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Jarju S, Wenlock RD, Danso M, Jobe D, Jagne YJ, Darboe A, Kumado M, Jallow Y, Touray M, Ceesay EA, Gaye H, Gaye B, Tunkara A, Kandeh S, Gomes M, Sylva EL, Toure F, Hornsby H, Lindsey BB, Nicklin MJ, Sayers JR, Sesay AK, Kucharski A, Hodgson D, Kampmann B, de Silva TI. High SARS-CoV-2 incidence and asymptomatic fraction during Delta and Omicron BA.1 waves in The Gambia. Nat Commun 2024; 15:3814. [PMID: 38714680 PMCID: PMC11076623 DOI: 10.1038/s41467-024-48098-3] [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: 01/06/2024] [Accepted: 04/19/2024] [Indexed: 05/10/2024] Open
Abstract
Little is known about SARS-CoV-2 infection risk in African countries with high levels of infection-driven immunity and low vaccine coverage. We conducted a prospective cohort study of 349 participants from 52 households in The Gambia between March 2021 and June 2022, with routine weekly SARS-CoV-2 RT-PCR and 6-monthly SARS-CoV-2 serology. Attack rates of 45% and 57% were seen during Delta and Omicron BA.1 waves respectively. Eighty-four percent of RT-PCR-positive infections were asymptomatic. Children under 5-years had a lower incidence of infection than 18-49-year-olds. One prior SARS-CoV-2 infection reduced infection risk during the Delta wave only, with immunity from ≥2 prior infections required to reduce the risk of infection with early Omicron lineage viruses. In an African population with high levels of infection-driven immunity and low vaccine coverage, we find high attack rates during SARS-CoV-2 waves, with a high proportion of asymptomatic infections and young children remaining relatively protected from infection.
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Affiliation(s)
- Sheikh Jarju
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Rhys D Wenlock
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Madikoi Danso
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Dawda Jobe
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Ya Jankey Jagne
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Alansana Darboe
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Michelle Kumado
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Yusupha Jallow
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Mamlie Touray
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Ebrima A Ceesay
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Hoja Gaye
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Biran Gaye
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Abdoulie Tunkara
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Sheriff Kandeh
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Marie Gomes
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Ellen Lena Sylva
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Fatoumata Toure
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Hailey Hornsby
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield, UK
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK
| | - Benjamin B Lindsey
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield, UK
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK
| | - Martin J Nicklin
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield, UK
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK
| | - Jon R Sayers
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield, UK
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK
| | - Abdul K Sesay
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia
| | - Adam Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - David Hodgson
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia.
- Institute for International Health, Charité Universitätsmedizin, Berlin, Germany.
| | - Thushan I de Silva
- Vaccines and Immunity Theme, Medical Research Council The Gambia at the London School of Hygiene and Tropical Medicine, PO Box 273, Banjul, The Gambia.
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield, UK.
- The Florey Institute of Infection, The University of Sheffield, Sheffield, UK.
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2
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Liu J, Garcia Bardales PF, Islam K, Jarju S, Juma J, Mhango C, Naumanga Q, Qureshi S, Sonye C, Ahmed N, Aziz F, Bhuiyan MTR, Charles M, Cunliffe NA, Abdou M, Galagan SR, Gitteh E, Guindo I, Jahangir Hossain M, Jabang AMJ, Jere KC, Kawonga F, Keita M, Keita NY, Kotloff KL, Shapiama Lopez WV, Munga S, Paredes Olortegui M, Omore R, Pavlinac PB, Qadri F, Qamar FN, Azadul Alam Raz SM, Riziki L, Schiaffino F, Stroup S, Traore SN, Pinedo Vasquez T, Yousafzai MT, Antonio M, Cornick JE, Kabir F, Khanam F, Kosek MN, Ochieng JB, Platts-Mills JA, Tennant SM, Houpt ER. Shigella Detection and Molecular Serotyping With a Customized TaqMan Array Card in the Enterics for Global Health (EFGH): Shigella Surveillance Study. Open Forum Infect Dis 2024; 11:S34-S40. [PMID: 38532960 PMCID: PMC10962731 DOI: 10.1093/ofid/ofad574] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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] [Indexed: 03/28/2024] Open
Abstract
Background Quantitative polymerase chain reaction (qPCR) targeting ipaH has been proven to be highly efficient in detecting Shigella in clinical samples compared to culture-based methods, which underestimate Shigella burden by 2- to 3-fold. qPCR assays have also been developed for Shigella speciation and serotyping, which is critical for both vaccine development and evaluation. Methods The Enterics for Global Health (EFGH) Shigella surveillance study will utilize a customized real-time PCR-based TaqMan Array Card (TAC) interrogating 82 targets, for the detection and differentiation of Shigella spp, Shigella sonnei, Shigella flexneri serotypes, other diarrhea-associated enteropathogens, and antimicrobial resistance (AMR) genes. Total nucleic acid will be extracted from rectal swabs or stool samples, and assayed on TAC. Quantitative analysis will be performed to determine the likely attribution of Shigella and other particular etiologies of diarrhea using the quantification cycle cutoffs derived from previous studies. The qPCR results will be compared to conventional culture, serotyping, and phenotypic susceptibility approaches in EFGH. Conclusions TAC enables simultaneous detection of diarrheal etiologies, the principal pathogen subtypes, and AMR genes. The high sensitivity of the assay enables more accurate estimation of Shigella-attributed disease burden, which is critical to informing policy and in the design of future clinical trials.
