematic analysis for the Global Burden of Disease Study 2017. Lancet Infect Dis 2019; 19:369-381. [PMID: 30792131 PMCID: PMC6437314 DOI: 10.1016/s1473-3099(18)30685-6] [Citation(s) in RCA: 372] [Impact Index Per Article: 74.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 10/17/2018] [Accepted: 11/01/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Efforts to quantify the global burden of enteric fever are valuable for understanding the health lost and the large-scale spatial distribution of the disease. We present the estimates of typhoid and paratyphoid fever burden from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017, and the approach taken to produce them. METHODS For this systematic analysis we broke down the relative contributions of typhoid and paratyphoid fevers by country, year, and age, and analysed trends in incidence and mortality. We modelled the combined incidence of typhoid and paratyphoid fevers and split these total cases proportionally between typhoid and paratyphoid fevers using aetiological proportion models. We estimated deaths using vital registration data for countries with sufficiently high data completeness and using a natural history approach for other locations. We also estimated disability-adjusted life-years (DALYs) for typhoid and paratyphoid fevers. FINDINGS Globally, 14·3 million (95% uncertainty interval [UI] 12·5-16·3) cases of typhoid and paratyphoid fevers occurred in 2017, a 44·6% (42·2-47·0) decline from 25·9 million (22·0-29·9) in 1990. Age-standardised incidence rates declined by 54·9% (53·4-56·5), from 439·2 (376·7-507·7) per 100 000 person-years in 1990, to 197·8 (172·0-226·2) per 100 000 person-years in 2017. In 2017, Salmonella enterica serotype Typhi caused 76·3% (71·8-80·5) of cases of enteric fever. We estimated a global case fatality of 0·95% (0·54-1·53) in 2017, with higher case fatality estimates among children and older adults, and among those living in lower-income countries. We therefore estimated 135·9 thousand (76·9-218·9) deaths from typhoid and paratyphoid fever globally in 2017, a 41·0% (33·6-48·3) decline from 230·5 thousand (131·2-372·6) in 1990. Overall, typhoid and paratyphoid fevers were responsible for 9·8 million (5·6-15·8) DALYs in 2017, down 43·0% (35·5-50·6) from 17·2 million (9·9-27·8) DALYs in 1990. INTERPRETATION Despite notable progress, typhoid and paratyphoid fevers remain major causes of disability and death, with billions of people likely to be exposed to the pathogens. Although improvements in water and sanitation remain essential, increased vaccine use (including with typhoid conjugate vaccines that are effective in infants and young children and protective for longer periods) and improved data and surveillance to inform vaccine rollout are likely to drive the greatest improvements in the global burden of the disease. FUNDING Bill & Melinda Gates Foundation.
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Turner P, Fox-Lewis A, Shrestha P, Dance DAB, Wangrangsimakul T, Cusack TP, Ling CL, Hopkins J, Roberts T, Limmathurotsakul D, Cooper BS, Dunachie S, Moore CE, Dolecek C, van Doorn HR, Guerin PJ, Day NPJ, Ashley EA. Microbiology Investigation Criteria for Reporting Objectively (MICRO): a framework for the reporting and interpretation of clinical microbiology data. BMC Med 2019; 17:70. [PMID: 30922309 PMCID: PMC6440102 DOI: 10.1186/s12916-019-1301-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 03/06/2019] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND There is a pressing need to understand better the extent and distribution of antimicrobial resistance on a global scale, to inform development of effective interventions. Collation of datasets for meta-analysis, mathematical modelling and temporo-spatial analysis is hampered by the considerable variability in clinical sampling, variable quality in laboratory practice and inconsistencies in antimicrobial susceptibility testing and reporting. METHODS The Microbiology Investigation Criteria for Reporting Objectively (MICRO) checklist was developed by an international working group of clinical and laboratory microbiologists, infectious disease physicians, epidemiologists and mathematical modellers. RESULTS In keeping with the STROBE checklist, but applicable to all study designs, MICRO defines items to be included in reports of studies involving human clinical microbiology data. It provides a concise and comprehensive reference for clinicians, researchers, reviewers and journals working on, critically appraising, and publishing clinical microbiology datasets. CONCLUSIONS Implementation of the MICRO checklist will enhance the quality and scientific reporting of clinical microbiology data, increasing data utility and comparability to improve surveillance, grade data quality, facilitate meta-analyses and inform policy and interventions from local to global levels.
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Affiliation(s)
- Paul Turner
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew Fox-Lewis
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Poojan Shrestha
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Infectious Diseases Data Observatory, Oxford, UK
| | - David A. B. Dance
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People’s Democratic Republic
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Tri Wangrangsimakul
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Tomas-Paul Cusack
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People’s Democratic Republic
- National Infection Service, Public Health England, London, UK
| | - Clare L. Ling
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Jill Hopkins
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tamalee Roberts
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People’s Democratic Republic
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Ben S. Cooper
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Susanna Dunachie
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Catrin E. Moore
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - H. Rogier van Doorn
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit, Hanoi, Vietnam
| | - Philippe J. Guerin
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Infectious Diseases Data Observatory, Oxford, UK
| | - Nicholas P. J. Day
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Elizabeth A. Ashley
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar
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Hay SI, Rao PC, Dolecek C, Day NPJ, Stergachis A, Lopez AD, Murray CJL. Measuring and mapping the global burden of antimicrobial resistance. BMC Med 2018; 16:78. [PMID: 29860943 PMCID: PMC5985573 DOI: 10.1186/s12916-018-1073-z] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 05/11/2018] [Indexed: 12/14/2022] Open
Abstract
The increasing number and global distribution of pathogens resistant to antimicrobial drugs is potentially one of the greatest threats to global health, leading to health crises arising from infections that were once easy to treat. Infections resistant to antimicrobial treatment frequently result in longer hospital stays, higher medical costs, and increased mortality. Despite the long-standing recognition of antimicrobial resistance (AMR) across many settings, there is surprisingly poor information about its geographical distribution over time and trends in its population prevalence and incidence. This makes reliable assessments of the health burden attributable to AMR difficult, weakening the evidence base to drive forward research and policy agendas to combat AMR. The inclusion of mortality and morbidity data related to drug-resistant infections into the annual Global Burden of Disease Study should help fill this policy void.
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Affiliation(s)
- Simon I Hay
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Seattle, WA, 98121, USA.,Big Data Institute, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF, UK
| | - Puja C Rao
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Seattle, WA, 98121, USA
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand
| | - Nicholas P J Day
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand
| | - Andy Stergachis
- School of Pharmacy, University of Washington, H-362B Box 357631, Seattle, WA, 98195, USA
| | - Alan D Lopez
- Big Data Institute, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF, UK. .,Melbourne School of Population and Global Health, The University of Melbourne, Level 5, 207 Bouverie St, Carlton, VIC, 3053, Australia.
| | - Christopher J L Murray
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Seattle, WA, 98121, USA
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Thompson CN, Karkey A, Dongol S, Arjyal A, Wolbers M, Darton T, Farrar JJ, Thwaites GE, Dolecek C, Basnyat B, Baker S. Treatment Response in Enteric Fever in an Era of Increasing Antimicrobial Resistance: An Individual Patient Data Analysis of 2092 Participants Enrolled into 4 Randomized, Controlled Trials in Nepal. Clin Infect Dis 2018; 64:1522-1531. [PMID: 28329181 PMCID: PMC5434338 DOI: 10.1093/cid/cix185] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/25/2017] [Indexed: 12/16/2022] Open
Abstract
Background. Enteric fever, caused by Salmonella Typhi and Salmonella Paratyphi A, is the leading cause of bacterial febrile disease in South Asia. Methods. Individual data from 2092 patients with enteric fever randomized into 4 trials in Kathmandu, Nepal, were pooled. All trials compared gatifloxacin with 1 of the following comparator drugs: cefixime, chloramphenicol, ofloxacin, or ceftriaxone. Treatment outcomes were evaluated according to antimicrobial if S. Typhi/Paratyphi were isolated from blood. We additionally investigated the impact of changing bacterial antimicrobial susceptibility on outcome. Results. Overall, 855 (41%) patients had either S. Typhi (n = 581, 28%) or S. Paratyphi A (n = 274, 13%) cultured from blood. There were 139 (6.6%) treatment failures with 1 death. Except for the last trial with ceftriaxone, the fluoroquinolone gatifloxacin was associated with equivalent or better fever clearance times and lower treatment failure rates in comparison to all other antimicrobials. However, we additionally found that the minimum inhibitory concentrations (MICs) against fluoroquinolones have risen significantly since 2005 and were associated with increasing fever clearance times. Notably, all organisms were susceptible to ceftriaxone throughout the study period (2005-2014), and the MICs against azithromycin declined, confirming the utility of these alternative drugs for enteric fever treatment. Conclusion. The World Health Organization and local government health ministries in South Asia still recommend fluoroquinolones for enteric fever. This policy should change based on the evidence provided here. Rapid diagnostics are urgently required given the large numbers of suspected enteric fever patients with a negative culture.
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Affiliation(s)
- Corinne N Thompson
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
| | - Abhilasha Karkey
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Lalitpur, and
| | - Sabina Dongol
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Lalitpur, and
| | - Amit Arjyal
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Lalitpur, and
| | - Marcel Wolbers
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
| | - Thomas Darton
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Jeremy J Farrar
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
| | - Guy E Thwaites
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
| | - Christiane Dolecek
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand ; and
| | - Buddha Basnyat
- Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Lalitpur, and
- Global Antibiotic Resistance Partnership, Nepal
| | - Stephen Baker
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
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Zellweger RM, Basnyat B, Shrestha P, Prajapati KG, Dongol S, Sharma PK, Koirala S, Darton TC, Dolecek C, Thompson CN, Thwaites GE, Baker SG, Karkey A. A 23-year retrospective investigation of Salmonella Typhi and Salmonella Paratyphi isolated in a tertiary Kathmandu hospital. PLoS Negl Trop Dis 2017; 11:e0006051. [PMID: 29176850 PMCID: PMC5720835 DOI: 10.1371/journal.pntd.0006051] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 12/07/2017] [Accepted: 10/19/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Salmonella serovars Typhi (S. Typhi) and Paratyphi A (S. Paratyphi A), the causative agents of enteric fever, have been routinely isolated organisms from the blood of febrile patients in the Kathmandu Valley since the early 1990s. Susceptibility against commonly used antimicrobials for treating enteric fever has gradually changed throughout South Asia since this time, posing serious treatment challenges. Here, we aimed to longitudinally describe trends in the isolation of Salmonella enterica and assess changes in their antimicrobial susceptibility in Kathmandu over a 23-year period. METHODS We conducted a retrospective analysis of standardised microbiological data from April 1992 to December 2014 at a single healthcare facility in Kathmandu, examining time trends of Salmonella-associated bacteraemia and the corresponding antimicrobial susceptibility profiles of the isolated organisms. RESULTS Over 23 years there were 30,353 positive blood cultures. Salmonella enterica accounted for 65.4% (19,857/30,353) of all the bacteria positive blood cultures. S. Typhi and S. Paratyphi A were the dominant serovars, constituting 68.5% (13,592/19,857) and 30.5% (6,057/19,857) of all isolated Salmonellae. We observed (i) a peak in the number of Salmonella-positive cultures in 2002, a year of heavy rainfall and flooding in the Kathmandu Valley, followed by a decline toward pre-flood baseline by 2014, (ii) an increase in the proportion of S. Paratyphi in all Salmonella-positive cultures between 1992 and 2014, (iii) a decrease in the prevalence of MDR for both S. Typhi and S. Paratyphi, and (iv) a recent increase in fluoroquinolone non-susceptibility in both S. Typhi and S. Paratyphi isolates. CONCLUSIONS Our work describes significant changes in the epidemiology of Salmonella enterica in the Kathmandu Valley during the last quarter of a century. We highlight the need to examine current treatment protocols for enteric fever and suggest a change from fluoroquinolone monotherapy to combination therapies of macrolides or cephalosporins along with older first-line antimicrobials that have regained their efficacy.
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Affiliation(s)
- Raphaël M. Zellweger
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
- Global Antibiotic Resistance Partnership, Centre for Disease Dynamics Economics and Policy, Washington DC, Unites States of America
| | - Poojan Shrestha
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | | | - Sabina Dongol
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Paban K. Sharma
- Patan Academy of Health Sciences, Patan Hospital, Kathmandu, Nepal
| | - Samir Koirala
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Thomas C. Darton
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
| | - Corinne N. Thompson
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Guy E. Thwaites
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
| | - Stephen G. Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
- The Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Abhilasha Karkey
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
- Global Antibiotic Resistance Partnership, Centre for Disease Dynamics Economics and Policy, Washington DC, Unites States of America
- * E-mail:
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Darton TC, Meiring JE, Tonks S, Khan MA, Khanam F, Shakya M, Thindwa D, Baker S, Basnyat B, Clemens JD, Dougan G, Dolecek C, Dunstan SJ, Gordon MA, Heyderman RS, Holt KE, Pitzer VE, Qadri F, Zaman K, Pollard AJ. The STRATAA study protocol: a programme to assess the burden of enteric fever in Bangladesh, Malawi and Nepal using prospective population census, passive surveillance, serological studies and healthcare utilisation surveys. BMJ Open 2017; 7:e016283. [PMID: 28674145 PMCID: PMC5726077 DOI: 10.1136/bmjopen-2017-016283] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION Invasive infections caused by Salmonella enterica serovar Typhi and Paratyphi A are estimated to account for 12-27 million febrile illness episodes worldwide annually. Determining the true burden of typhoidal Salmonellae infections is hindered by lack of population-based studies and adequate laboratory diagnostics.The Strategic Typhoid alliance across Africa and Asia study takes a systematic approach to measuring the age-stratified burden of clinical and subclinical disease caused by typhoidal Salmonellae infections at three high-incidence urban sites in Africa and Asia. We aim to explore the natural history of Salmonella transmission in endemic settings, addressing key uncertainties relating to the epidemiology of enteric fever identified through mathematical models, and enabling optimisation of vaccine strategies. METHODS/DESIGN Using census-defined denominator populations of ≥100 000 individuals at sites in Malawi, Bangladesh and Nepal, the primary outcome is to characterise the burden of enteric fever in these populations over a 24-month period. During passive surveillance, clinical and household data, and laboratory samples will be collected from febrile individuals. In parallel, healthcare utilisation and water, sanitation and hygiene surveys will be performed to characterise healthcare-seeking behaviour and assess potential routes of transmission. The rates of both undiagnosed and subclinical exposure to typhoidal Salmonellae (seroincidence), identification of chronic carriage and population seroprevalence of typhoid infection will be assessed through age-stratified serosurveys performed at each site. Secondary attack rates will be estimated among household contacts of acute enteric fever cases and possible chronic carriers. ETHICS AND DISSEMINATION This protocol has been ethically approved by the Oxford Tropical Research Ethics Committee, the icddr,b Institutional Review Board, the Malawian National Health Sciences Research Committee and College of Medicine Research Ethics Committee and Nepal Health Research Council. The study is being conducted in accordance with the principles of the Declaration of Helsinki and Good Clinical Practice. Informed consent was obtained before study enrolment. Results will be submitted to international peer-reviewed journals and presented at international conferences. TRIAL REGISTRATION NUMBER ISRCTN 12131979. ETHICS REFERENCES Oxford (Oxford Tropical Research Ethics Committee 39-15).Bangladesh (icddr,b Institutional Review Board PR-15119).Malawi (National Health Sciences Research Committee 15/5/1599).Nepal (Nepal Health Research Council 306/2015).