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Affiliation(s)
- Jie Liu
- School of Public Health, Qingdao University, Qingdao, China
| | | | - Kamrul Islam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Jane Juma
- Centre pour le Développement des Vaccins du Mali (CVD-Mali), Bamako, Mali
| | | | - Queen Naumanga
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Sonia Qureshi
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Catherine Sonye
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Naveed Ahmed
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Fatima Aziz
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Md Taufiqur Rahman Bhuiyan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mary Charles
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
| | - Nigel A Cunliffe
- Institute of Infection, Veterinary and Ecological Sciences, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, United Kingdom
| | - Mahamadou Abdou
- Centre pour le Développement des Vaccins du Mali (CVD-Mali), Bamako, Mali
| | - Sean R Galagan
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Ensa Gitteh
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Ibrehima Guindo
- Centre pour le Développement des Vaccins du Mali (CVD-Mali), Bamako, Mali
| | - M Jahangir Hossain
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Abdoulie M J Jabang
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Khuzwayo C Jere
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, United Kingdom
- Department of Medical Laboratory Sciences, School of Life Sciences and Health Professions, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Flywell Kawonga
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
| | - Mariama Keita
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | | | - Karen L Kotloff
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | - Stephen Munga
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | | | - Richard Omore
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Patricia B Pavlinac
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Farah Naz Qamar
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - S M Azadul Alam Raz
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Laura Riziki
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Francesca Schiaffino
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
- Faculty of Veterinary Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Suzanne Stroup
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | | | | | | | - Martin Antonio
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Centre for Epidemic Preparedness and Response, London School of Hygiene & Tropical Medicine, London, UK
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jennifer E Cornick
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, United Kingdom
| | - Furqan Kabir
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Farhana Khanam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Margaret N Kosek
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | | | - James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Sharon M Tennant
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
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3
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Conteh B, Badji H, Jallow AF, Karim M, Manneh A, Keita B, Sarwar G, Ceesay BE, Jarju S, Jabang AMJ, Baldeh E, Ikumapayi UN, Secka O, Antonio M, Roca A, D’Alessandro U, Kotloff KL, Hossain MJ. The Enterics for Global Health (EFGH) Shigella Surveillance Study in The Gambia. Open Forum Infect Dis 2024; 11:S84-S90. [PMID: 38532959 PMCID: PMC10962724 DOI: 10.1093/ofid/ofae049] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
Background The Gambia, located in West Africa, is one of 7 country sites conducting the Enterics for Global Health (EFGH) Shigella Surveillance Study to establish incidence and consequence of Shigella-associated medically attended diarrhea among children 6-35 months old. Methods Here we describe the study site and research experience, sociodemographic characteristics of the study catchment area, facilities of recruitment for diarrhea case surveillance, and known care-seeking behavior for diarrheal illness. We also describe The Gambia's healthcare system and financing, current vaccine schedule and Shigella vaccine adaptation, local diarrhea management guidelines and challenges, and antibiotic resistance patterns in the region. Conclusions The EFGH study in The Gambia will contribute to the multisite network of Shigella surveillance study and prepare the site for future vaccine trials. In addition, the data produced will inform policy makers about prevention strategies and upcoming Shigella vaccine studies among children in this setting.
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Affiliation(s)
- Bakary Conteh
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Henry Badji
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Abdoulie F Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Mehrab Karim
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Alhagie Manneh
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Belali Keita
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Golam Sarwar
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Bubacarr E Ceesay
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Abdoulie M J Jabang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Ebrima Baldeh
- Regional Health Directorate Upper River Region, Ministry of Health and Social Welfare, Basse, The Gambia
| | - Usman N Ikumapayi
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Ousman Secka
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Martin Antonio
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Anna Roca
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Umberto D’Alessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Karen L Kotloff
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - M Jahangir Hossain
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
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4
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Butcher R, Jarju S, Obayemi D, Bashorun AO, Vasileva H, Bransbury-Hare H, Agboghoroma O, Drammeh L, Holland M, Harding-Esch E, Clarke E. Prevalence of five treatable sexually transmitted infections among women in Lower River region of The Gambia. BMC Infect Dis 2023; 23:471. [PMID: 37442966 DOI: 10.1186/s12879-023-08399-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND The prevalence of sexually transmitted infections (STIs) in sub-Saharan Africa is poorly described. We aimed to determine the prevalence of five treatable STIs (Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, Mycoplasma genitalium, Treponema pallidum) in a sample of Gambian women from the general population. METHODS Archived specimens from 420 women aged 15 - 69 years living in The Gambia enrolled in a clinical trial of human papilloma virus vaccine schedules were tested in this study. Urine samples were tested for C. trachomatis, N. gonorrhoeae, T. vaginalis and M. genitalium using a commercially available, open-platform multiplex PCR kit. A fragment of the ompA gene was amplified from C. trachomatis-positive samples and sequenced. Serum samples were tested for T. pallidum using the Chembio DPP Syphilis Screen and Confirm test. RESULTS Overall, 41/420 (9.8%) women tested positive for at least one STI. 32 (7.6%), 9 (2.1%), 1 (0.2%), 1 (0.2%) and 0 (0.0%) tested positive for T. vaginalis, C. trachomatis, N gonorrhoeae, M. genitalium and T. pallidum, respectively. ompA gene sequence was available from five C. trachomatis infections: four were genovar D,one was genovar G and one was genovar F. CONCLUSIONS STIs are endemic in The Gambia. Monitoring systems should be established.