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Affiliation(s)
- Thomas C Darton
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Sheffield, UK
| | - James E Meiring
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susan Tonks
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | | | - Farhana Khanam
- International Centre for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - Mila Shakya
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Deus Thindwa
- Malawi Liverpool Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- The Wellcome Trust Sanger Institute, Cambridgeshire, UK
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - John D Clemens
- International Centre for Diarrhoeal Diseases Research, Dhaka, Bangladesh
- UCLA Fielding School of Public Health, Los Angeles, USA
| | - Gordon Dougan
- The Wellcome Trust Sanger Institute, Cambridgeshire, UK
| | - Christiane Dolecek
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Sarah J Dunstan
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Melita A Gordon
- Malawi Liverpool Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Robert S Heyderman
- Malawi Liverpool Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Division of Infection and Immunity, University College London, London, UK
| | - Kathryn E Holt
- Centre for Systems Genomics, University of Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Victoria, Australia
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut, USA
| | - Firdausi Qadri
- International Centre for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - K Zaman
- International Centre for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - Andrew J Pollard
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
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Dolecek C. Typhoid Fever and Other Enteric Fevers. Infect Dis (Lond) 2017. [DOI: 10.1016/b978-0-7020-6285-8.00115-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Abrahamian FM, Aldape MJ, Aldasoro E, Allen UD, Al-Sum H, Anadkat MJ, Anders K, Angelakis E, Angus BJ, Antoniadou A, Arena F, Arends JE, Arribas JR, Artenstein AW, Atherton JC, Aucott JN, Aw TC, Babcock HM, Bailey R, Bailey TC, Banks AZ, Barillo DJ, Barrette EP, Bauer MP, Bayston R, Beard CB, Beardsley J, Beeching NJ, Bégué RE, Beldi G, Benson CA, Berbari EF, Berenger JM, Berger C, Bernardino JI, Bille J, Billioux AC, Bitnun A, Blair I, Blanche S, Bleck TP, Bleeker-Rovers CP, Bleijenberg G, Bloch KC, Blum J, Blumberg EA, Bonomo RA, Bonten MJ, Bourayou R, Bouza E, Brandt KA, Bretelle F, Brisse S, Britton WJ, Brook I, Brouwer MC, Browne SK, Bryant AE, Bühler S, Bulger EM, Buller RML, Burke LA, Burri C, Butler MW, Calandra T, Calfee DP, Calvo-Cano A, Cameron DW, Carcillo JA, Carson G, Chambers ST, Charrel RN, Nguyen VCV, Chevaliez S, Chiller TM, Christaki E, Chung KK, Clifford DB, Clumeck N, Cohen J, Collinge J, Conlon CP, Conrad C, Cooke FJ, Cope JR, Corey GR, Cross JH, Cunha BA, Cunha CB, D'Journo B, Daikos GL, Daniels JM, Davidson RN, Day NP, De Cock KM, de Silva TI, de Vries HJ, de Wit S, Delaloye J, Denning DW, Dennis DT, Dhanireddy S, Dielubanza EJ, Diemert DJ, Doganay M, Doherty T, Dolecek C, Dondorp AM, Douglas A, Drancourt M, Dubourg G, Dudley MN, Durand G, Eckhardt BJ, Efstratiou A, Ekkelenkamp MB, Eranki A, Erdem H, Escota GV, Evans HL, Eziefula AC, Fenollar F, Fenwick A, Fierer J, Finch RG, Fleckenstein JM, Forstner C, Foschi F, Fournier PE, French MA, Gage KL, Garcia LS, Gascon J, Gastañaduy AS, Gautret P, Geisler WM, Ghanem KG, Giani T, Giannella M, Gilliam BL, Gilliet M, Glaser CA, Glupczynski Y, Gnann JW, Goldstein EJ, Gottstein B, Gouriet F, Gravitt PE, Green MD, Green ST, Groll AH, Gulick RM, Gupta A, Habib G, Harbarth S, Harris M, Hayden FG, Hetem DJ, Hill PC, Hirschel B, Hodowanec AC, Hoffart L, Hoffmann C, Holland SM, Horby PW, Horne DJ, Hraiech S, Hull MW, Huttner A, Ingram RJ, Islam J, Ison MG, James SH, Jenkins C, Jenkins SG, Jensen JS, Johnston C, Jones TB, Jordan SJ, Julian KG, Kato Y, Kauffman CA, Kaye KS, Keane MP, Keeney J, Kelly P, Kent SJ, Kern WV, Keynan Y, Kim AA, Koné-Paut I, Kosmidis C, Kroes AC, Kroon FP, Ksiazek TG, Kuhlmann FM, Kuijper EJ, Kwon JH, Kyei GB, Lacombe K, Lagacé-Wiens P, Lagier JC, Lamagni T, Landraud L, Lanternier F, LaPlante KL, Lawn SD, Lawrence SJ, Leblebicioglu H, Lee N, Leggett JE, Lehours P, Levy