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Affiliation(s)
- Robert Butcher
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK.
| | - Sheikh Jarju
- MRC Unit The Gambia at London School of Hygiene & Tropical Medicine, London, UK
| | - Dolapo Obayemi
- MRC Unit The Gambia at London School of Hygiene & Tropical Medicine, London, UK
| | | | - Hristina Vasileva
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
| | - Hannah Bransbury-Hare
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Lamin Drammeh
- MRC Unit The Gambia at London School of Hygiene & Tropical Medicine, London, UK
| | - Martin Holland
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
| | - Emma Harding-Esch
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
| | - Ed Clarke
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
- MRC Unit The Gambia at London School of Hygiene & Tropical Medicine, London, UK
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5
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Jarju S, Senghore E, Brotherton H, Affleck L, Saidykhan A, Jallow S, Krubally E, Sinjanka E, Ndene MN, Bajo F, Sanyang MM, Saidy B, Bah A, Mohammed NI, Forrest K, Clarke E, Dalessandro U, Sesay AK, Usuf E, Cerami C, Roca A, Kampmann B, de Silva TI. Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia. Gates Open Res 2023; 6:148. [PMID: 36726685 PMCID: PMC9883272 DOI: 10.12688/gatesopenres.14155.3] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Background: In many countries, non-pharmaceutical interventions to limit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission resulted in significant reductions in other respiratory viruses. However, similar data from Africa are limited. We explored the extent to which viruses such as influenza and rhinovirus co-circulated with SARS-CoV-2 in The Gambia during the COVID-19 pandemic. Methods: Between April 2020 and March 2022, respiratory viruses were detected using RT-PCR in nasopharyngeal swabs from 1397 participants with influenza-like illness. An assay to detect SARS-CoV-2 and a viral multiplex RT-PCR assay was used as previously described to detect influenza A and B, respiratory syncytial virus (RSV) A and B, parainfluenza viruses 1-4, human metapneumovirus (HMPV), adenovirus, seasonal coronaviruses (229E, OC43, NL63) and human rhinovirus. Results: Overall virus positivity was 44.2%, with prevalence higher in children <5 years (80%) compared to children aged 5-17 years (53.1%), adults aged 18-50 (39.5%) and >50 years (39.9%), p<0.0001. After SARS-CoV-2 (18.3%), rhinoviruses (10.5%) and influenza viruses (5.5%) were the most prevalent. SARS-CoV-2 positivity was lower in children <5 (4.3%) and 5-17 years (12.7%) than in adults aged 18-50 (19.3%) and >50 years (24.3%), p<0.0001. In contrast, rhinoviruses were most prevalent in children <5 years (28.7%), followed by children aged 5-17 (15.8%), adults aged 18-50 (8.3%) and >50 years (6.3%), p<0.0001. Four SARS-CoV-2 waves occurred, with 36.1%-52.4% SARS-CoV-2 positivity during peak months. Influenza infections were observed in both 2020 and 2021 during the rainy season as expected (peak positivity 16.4%-23.5%). Peaks of rhinovirus were asynchronous to the months when SARS-CoV-2 and influenza peaked. Conclusion: Our data show that many respiratory viruses continued to circulate during the COVID-19 pandemic in The Gambia, including human rhinoviruses, despite the presence of NPIs during the early stages of the pandemic, and influenza peaks during expected months.
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Affiliation(s)
- Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Elina Senghore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Helen Brotherton
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Lucy Affleck
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Saidykhan
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Samba Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ebrima Krubally
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Edrisa Sinjanka
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Morris Ngor Ndene
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Fabakary Bajo
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Musa M Sanyang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Binta Saidy
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Bah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Nuredin I Mohammed
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Karen Forrest
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ed Clarke
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Umberto Dalessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Abdul K Sesay
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Effua Usuf
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Carla Cerami
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Anna Roca
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Thushan I de Silva
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- 4. Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
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6
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Kanteh A, Jallow HS, Manneh J, Sanyang B, Kujabi MA, Ndure SL, Jarju S, Sey AP, Damilare K D, Bah Y, Sambou S, Jarju G, Manjang B, Jagne A, Bittaye SO, Bittaye M, Forrest K, Tiruneh DA, Samateh AL, Jagne S, Hué S, Mohammed N, Amambua-Ngwa A, Kampmann B, D'Alessandro U, de Silva TI, Roca A, Sesay AK. Genomic epidemiology of SARS-CoV-2 infections in The Gambia: an analysis of routinely collected surveillance data between March, 2020, and January, 2022. Lancet Glob Health 2023; 11:e414-e424. [PMID: 36796985 PMCID: PMC9928486 DOI: 10.1016/s2214-109x(22)00553-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 11/30/2022] [Accepted: 12/14/2022] [Indexed: 02/16/2023]
Abstract
BACKGROUND COVID-19, caused by SARS-CoV-2, is one of the deadliest pandemics of the past 100 years. Genomic sequencing has an important role in monitoring of the evolution of the virus, including the detection of new viral variants. We aimed to describe the genomic epidemiology of SARS-CoV-2 infections in The Gambia. METHODS Nasopharyngeal or oropharyngeal swabs collected from people with suspected cases of COVID-19 and international travellers were tested for SARS-CoV-2 with standard RT-PCR methods. SARS-CoV-2-positive samples were sequenced according to standard library preparation and sequencing protocols. Bioinformatic analysis was done using ARTIC pipelines and Pangolin was used to assign lineages. To construct phylogenetic trees, sequences were first stratified into different COVID-19 waves (waves 1-4) and aligned. Clustering analysis was done and phylogenetic trees constructed. FINDINGS Between March, 2020, and January, 2022, 11 911 confirmed cases of COVID-19 were recorded in The Gambia, and 1638 SARS-CoV-2 genomes were sequenced. Cases were broadly distributed into four waves, with more cases during the waves that coincided with the rainy season (July-October). Each wave occurred after the introduction of new viral variants or lineages, or both, generally those already established in Europe or in other African countries. Local transmission was higher during the first and third waves (ie, those that corresponded with the rainy season), in which the B.1.416 lineage and delta (AY.34.1) were dominant, respectively. The second wave was driven by the alpha and eta variants and the B.1.1.420 lineage. The fourth wave was driven by the omicron variant and was predominantly associated with the BA.1.1 lineage. INTERPRETATION More cases of SARS-CoV-2 infection were recorded in The Gambia during peaks of the pandemic that coincided with the rainy season, in line with transmission patterns for other respiratory viruses. The introduction of new lineages or variants preceded epidemic waves, highlighting the importance of implementing well structured genomic surveillance at a national level to detect and monitor emerging and circulating variants. FUNDING Medical Research Unit The Gambia at London School of Hygiene & Tropical Medicine, UK Research and Innovation, WHO.
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Affiliation(s)
- Abdoulie Kanteh
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Haruna S Jallow
- National Public Health Reference Laboratory, Ministry of Health, Banjul, The Gambia
| | - Jarra Manneh
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Bakary Sanyang
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Mariama A Kujabi
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Sainabou Laye Ndure
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Alhagie Papa Sey
- National Public Health Reference Laboratory, Ministry of Health, Banjul, The Gambia
| | - Dabiri Damilare K
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Yaya Bah
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | | | | | | | | | | | | | - Karen Forrest
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | | | | | - Sheriffo Jagne
- National Public Health Reference Laboratory, Ministry of Health, Banjul, The Gambia
| | - Stéphane Hué
- Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Nuredin Mohammed
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Alfred Amambua-Ngwa
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Thushan I de Silva
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Anna Roca
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Abdul Karim Sesay
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia.
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7
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Okomo UA, Darboe S, Bah SY, Ayorinde A, Jarju S, Sesay AK, Kebbeh N, Gai A, Dibbasey T, Grey-Johnson M, Le Doare K, Holt KE, Lawn JE, Kampmann B. Maternal colonization and early-onset neonatal bacterial sepsis in the Gambia, West Africa: a genomic analysis of vertical transmission. Clin Microbiol Infect 2023; 29:386.e1-386.e9. [PMID: 36243352 DOI: 10.1016/j.cmi.2022.10.012] [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: 02/08/2022] [Revised: 09/14/2022] [Accepted: 10/06/2022] [Indexed: 11/03/2022]
Abstract
OBJECTIVES To define bacterial aetiology of neonatal sepsis and estimate the prevalence of neonatal infection from maternal genital tract bacterial carriage among mother-newborn pairs. METHODS We carried out a cross-sectional study of newborns with clinical sepsis admitted to three hospitals in the Gambia neonatal wards. Neonatal blood cultures and maternal genital swabs were obtained at recruitment. We used whole-genome sequencing to explore vertical transmission for neonates with microbiologically confirmed bloodstream infection by comparing phenotypically-matched paired neonatal blood cultures and maternal genital tract bacterial isolates. RESULTS We enrolled 203 maternal-newborn pairs. Two-thirds (67%; 137/203) of neonates presented with early-onset sepsis (days 0-6 after birth) of which 26% (36/137) were because of a clinically-significant bacterial pathogen. Blood culture isolates from newborns with early-onset sepsis because of Staphylococcus aureus (n = 5), Klebsiella pneumonia (n = 2), and Enterococcus faecalis (n = 1), phenotypically matched their maternal genital tract isolates. Pairwise single-nucleotide variants comparisons showed differences of 12 to 52 single-nucleotide variants only between maternal and newborn S. aureus isolates, presumably representing vertical transmission with a transmission rate of 14% (5/36). CONCLUSIONS We found a low prevalence of vertical transmission of maternal genital tract colonization in maternal-newborn pairs for early-onset neonatal sepsis in the West African context. Identifying infection acquisition pathways among newborns is essential to prioritize preventive interventions, which could be targeted at the mother or infection control in the hospital environment, depending on the major pathways of transmission.