PY, Leyh RG, Lillis RA, Limmathurotsakul D, Lin J, Lindquist HA, Lipsky BA, Liscynesky C, Looney D, Lortholary O, Lowy FD, Luft BJ, Mackowiak PA, MacPherson PA, Maghraoui-Slim V, Mallon PW, Mangino JE, Manuel O, Marchetti O, Marks KM, Marr KA, Marrazzo J, Marschall J, Martin DH, Matonti F, Matulewicz RS, Mayer KH, McCulloh RJ, McGready R, Mdodo R, Mead S, Mégraud F, Meintjes G, Metcalf SC, Michaels MG, Migliori GB, Miles MA, Miller A, Mimiaga MJ, Mingeot-Leclercq MP, Misch EA, Mitreva M, Montaner JS, Moore CB, Muñoz P, Muñoz J, Murray CK, Musso D, Mutengo M, Mutizwa MM, Naber KG, Natarajan P, Neme S, Newton PN, Nichols RA, Nicolle LE, Nosten F, Notarangelo LD, Nutman TB, Nyirjesy P, O'Connell PR, Opal SM, Ormerod LP, Osmon DR, Pankert MB, Pantaleo G, Papazian L, Parente DM, Parola P, Parsaei S, Pascual MA, Patel R, Patrozou E, Pawlotsky JM, Peacock SJ, Pechère JC, Pelegrin I, Peters BS, Peters EJ, Petersen JM, Petersen LR, Petraitis V, Pham LL, Picado A, Pilatz A, Pilmis B, Pinazo MJ, Pletz MW, Pogue JM, Polgreen EL, Polgreen PM, Posfay-Barbe KM, Powderly WG, Presti R, Prod'hom G, Puolakkainen M, Quinn TC, Raoult D, Razonable RR, Read RC, Redfield RR, Rentenaar RJ, Reynolds SJ, Ribi C, Richardson MD, Ritter ML, Roch A, Rockstroh JK, Rojek A, Romero JR, Rooijakkers SH, Rosenbluth D, Rosenzweig SD, Rossolini GM, Rubinstein E, Ryan G, Safren SA, Sahasrabuddhe VV, Saikku PA, Sajadi MM, Salvaggio MR, Santos CA, Satlin MJ, Schaeffer AJ, Schimmer C, Schooley RT, Schumacher RF, Sha BE, Shapiro DS, Sheehan G, Shlaes DM, Shoham S, Simmons CP, Simon DW, Simon MS, Simonsen KA, Slack MP, Smith TT, Sobel JD, Souli M, Sridhar S, Steckelberg JM, Stevens DL, Strah H, Sturm AW, Sungkanuparph S, Tabrizi SJ, Tacconelli E, Tan CS, Taplitz RA, Thomas G, Thomas LD, Thuny F, Thwaites G, Tissot F, Tønjum T, Torriani FJ, Toso C, Tulkens PM, Tunkel AR, Turner CE, Ustianowski AP, van Bambeke F, van Crevel R, van de Beek D, van Delden C, van der Eerden MM, van der Meer JW, van der Poll T, van Ingen J, van Putten J, Vaudaux BP, Vermund SH, Viscidi RP, Visvanathan K, Visvesvara GS, von Seidlein L, Wagenlehner FM, Wald A, Walsh TJ, Warhurst DC, Warnock DW, Warrell DA, Warrell MJ, Warris A, Watkins RR, Weatherall DJ, Weber R, Weidner W, White JR, White PJ, Whitehorn J, Whitley RJ, Whitty CJ, Wiersinga WJ, Wilcox MH, Williams TN, Wilson CC, Wilson ME, Wisplinghoff H, Wood R, Wunderink RG, Wyles D, Yang ZT, Yoder JS, Zaidi NA, Zimmer AJ, Zuckerman JN, Zumla A. List of Contributors. Infect Dis (Lond) 2017. [DOI: 10.1016/b978-0-7020-6285-8.00234-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Pearson RD, Amato R, Auburn S, Miotto O, Almagro-Garcia J, Amaratunga C, Suon S, Mao S, Noviyanti R, Trimarsanto H, Marfurt J, Anstey NM, William T, Boni MF, Dolecek C, Hien TT, White NJ, Michon P, Siba P, Tavul L, Harrison G, Barry A, Mueller I, Ferreira MU, Karunaweera N, Randrianarivelojosia M, Gao Q, Hubbart C, Hart L, Jeffery B, Drury E, Mead D, Kekre M, Campino S, Manske M, Cornelius VJ, MacInnis B, Rockett KA, Miles A, Rayner JC, Fairhurst RM, Nosten F, Price RN, Kwiatkowski DP. Genomic analysis of local variation and recent evolution in Plasmodium vivax. Nat Genet 2016; 48:959-964. [PMID: 27348299 PMCID: PMC4966634 DOI: 10.1038/ng.3599] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 05/27/2016] [Indexed: 01/12/2023]
Abstract
The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for the elimination of malaria. To characterize the genetic diversity of this parasite in individual infections and across the population, we performed deep genome sequencing of >200 clinical samples collected across the Asia-Pacific region and analyzed data on >300,000 SNPs and nine regions of the genome with large copy number variations. Individual infections showed complex patterns of genetic structure, with variation not only in the number of dominant clones but also in their level of relatedness and inbreeding. At the population level, we observed strong signals of recent evolutionary selection both in known drug resistance genes and at new loci, and these varied markedly between geographical locations. These findings demonstrate a dynamic landscape of local evolutionary adaptation in the parasite population and provide a foundation for genomic surveillance to guide effective strategies for control and elimination of P. vivax.
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Affiliation(s)
- Richard D Pearson
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Roberto Amato
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territories 0811, Australia
| | - Olivo Miotto
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok 10400, Thailand
| | - Jacob Almagro-Garcia
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA
| | - Seila Suon
- National Centre for Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | - Sivanna Mao
- Sampov Meas Referral Hospital, Pursat, Cambodia
| | - Rintis Noviyanti
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia
| | | | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territories 0811, Australia
| | - Nicholas M Anstey
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territories 0811, Australia
| | - Timothy William
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit and Queen Elizabeth Hospital Clinical Research Centre, Kota Kinabalu, Sabah, Malaysia
| | - Maciej F Boni
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Tinh Tran Hien
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok 10400, Thailand
| | - Pascal Michon
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
- Faculty of Medicine and Health Sciences, Divine Word University, Madang, Papua New Guinea
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Gabrielle Harrison
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute for Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Alyssa Barry
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute for Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Ivo Mueller
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute for Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nadira Karunaweera
- Department of Parasitology, Faculty of Medicine, University of Colombo, Sri Lanka
| | | | - Qi Gao
- Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu, People's Republic of China
| | - Christina Hubbart
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Lee Hart
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Ben Jeffery
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Eleanor Drury
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Daniel Mead
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Mihir Kekre
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Susana Campino
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Magnus Manske
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Victoria J Cornelius
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Bronwyn MacInnis
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Kirk A Rockett
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Alistair Miles
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Julian C Rayner
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Rick M Fairhurst
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA
| | - Francois Nosten
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok 10400, Thailand
- Shoklo Malaria Research Unit, Mae Sot, Tak 63110, Thailand
| | - Ric N Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territories 0811, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7LJ, UK
| | - Dominic P Kwiatkowski
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
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42
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Pham Thanh D, Karkey A, Dongol S, Ho Thi N, Thompson CN, Rabaa MA, Arjyal A, Holt KE, Wong V, Tran Vu Thieu N, Voong Vinh P, Ha Thanh T, Pradhan A, Shrestha SK, Gajurel D, Pickard D, Parry CM, Dougan G, Wolbers M, Dolecek C, Thwaites GE, Basnyat B, Baker S. A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure. eLife 2016; 5:e14003. [PMID: 26974227 PMCID: PMC4805543 DOI: 10.7554/elife.14003] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/19/2016] [Indexed: 01/22/2023] Open
Abstract
The interplay between bacterial antimicrobial susceptibility, phylogenetics and patient outcome is poorly understood. During a typhoid clinical treatment trial in Nepal, we observed several treatment failures and isolated highly fluoroquinolone-resistant Salmonella Typhi (S. Typhi). Seventy-eight S. Typhi isolates were genome sequenced and clinical observations, treatment failures and fever clearance times (FCTs) were stratified by lineage. Most fluoroquinolone-resistant S. Typhi belonged to a specific H58 subclade. Treatment failure with S. Typhi-H58 was significantly less frequent with ceftriaxone (3/31; 9.7%) than gatifloxacin (15/34; 44.1%)(Hazard Ratio 0.19, p=0.002). Further, for gatifloxacin-treated patients, those infected with fluoroquinolone-resistant organisms had significantly higher median FCTs (8.2 days) than those infected with susceptible (2.96) or intermediately resistant organisms (4.01)(p<0.001). H58 is the dominant S. Typhi clade internationally, but there are no data regarding disease outcome with this organism. We report an emergent new subclade of S. Typhi-H58 that is associated with fluoroquinolone treatment failure. Clinical trial registration: ISRCTN63006567. DOI:http://dx.doi.org/10.7554/eLife.14003.001 People who ingest a type of bacteria called Salmonella Typhi can develop the symptoms of typhoid fever. This disease is common in low-income settings in Asia and Africa, and causes a high rate of death in people who are not treated with antimicrobial drugs. During a study in Nepal, Thanh et al. tried to evaluate which of two antimicrobials was better for treating typhoid fever. One of the drugs – called gatifloxacin – did not work in some of the patients. To understand why this treatment failed, Thanh et al. decoded the entire DNA sequences of all the Salmonella Typhi bacteria isolated during the study. Comparing this genetic data to the clinical data of the patients identified a new variant of Salmonella Typhi. These bacteria have a specific combination of genetic mutations that render them resistant to the family of drugs that gatifloxacin belongs to – the fluoroquinolones. Patients infected with the variant bacteria and treated with gatifloxacin were highly likely to completely fail treatment and have longer-lasting fevers. On further investigation Thanh et al. found these organisms were likely recently introduced into Nepal from India. Fluoroquinolones are amongst the most effective and common antimicrobials used to treat typhoid fever and other bacterial infections. However, the presence of bacteria that are resistant to these compounds in South Asia means that they should no longer be the first choice of drug to treat typhoid fever in this location. DOI:http://dx.doi.org/10.7554/eLife.14003.002
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Affiliation(s)
- Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Abhilasha Karkey
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Sabina Dongol
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Nhan Ho Thi
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Corinne N Thompson
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom.,The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Maia A Rabaa
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
| | - Amit Arjyal
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
| | - Vanessa Wong
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Nga Tran Vu Thieu
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phat Voong Vinh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tuyen Ha Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | | | - Derek Pickard
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Christopher M Parry
- The London School of Hygiene and Tropical Medicine, London, United Kingdom.,School of Tropical Medicine and Global Health, Department of Clinical Research, Nagasaki University, Nagasaki, Japan
| | - Gordon Dougan
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Marcel Wolbers
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
| | - Christiane Dolecek
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom.,Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Guy E Thwaites
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom.,The London School of Hygiene and Tropical Medicine, London, United Kingdom
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43
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Thuan PD, Ca NTN, Van Toi P, Nhien NTT, Thanh NV, Anh ND, Phu NH, Thai CQ, Hong Thai L, Hoa NT, Thanh Dong L, Loi MA, Son DH, Khanh TTN, Dolecek C, Nhan HT, Wolbers M, Thwaites G, Farrar J, White NJ, Hien TT. A Randomized Comparison of Chloroquine Versus Dihydroartemisinin-Piperaquine for the Treatment of Plasmodium vivax Infection in Vietnam. Am J Trop Med Hyg 2016; 94:879-885. [PMID: 26856909 PMCID: PMC4824232 DOI: 10.4269/ajtmh.15-0740] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 12/14/2015] [Indexed: 01/20/2023] Open
Abstract
A total of 128 Vietnamese patients with symptomatic Plasmodium vivax mono-infections were enrolled in a prospective, open-label, randomized trial to receive either chloroquine or dihydroartemisinin–piperaquine (DHA-PPQ). The proportions of patients with adequate clinical and parasitological responses were 47% in the chloroquine arm (31 of 65 patients) and 66% in the DHA-PPQ arm (42 of 63 patients) in the Kaplan–Meier intention-to-treat analysis (absolute difference 19%, 95% confidence interval = 0–37%), thus establishing non-inferiority of DHA-PPQ. Fever clearance time (median 24 versus 12 hours, P = 0.02), parasite clearance time (median 36 versus 18 hours, P < 0.001), and parasite clearance half-life (mean 3.98 versus 1.80 hours, P < 0.001) were all significantly shorter in the DHA-PPQ arm. All cases of recurrent parasitemia in the chloroquine arm occurred from day 33 onward, with corresponding whole blood chloroquine concentration lower than 100 ng/mL in all patients. Chloroquine thus remains efficacious for the treatment of P. vivax malaria in southern Vietnam, but DHA-PPQ provides more rapid symptomatic and parasitological recovery.
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Affiliation(s)
- Phung Duc Thuan
- *Address correspondence to Phung Duc Thuan, Oxford University Clinical Research Unit, 764 Vo Van Kiet, District 5, Ho Chi Minh city, Vietnam. E-mail:
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44
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Wong VK, Baker S, Pickard DJ, Parkhill J, Page AJ, Feasey NA, Kingsley RA, Thomson NR, Keane JA, Weill FX, Edwards DJ, Hawkey J, Harris SR, Mather AE, Cain AK, Hadfield J, Hart PJ, Thieu NTV, Klemm EJ, Glinos DA, Breiman RF, Watson CH, Kariuki S, Gordon MA, Heyderman RS, Okoro C, Jacobs J, Lunguya O, Edmunds WJ, Msefula C, Chabalgoity JA, Kama M, Jenkins K, Dutta S, Marks F, Campos J, Thompson C, Obaro S, MacLennan CA, Dolecek C, Keddy KH, Smith AM, Parry CM, Karkey A, Mulholland EK, Campbell JI, Dongol S, Basnyat B, Dufour M, Bandaranayake D, Naseri TT, Singh SP, Hatta M, Newton P, Onsare RS, Isaia L, Dance D, Davong V, Thwaites G, Wijedoru L, Crump JA, De Pinna E, Nair S, Nilles EJ, Thanh DP, Turner P, Soeng S, Valcanis M, Powling J, Dimovski K, Hogg G, Farrar J, Holt KE, Dougan G. Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events. Nat Genet 2015; 47:632-9. [PMID: 25961941 PMCID: PMC4921243 DOI: 10.1038/ng.3281] [Citation(s) in RCA: 298] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 03/23/2015] [Indexed: 11/09/2022]
Abstract
The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome sequence analysis of 1,832 Salmonella enterica serovar Typhi (S. Typhi) identifies a single dominant MDR lineage, H58, that has emerged and spread throughout Asia and Africa over the last 30 years. Our analysis identifies numerous transmissions of H58, including multiple transfers from Asia to Africa and an ongoing, unrecognized MDR epidemic within Africa itself. Notably, our analysis indicates that H58 lineages are displacing antibiotic-sensitive isolates, transforming the global population structure of this pathogen. H58 isolates can harbor a complex MDR element residing either on transmissible IncHI1 plasmids or within multiple chromosomal integration sites. We also identify new mutations that define the H58 lineage. This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is applicable to similar MDR lineages emerging in other bacterial species.