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Affiliation(s)
- Uduak A Okomo
- Vaccines and Immunity Theme, MRC Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia; MARCH Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - Saffiatou Darboe
- Disease Control and Elimination Theme, MRC Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Saikou Y Bah
- Vaccines and Immunity Theme, MRC Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia; Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
| | - Abigail Ayorinde
- Vaccines and Immunity Theme, MRC Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Sheikh Jarju
- Vaccines and Immunity Theme, MRC Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Abdul Karim Sesay
- Vaccines and Immunity Theme, MRC Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Ngange Kebbeh
- Disease Control and Elimination Theme, MRC Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Abdou Gai
- Department of Paediatrics, Edward Francis Small Teaching Hospital, Banjul, Gambia
| | - Tida Dibbasey
- Department of Paediatrics, Edward Francis Small Teaching Hospital, Banjul, Gambia
| | - Mary Grey-Johnson
- Department of Paediatrics, Edward Francis Small Teaching Hospital, Banjul, Gambia
| | - Kirsty Le Doare
- Institute of Infection and Immunity, St George's University of London, Cranmer Terrace, London, United Kingdom
| | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Joy E Lawn
- MARCH Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Beate Kampmann
- Vaccines and Immunity Theme, MRC Unit the Gambia at London School of Hygiene and Tropical Medicine, Fajara, Gambia; The Vaccine Centre, and Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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8
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Jarju S, Senghore E, Brotherton H, Affleck L, Saidykhan A, Jallow S, Krubally E, Sinjanka E, Ndene MN, Bajo F, Sanyang MM, Saidy B, Bah A, Mohammed NI, Forrest K, Clarke E, Dalessandro U, Sesay AK, Usuf E, Cerami C, Roca A, Kampmann B, de Silva TI. Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia. Gates Open Res 2023; 6:148. [PMID: 36726685 PMCID: PMC9883272 DOI: 10.12688/gatesopenres.14155.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
Background: In many countries, non-pharmaceutical interventions to limit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission resulted in significant reductions in other respiratory viruses. However, similar data from Africa are limited. We explored the extent to which viruses such as influenza and rhinovirus co-circulated with SARS-CoV-2 in The Gambia during the COVID-19 pandemic. Methods: Between April 2020 and March 2022, respiratory viruses were detected using RT-PCR in nasopharyngeal swabs from 1397 participants with influenza-like illness. An assay to detect SARS-CoV-2 and a viral multiplex RT-PCR assay was used as previously described to detect influenza A and B, respiratory syncytial virus (RSV) A and B, parainfluenza viruses 1-4, human metapneumovirus (HMPV), adenovirus, seasonal coronaviruses (229E, OC43, NL63) and human rhinovirus. Results: Overall virus positivity was 44.2%, with prevalence higher in children <5 years (80%) compared to children aged 5-17 years (53.1%), adults aged 18-50 (39.5%) and >50 years (39.9%), p<0.0001. After SARS-CoV-2 (18.3%), rhinoviruses (10.5%) and influenza viruses (5.5%) were the most prevalent. SARS-CoV-2 positivity was lower in children <5 (4.3%) and 5-17 years (12.7%) than in adults aged 18-50 (19.3%) and >50 years (24.3%), p<0.0001. In contrast, rhinoviruses were most prevalent in children <5 years (28.7%), followed by children aged 5-17 (15.8%), adults aged 18-50 (8.3%) and >50 years (6.3%), p<0.0001. Four SARS-CoV-2 waves occurred, with 36.1%-52.4% SARS-CoV-2 positivity during peak months. Influenza infections were observed in both 2020 and 2021 during the rainy season as expected (peak positivity 16.4%-23.5%). Peaks of rhinovirus were asynchronous to the months when SARS-CoV-2 and influenza peaked. Conclusion: Our data show that many respiratory viruses continued to circulate during the COVID-19 pandemic in The Gambia, including human rhinoviruses, despite the presence of NPIs during the early stages of the pandemic, and influenza peaks during expected months.