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Affiliation(s)
- Vanessa K Wong
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Department of Microbiology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, UK
| | - Stephen Baker
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [3] Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | | | | | | | - Robert A Kingsley
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Institute of Food Research, Norwich Research Park, Norwich, UK
| | - Nicholas R Thomson
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | | | - David J Edwards
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Jane Hawkey
- 1] Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia. [2] Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | | | | | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Peter J Hart
- Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Nga Tran Vu Thieu
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Robert F Breiman
- 1] Kenya Medical Research Institute (KEMRI), Nairobi, Kenya. [2] Centers for Disease Control and Prevention, Atlanta, Georgia, USA. [3] Emory Global Health Institute, Atlanta, Georgia, USA
| | - Conall H Watson
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Samuel Kariuki
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Melita A Gordon
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Robert S Heyderman
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | | | - Jan Jacobs
- 1] Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium. [2] Department of Microbiology and Immunology, Katholieke Universiteit (KU) Leuven, University of Leuven, Leuven, Belgium
| | - Octavie Lunguya
- 1] National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo. [2] University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - W John Edmunds
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Chisomo Msefula
- 1] Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi. [2] Microbiology Department, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Jose A Chabalgoity
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Montevideo, Uruguay
| | | | | | - Shanta Dutta
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Florian Marks
- International Vaccine Institute, Department of Epidemiology, Seoul, Republic of Korea
| | - Josefina Campos
- Enteropathogen Division, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) Carlos G. Malbran Institute, Buenos Aires, Argentina
| | - Corinne Thompson
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Stephen Obaro
- 1] Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA. [2] University of Abuja Teaching Hospital, Abuja, Nigeria. [3] Bingham University, Karu, Nigeria
| | - Calman A MacLennan
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK. [3] Novartis Vaccines Institute for Global Health, Siena, Italy
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Karen H Keddy
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa
| | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa
| | - Christopher M Parry
- 1] Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK. [2] Graduate School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Abhilasha Karkey
- Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - E Kim Mulholland
- 1] Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK. [2] Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | - James I Campbell
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Sabina Dongol
- Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - Buddha Basnyat
- Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - Muriel Dufour
- Enteric and Leptospira Reference Laboratory, Institute of Environmental Science and Research, Ltd. (ESR), Porirua, New Zealand
| | - Don Bandaranayake
- National Centre for Biosecurity and Infectious Disease, Institute of Environmental Science and Research, Porirua, New Zealand
| | | | - Shalini Pravin Singh
- National Influenza Center, World Health Organization, Center for Communicable Disease Control, Suva, Fiji
| | - Mochammad Hatta
- Department of Microbiology, Hasanuddin University, Makassar, Indonesia
| | - Paul Newton
- 1] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [2] Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | | | | | - David Dance
- 1] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [2] Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Viengmon Davong
- Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Guy Thwaites
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Lalith Wijedoru
- 1] Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. [2] Paediatric Emergency Medicine, Chelsea and Westminster Hospital, London, UK
| | - John A Crump
- Centre for International Health and Otago International Health Research Network, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Elizabeth De Pinna
- Salmonella Reference Service, Public Health England, Colindale, London, UK
| | - Satheesh Nair
- Salmonella Reference Service, Public Health England, Colindale, London, UK
| | - Eric J Nilles
- Emerging Disease Surveillance and Response, Division of Pacific Technical Support, World Health Organization, Suva, Fiji
| | - Duy Pham Thanh
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Paul Turner
- 1] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [2] Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. [3] Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Sona Soeng
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Mary Valcanis
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Joan Powling
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Karolina Dimovski
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Geoff Hogg
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jeremy Farrar
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
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45
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Thompson CN, Blacksell SD, Paris DH, Arjyal A, Karkey A, Dongol S, Giri A, Dolecek C, Day N, Baker S, Thwaites G, Farrar J, Basnyat B. Undifferentiated febrile illness in Kathmandu, Nepal. Am J Trop Med Hyg 2015; 92:875-878. [PMID: 25667056 PMCID: PMC4385789 DOI: 10.4269/ajtmh.14-0709] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 12/16/2014] [Indexed: 01/07/2023] Open
Abstract
Undifferentiated febrile illnesses (UFIs) are common in low- and middle-income countries. We prospectively investigated the causes of UFIs in 627 patients presenting to a tertiary referral hospital in Kathmandu, Nepal. Patients with microbiologically confirmed enteric fever (218 of 627; 34.8%) randomized to gatifloxacin or ofloxacin treatment were previously reported. We randomly selected 125 of 627 (20%) of these UFI patients, consisting of 96 of 409 (23%) cases with sterile blood cultures and 29 of 218 (13%) cases with enteric fever, for additional diagnostic investigations. We found serological evidence of acute murine typhus in 21 of 125 (17%) patients, with 12 of 21 (57%) patients polymerase chain reaction (PCR)-positive for Rickettsia typhi. Three UFI cases were quantitative PCR-positive for Rickettsia spp., two UFI cases were seropositive for Hantavirus, and one UFI case was seropositive for Q fever. Fever clearance time (FCT) for rickettsial infection was 44.5 hours (interquartile range = 26–66 hours), and there was no difference in FCT between ofloxacin or gatifloxacin. Murine typhus represents an important cause of predominantly urban UFIs in Nepal, and fluoroquinolones seem to be an effective empirical treatment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Buddha Basnyat
- *Address correspondence to Buddha Basnyat, Oxford University Clinical Research Unit–Nepal, Patan Academy of Health Sciences, Patan Hospital, Lagankhel Rodd, 44700, Lalitpur, Nepal. E-mail:
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Dunstan SJ, Hue NT, Han B, Li Z, Tram TTB, Sim KS, Parry CM, Chinh NT, Vinh H, Lan NPH, Thieu NTV, Vinh PV, Koirala S, Dongol S, Arjyal A, Karkey A, Shilpakar O, Dolecek C, Foo JN, Phuong LT, Lanh MN, Do T, Aung T, Hon DN, Teo YY, Hibberd ML, Anders KL, Okada Y, Raychaudhuri S, Simmons CP, Baker S, de Bakker PIW, Basnyat B, Hien TT, Farrar JJ, Khor CC. Variation at HLA-DRB1 is associated with resistance to enteric fever. Nat Genet 2014; 46:1333-6. [PMID: 25383971 PMCID: PMC5099079 DOI: 10.1038/ng.3143] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 10/15/2014] [Indexed: 12/18/2022]
Abstract
Enteric fever affects more than 25 million people annually and results from systemic infection with Salmonella enterica serovar Typhi or Paratyphi pathovars A, B or C(1). We conducted a genome-wide association study of 432 individuals with blood culture-confirmed enteric fever and 2,011 controls from Vietnam. We observed strong association at rs7765379 (odds ratio (OR) for the minor allele = 0.18, P = 4.5 × 10(-10)), a marker mapping to the HLA class II region, in proximity to HLA-DQB1 and HLA-DRB1. We replicated this association in 595 enteric fever cases and 386 controls from Nepal and also in a second independent collection of 151 cases and 668 controls from Vietnam. Imputation-based fine-mapping across the extended MHC region showed that the classical HLA-DRB1*04:05 allele (OR = 0.14, P = 2.60 × 10(-11)) could entirely explain the association at rs7765379, thus implicating HLA-DRB1 as a major contributor to resistance against enteric fever, presumably through antigen presentation.