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Affiliation(s)
- Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Elina Senghore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Helen Brotherton
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Lucy Affleck
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Saidykhan
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Samba Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ebrima Krubally
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Edrisa Sinjanka
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Morris Ngor Ndene
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Fabakary Bajo
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Musa M Sanyang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Binta Saidy
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Bah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Nuredin I Mohammed
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Karen Forrest
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ed Clarke
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Umberto Dalessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Abdul K Sesay
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Effua Usuf
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Carla Cerami
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Anna Roca
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Thushan I de Silva
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- 4. Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
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9
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Fischer C, Maponga TG, Yadouleton A, Abílio N, Aboce E, Adewumi P, Afonso P, Akorli J, Andriamandimby SF, Anga L, Ashong Y, Beloufa MA, Bensalem A, Birtles R, Boumba ALM, Bwanga F, Chaponda M, Chibukira P, Chico RM, Chileshe J, Chongwe G, Cissé A, D'Alessandro U, de Lamballerie XN, de Morais JFM, Derrar F, Dia N, Diarra Y, Doumbia L, Drosten C, Dussart P, Echodu R, Eggers Y, Eloualid A, Faye O, Feldt T, Frühauf A, Halatoko A, Ilouga PV, Ismael N, Jambou R, Jarju S, Kamprad A, Katowa B, Kayiwa J, King'wara L, Koita O, Lacoste V, Lagare A, Landt O, Lekana-Douki SE, Lekana-Douki JB, Iipumbu E, Loemba H, Lutwama J, Mamadou S, Maman I, Manyisa B, Martinez PA, Matoba J, Mhuulu L, Moreira-Soto A, Mwangi J, N'dilimabaka N, Nassuna CA, Ndiath MO, Nepolo E, Njouom R, Nourlil J, Nyanjom SG, Odari EO, Okeng A, Ouoba JB, Owusu M, Donkor IO, Phadu KK, Phillips RO, Preiser W, Ruhanya V, Salah F, Salifou S, Sall AA, Sylverken AA, Tagnouokam-Ngoupo PA, Tarnagda Z, Tchikaya FO, Tufa TB, Drexler JF. Retraction. Science 2022; 378:1284-1285. [PMID: 36537892 DOI: 10.1126/science.adg2821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Carlo Fischer
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Tongai Gibson Maponga
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa
| | - Anges Yadouleton
- Laboratoire dés fievres hemorragiques virales de Cotonou, Akpakpa, Benin
| | - Nuro Abílio
- Instituto Nacional de Saúde, Maputo, Mozambique
| | | | - Praise Adewumi
- Laboratoire dés fievres hemorragiques virales de Cotonou, Akpakpa, Benin
| | - Pedro Afonso
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Jewelna Akorli
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Latifa Anga
- Institut Pasteur du Maroc, Casablanca, Morocco
| | - Yvonne Ashong
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Aicha Bensalem
- Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria
| | - Richard Birtles
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda.,School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Anicet Luc Magloire Boumba
- Faculty of Health Sciences, Marien Ngouabi University, Pointe-Noire, Congo.,Molecular Diagnostic Laboratory HDL, Pointe-Noire, Congo
| | - Freddie Bwanga
- MBN Clinical Laboratories, Kampala, Uganda.,Makerere University College of Health Sciences, Kampala, Uganda
| | - Mike Chaponda
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Paradzai Chibukira
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | | | - Justin Chileshe
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Gershom Chongwe
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Assana Cissé
- Laboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso
| | - Umberto D'Alessandro
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | | | | | - Fawzi Derrar
- Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria
| | - Ndongo Dia
- Institut Pasteur de Dakar (IPD), Dakar, Senegal
| | - Youssouf Diarra
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Lassina Doumbia
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Christian Drosten
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany.,German Centre for Infection Research (DZIF), associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Richard Echodu
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda
| | - Yannik Eggers
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | | | - Torsten Feldt
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Anna Frühauf
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | | | | | | | - Ronan Jambou
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | - Sheikh Jarju
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Antje Kamprad
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Ben Katowa
- Macha Research Trust, Choma, Zambia.,School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - John Kayiwa
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Leonard King'wara
- National Public Health Reference Laboratory, Ministry of Health, Nairobi, Kenya
| | - Ousmane Koita
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | | | - Adamou Lagare
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | | | | | | | - Etuhole Iipumbu
- School of Medicine, University of Namibia, Windhoek, Namibia
| | - Hugues Loemba
- Molecular Diagnostic Laboratory HDL, Pointe-Noire, Congo.,Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Santou Mamadou
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | | | - Brendon Manyisa
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | - Pedro A Martinez
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Japhet Matoba
- Macha Research Trust, Choma, Zambia.,School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Lusia Mhuulu
- School of Medicine, University of Namibia, Windhoek, Namibia
| | - Andres Moreira-Soto
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Judy Mwangi
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda.,School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Nadine N'dilimabaka