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Affiliation(s)
- Sarah J Dunstan
- 1] Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [3] Nossal Institute of Global Health, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nguyen Thi Hue
- 1] Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. [2] Faculty of Biology, University of Science, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Buhm Han
- 1] Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea. [2] Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA. [3] Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA. [4] Partners Center for Personalized Genetic Medicine, Boston, Massachusetts, USA
| | - Zheng Li
- Genome Institute of Singapore, Singapore
| | - Trinh Thi Bich Tram
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | - Christopher M Parry
- 1] Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. [2] Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Ha Vinh
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | - Nga Tran Vu Thieu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Phat Voong Vinh
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Samir Koirala
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Sciences, Patan Hospital, Patan, Nepal
| | - Sabina Dongol
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Sciences, Patan Hospital, Patan, Nepal
| | - Amit Arjyal
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Sciences, Patan Hospital, Patan, Nepal
| | - Abhilasha Karkey
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Sciences, Patan Hospital, Patan, Nepal
| | - Olita Shilpakar
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Sciences, Patan Hospital, Patan, Nepal
| | - Christiane Dolecek
- 1] Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | | | | | | | - Tan Do
- Vietnam National Institute of Ophthalmology, Hanoi, Vietnam
| | - Tin Aung
- Singapore Eye Research Institute, Singapore
| | - Do Nu Hon
- Vietnam National Institute of Ophthalmology, Hanoi, Vietnam
| | - Yik Ying Teo
- 1] Department of Statistics and Applied Probability, National University of Singapore, Singapore. [2] Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Martin L Hibberd
- 1] Genome Institute of Singapore, Singapore. [2] London School of Tropical Medicine and Hygiene, London, UK
| | - Katherine L Anders
- 1] Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Yukinori Okada
- 1] Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. [2] Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Soumya Raychaudhuri
- 1] Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA. [3] Partners Center for Personalized Genetic Medicine, Boston, Massachusetts, USA. [4] Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, Massachusetts, USA. [5] Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - Cameron P Simmons
- 1] Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [3] Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen Baker
- 1] Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [3] London School of Tropical Medicine and Hygiene, London, UK
| | - Paul I W de Bakker
- 1] Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands. [2] Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Buddha Basnyat
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Sciences, Patan Hospital, Patan, Nepal
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Jeremy J Farrar
- 1] Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Chiea Chuen Khor
- 1] Genome Institute of Singapore, Singapore. [2] Singapore Eye Research Institute, Singapore. [3] Saw Swee Hock School of Public Health, National University of Singapore, Singapore. [4] Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore. [5] Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Näsström E, Vu Thieu NT, Dongol S, Karkey A, Voong Vinh P, Ha Thanh T, Johansson A, Arjyal A, Thwaites G, Dolecek C, Basnyat B, Baker S, Antti H. Salmonella Typhi and Salmonella Paratyphi A elaborate distinct systemic metabolite signatures during enteric fever. eLife 2014; 3. [PMID: 24902583 PMCID: PMC4077204 DOI: 10.7554/elife.03100] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/26/2014] [Indexed: 12/31/2022] Open
Abstract
The host-pathogen interactions induced by Salmonella Typhi and Salmonella Paratyphi A during enteric fever are poorly understood. This knowledge gap, and the human restricted nature of these bacteria, limit our understanding of the disease and impede the development of new diagnostic approaches. To investigate metabolite signals associated with enteric fever we performed two dimensional gas chromatography with time-of-flight mass spectrometry (GCxGC/TOFMS) on plasma from patients with S. Typhi and S. Paratyphi A infections and asymptomatic controls, identifying 695 individual metabolite peaks. Applying supervised pattern recognition, we found highly significant and reproducible metabolite profiles separating S. Typhi cases, S. Paratyphi A cases, and controls, calculating that a combination of six metabolites could accurately define the etiological agent. For the first time we show that reproducible and serovar specific systemic biomarkers can be detected during enteric fever. Our work defines several biologically plausible metabolites that can be used to detect enteric fever, and unlocks the potential of this method in diagnosing other systemic bacterial infections.
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Affiliation(s)
- Elin Näsström
- Department of Chemistry, Computational Life Science Cluster, Umeå University, Umeå, Sweden
| | - Nga Tran Vu Thieu
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Sabina Dongol
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Abhilasha Karkey
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Phat Voong Vinh
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Tuyen Ha Thanh
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Anders Johansson
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Amit Arjyal
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Christiane Dolecek
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Stephen Baker
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Henrik Antti
- Department of Chemistry, Computational Life Science Cluster, Umeå University, Umeå, Sweden
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48
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Tanomsing N, Mayxay M, Newton PN, Nosten F, Dolecek C, Hien TT, White NJ, Day NPJ, Dondorp AM, Imwong M. Genetic variability of Plasmodium malariae dihydropteroate synthase (dhps) in four Asian countries. PLoS One 2014; 9:e93942. [PMID: 24699454 PMCID: PMC3974843 DOI: 10.1371/journal.pone.0093942] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 03/09/2014] [Indexed: 11/27/2022] Open
Abstract
The dihydropteroate synthase (dhps) genes of 44 P. malariae strains from four Asian countries were isolated. Only a limited number of polymorphisms were observed. Comparison with homologous mutations in other Plasmodium species showed that these polymorphisms are unlikely to be associated with sulfadoxine resistance.