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Mamadou Ousmane Ndiath
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Emmanuel Nepolo
- School of Medicine, University of Namibia, Windhoek, Namibia
| | | | | | - Steven Ger Nyanjom
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Eddy Okoth Odari
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | | | | | - Michael Owusu
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Irene Owusu Donkor
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Karabo Kristen Phadu
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa
| | - Richard Odame Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa.,National Health Laboratory Service Tygerberg Business Unit, Cape Town, South Africa
| | - Vurayai Ruhanya
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | | | | | | | - Augustina Angelina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana.,Department of Theoretical and Applied Biology, KNUST, Kumasi, Ghana
| | | | - Zekiba Tarnagda
- Laboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso
| | | | - Tafese Beyene Tufa
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany.,German Centre for Infection Research (DZIF), associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany
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10
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Jarju S, Senghore E, Brotherton H, Affleck L, Saidykhan A, Jallow S, Krubally E, Sinjanka E, Ndene MN, Bajo F, Sanyang MM, Saidy B, Bah A, Mohammed NI, Forrest K, Clarke E, Dalessandro U, Sesay AK, Usuf E, Cerami C, Roca A, Kampmann B, de Silva TI. Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia. Gates Open Res 2022; 6:148. [PMID: 36726685 PMCID: PMC9883272 DOI: 10.12688/gatesopenres.14155.1] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Background: In many countries, non-pharmaceutical interventions to limit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission resulted in significant reductions in other respiratory viruses. However, similar data from Africa are limited. We explored the extent to which viruses such as influenza and rhinovirus co-circulated with SARS-CoV-2 in The Gambia during the COVID-19 pandemic. Methods: Between April 2020 and March 2022, respiratory viruses were detected using RT-PCR in nasopharyngeal swabs from 1397 participants with influenza-like illness. An assay to detect SARS-CoV-2 and a viral multiplex RT-PCR assay was used as previously described to detect influenza A and B, respiratory syncytial virus (RSV) A and B, parainfluenza viruses 1-4, human metapneumovirus (HMPV), adenovirus, seasonal coronaviruses (229E, OC43, NL63) and human rhinovirus. Results: Overall virus positivity was 44.2%, with prevalence higher in children <5 years (80%) compared to children aged 5-17 years (53.1%), adults aged 18-50 (39.5%) and >50 years (39.9%), p<0.0001. After SARS-CoV-2 (18.3%), rhinoviruses (10.5%) and influenza viruses (5.5%) were the most prevalent. SARS-CoV-2 positivity was lower in children <5 (4.3%) and 5-17 years (12.7%) than in adults aged 18-50 (19.3%) and >50 years (24.3%), p<0.0001. In contrast, rhinoviruses were most prevalent in children <5 years (28.7%), followed by children aged 5-17 (15.8%), adults aged 18-50 (8.3%) and >50 years (6.3%), p<0.0001. Four SARS-CoV-2 waves occurred, with 36.1%-52.4% SARS-CoV-2 positivity during peak months. Influenza infections were observed in both 2020 and 2021 during the rainy season as expected (peak positivity 16.4%-23.5%). Peaks of rhinovirus were asynchronous to the months when SARS-CoV-2 and influenza peaked. Conclusion: Our data show that many respiratory viruses continued to circulate during the COVID-19 pandemic in The Gambia, including human rhinoviruses, despite the presence of NPIs during the early stages of the pandemic, and influenza peaks during expected months.
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Affiliation(s)
- Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Elina Senghore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Helen Brotherton
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Lucy Affleck
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Saidykhan
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Samba Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ebrima Krubally
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Edrisa Sinjanka
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Morris Ngor Ndene
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Fabakary Bajo
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Musa M Sanyang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Binta Saidy
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Bah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Nuredin I Mohammed
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Karen Forrest
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ed Clarke
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Umberto Dalessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Abdul K Sesay
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Effua Usuf
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Carla Cerami
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Anna Roca
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Thushan I de Silva
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- 4. Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
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11
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Fischer C, Maponga TG, Yadouleton A, Abílio N, Aboce E, Adewumi P, Afonso P, Akorli J, Andriamandimby SF, Anga L, Ashong Y, Beloufa MA, Bensalem A, Birtles R, Boumba ALM, Bwanga F, Chaponda M, Chibukira P, Chico RM, Chileshe J, Chongwe G, Cissé A, D'Alessandro U, de Lamballerie XN, de Morais JFM, Derrar F, Dia N, Diarra Y, Doumbia L, Drosten C, Dussart P, Echodu R, Eggers Y, Eloualid A, Faye O, Feldt T, Frühauf A, Halatoko A, Ilouga PV, Ismael N, Jambou R, Jarju S, Kamprad A, Katowa B, Kayiwa J, King'wara L, Koita O, Lacoste V, Lagare A, Landt O, Lekana-Douki SE, Lekana-Douki JB, Iipumbu E, Loemba H, Lutwama J, Mamadou S, Maman I, Manyisa B, Martinez PA, Matoba J, Mhuulu L, Moreira-Soto A, Mwangi J, N Dilimabaka N, Nassuna CA, Ndiath MO, Nepolo E, Njouom R, Nourlil J, Nyanjom SG, Odari EO, Okeng A, Ouoba JB, Owusu M, Owusu Donkor I, Phadu KK, Phillips RO, Preiser W, Ruhanya V, Salah F, Salifou S, Sall AA, Sylverken AA, Tagnouokam-Ngoupo PA, Tarnagda Z, Tchikaya FO, Tufa TB, Drexler JF. RETRACTED: Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa. Science 2022; 378:eadd8737. [PMID: 36454863 DOI: 10.1126/science.add8737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection.