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Affiliation(s)
- Naowarat Tanomsing
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Faculty of Postgraduate Studies, University of Health Sciences, Vientiane, Lao PDR
- Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Paul N. Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Francois Nosten
- Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Christiane Dolecek
- Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Tran Tinh Hien
- Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Nicholas J. White
- Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nicholas P. J. Day
- Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Arjen M. Dondorp
- Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- * E-mail:
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49
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Koirala S, Basnyat B, Arjyal A, Shilpakar O, Shrestha K, Shrestha R, Shrestha UM, Agrawal K, Koirala KD, Thapa SD, Karkey A, Dongol S, Giri A, Shakya M, Pathak KR, Campbell J, Baker S, Farrar J, Wolbers M, Dolecek C. Gatifloxacin versus ofloxacin for the treatment of uncomplicated enteric fever in Nepal: an open-label, randomized, controlled trial. PLoS Negl Trop Dis 2013; 7:e2523. [PMID: 24282626 PMCID: PMC3837022 DOI: 10.1371/journal.pntd.0002523] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Accepted: 09/25/2013] [Indexed: 11/29/2022] Open
Abstract
Background Fluoroquinolones are the most commonly used group of antimicrobials for the treatment of enteric fever, but no direct comparison between two fluoroquinolones has been performed in a large randomised trial. An open-label randomized trial was conducted to investigate whether gatifloxacin is more effective than ofloxacin in the treatment of uncomplicated enteric fever caused by nalidixic acid-resistant Salmonella enterica serovars Typhi and Paratyphi A. Methodology and Principal Findings Adults and children clinically diagnosed with uncomplicated enteric fever were enrolled in the study to receive gatifloxacin (10 mg/kg/day) in a single dose or ofloxacin (20 mg/kg/day) in two divided doses for 7 days. Patients were followed for six months. The primary outcome was treatment failure in patients infected with nalidixic acid resistant isolates. 627 patients with a median age of 17 (IQR 9–23) years were randomised. Of the 218 patients with culture confirmed enteric fever, 170 patients were infected with nalidixic acid-resistant isolates. In the ofloxacin group, 6 out of 83 patients had treatment failure compared to 5 out of 87 in the gatifloxacin group (hazard ratio [HR] of time to failure 0.81, 95% CI 0.25 to 2.65, p = 0.73). The median time to fever clearance was 4.70 days (IQR 2.98–5.90) in the ofloxacin group versus 3.31 days (IQR 2.29–4.75) in the gatifloxacin group (HR = 1.59, 95% CI 1.16 to 2.18, p = 0.004). The results in all blood culture-confirmed patients and all randomized patients were comparable. Conclusion Gatifloxacin was not superior to ofloxacin in preventing failure, but use of gatifloxacin did result in more prompt fever clearance time compared to ofloxacin. Trial registration: ISRCTN 63006567 (www.controlled-trials.com). Enteric fever, which comprises of typhoid and paratyphoid fevers, is common in many developing countries. It is also sometimes seen in the Western world in returning travellers. This present study of uncomplicated enteric fever in an outpatient setting in a hospital in Kathmandu, Nepal compared the newer gatifloxacin with the widely-used ofloxacin (two drugs of the fluroquinolone class) in the treatment of this illness. Although fluroquinolones are commonly considered the main group of drugs in the treatment of enteric fever, there have not been comparisons of efficacy between two drugs in this same class in the treatment of enteric fever. Furthermore, certain strains of enteric fever organism called nalidixic-acid resistant strains are proving very difficult to treat in both the local population and the Western travellers. The study focused primarily on the efficacy of the 2 drugs against these particular strains. The results revealed that both drugs were effective but gatifloxacin decreased the patient's fever more rapidly than ofloxacin. Dysglycemia was noted in a 35-year-old woman taking gatifloxacin who did not disclose a pre-existing diagnosis of diabetes at time of enrollment, but not in any other healthy child or young adult.
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Affiliation(s)
- Samir Koirala
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Sciences, Patan Hospital, Patan, Nepal
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50
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Karkey A, Thompson CN, Tran Vu Thieu N, Dongol S, Le Thi Phuong T, Voong Vinh P, Arjyal A, Martin LB, Rondini S, Farrar JJ, Dolecek C, Basnyat B, Baker S. Differential epidemiology of Salmonella Typhi and Paratyphi A in Kathmandu, Nepal: a matched case control investigation in a highly endemic enteric fever setting. PLoS Negl Trop Dis 2013; 7:e2391. [PMID: 23991240 PMCID: PMC3749961 DOI: 10.1371/journal.pntd.0002391] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 07/17/2013] [Indexed: 01/08/2023] Open
Abstract
Background Enteric fever, a systemic infection caused by the bacteria Salmonella Typhi and Salmonella Paratyphi A, is endemic in Kathmandu, Nepal. Previous work identified proximity to poor quality water sources as a community-level risk for infection. Here, we sought to examine individual-level risk factors related to hygiene and sanitation to improve our understanding of the epidemiology of enteric fever in this setting. Methodology and principal findings A matched case-control analysis was performed through enrollment of 103 blood culture positive enteric fever patients and 294 afebrile community-based age and gender-matched controls. A detailed questionnaire was administered to both cases and controls and the association between enteric fever infection and potential exposures were examined through conditional logistic regression. Several behavioral practices were identified as protective against infection with enteric fever, including water storage and hygienic habits. Additionally, we found that exposures related to poor water and socioeconomic status are more influential in the risk of infection with S. Typhi, whereas food consumption habits and migration play more of a role in risk of S. Paratyphi A infection. Conclusions and significance Our work suggests that S. Typhi and S. Paratyphi A follow different routes of infection in this highly endemic setting and that sustained exposure to both serovars probably leads to the development of passive immunity. In the absence of a polyvalent vaccine against S. Typhi and S. Paratyphi A, we advocate better systems for water treatment and storage, improvements in the quality of street food, and vaccination with currently available S. Typhi vaccines. Enteric fever, caused by ingestion of bacteria Salmonella Typhi or Salmonella Paratyphi A, is common in regions with poor water quality and sanitation. We sought to identify individual-level risks for infection in Kathmandu, Nepal, a region endemic for enteric fever. In this study, we enrolled patients presenting to hospital who were blood-culture positive for enteric fever and a series of community controls matched for age, gender and residential ward. Our findings suggest that while some risks for infection with S. Typhi and S. Paratyphi A overlap, these organisms also have distinctive routes of infection in this setting; poor water and socioeconomic status seemed more influential in infection with S. Typhi, whereas food consumption habits and migratory status were shown to play a larger role in infection with S. Paratyphi A. Additionally, serological evaluation of IgG levels against the Vi (Salmonella Typhi) and the O:2 (Salmonella Paratyphi A) antigens demonstrated high titers against both antigens throughout life, suggesting frequent and constant exposure to these organisms in Kathmandu. As major improvements in sanitation infrastructure are unlikely in this setting, we recommend water treatment and storage-based prevention strategies, as well as street food quality regulation, and the promotion of vaccination with existing typhoid vaccines.
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Affiliation(s)
- Abhilasha Karkey
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Corinne N. Thompson
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Oxford University, Oxford, United Kingdom
| | - Nga Tran Vu Thieu
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Sabina Dongol
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Tu Le Thi Phuong
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phat Voong Vinh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Amit Arjyal
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | | | - Simona Rondini
- Novartis Institute Vaccines for Global Health, Siena, Italy
| | - Jeremy J. Farrar
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Oxford University, Oxford, United Kingdom
| | | | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Oxford University, Oxford, United Kingdom
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
- * E-mail:
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