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Affiliation(s)
- Carlo Fischer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Tongai Gibson Maponga
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa
| | - Anges Yadouleton
- Laboratoire dés fievres hemorragiques virales de Cotonou, Akpakpa, Benin
| | - Nuro Abílio
- Instituto Nacional de Saúde, Maputo, Mozambique
| | | | - Praise Adewumi
- Laboratoire dés fievres hemorragiques virales de Cotonou, Akpakpa, Benin
| | - Pedro Afonso
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Jewelna Akorli
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Latifa Anga
- Institut Pasteur du Maroc, Casablanca, Morocco
| | - Yvonne Ashong
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Aicha Bensalem
- Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria
| | - Richard Birtles
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda.,School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Anicet Luc Magloire Boumba
- Faculty of Health Sciences, Marien Ngouabi University, Pointe-Noire, Congo.,Molecular Diagnostic Laboratory HDL, Pointe-Noire, Congo
| | - Freddie Bwanga
- MBN Clinical Laboratories, Kampala, Uganda.,Makerere University College of Health Sciences, Kampala, Uganda
| | - Mike Chaponda
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Paradzai Chibukira
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | | | - Justin Chileshe
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Gershom Chongwe
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Assana Cissé
- Laboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso
| | - Umberto D'Alessandro
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | | | | | - Fawzi Derrar
- Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria
| | - Ndongo Dia
- Institut Pasteur de Dakar (IPD), Dakar, Senegal
| | - Youssouf Diarra
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Lassina Doumbia
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Christian Drosten
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany.,German Centre for Infection Research (DZIF), associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Richard Echodu
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda
| | - Yannik Eggers
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | | | - Torsten Feldt
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Anna Frühauf
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | | | | | | | - Ronan Jambou
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | - Sheikh Jarju
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Antje Kamprad
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Ben Katowa
- Macha Research Trust, Choma, Zambia.,School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - John Kayiwa
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Leonard King'wara
- National Public Health Reference Laboratory, Ministry of Health, Nairobi, Kenya
| | - Ousmane Koita
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | | | - Adamou Lagare
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | | | | | | | - Etuhole Iipumbu
- School of Medicine, University of Namibia, Windhoek, Namibia
| | - Hugues Loemba
- Molecular Diagnostic Laboratory HDL, Pointe-Noire, Congo.,Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Santou Mamadou
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | | | - Brendon Manyisa
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | - Pedro A Martinez
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Japhet Matoba
- Macha Research Trust, Choma, Zambia.,School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Lusia Mhuulu
- School of Medicine, University of Namibia, Windhoek, Namibia
| | - Andres Moreira-Soto
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Judy Mwangi
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda.,School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Nadine N Dilimabaka
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Mamadou Ousmane Ndiath
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Emmanuel Nepolo
- School of Medicine, University of Namibia, Windhoek, Namibia
| | | | | | - Steven Ger Nyanjom
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Eddy Okoth Odari
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | | | | | - Michael Owusu
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Irene Owusu Donkor
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Karabo Kristen Phadu
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa
| | - Richard Odame Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa.,National Health Laboratory Service Tygerberg Business Unit, Cape Town, South Africa
| | - Vurayai Ruhanya
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | | | | | | | - Augustina Angelina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana.,Department of Theoretical and Applied Biology, KNUST, Kumasi, Ghana
| | | | - Zekiba Tarnagda
- Laboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso
| | | | - Tafese Beyene Tufa
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jan Felix Drexler
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany.,German Centre for Infection Research (DZIF), associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany
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12
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Secka O, Oriero EC, Jarju S, Vilane A, Ndiath MO, Hofmann N, Nwakanma D. A report on preparation, expansion and future outlook of COVID-19 testing in Gambia. J Public Health Afr 2022; 13:1616. [PMID: 36277952 PMCID: PMC9585608 DOI: 10.4081/jphia.2022.1616] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 05/22/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The outbreak of COVID-19 disease and rapid spread of the virus outside China led to its declaration as a Public Health Emergency of International Concern (PHEIC) in January 2020. Key elements of the early intervention strategy focused on laboratory diagnosis and screening at points of entry and imposition of restrictions in crossborder activities. OBJECTIVE We report the role the Medical Research Council Unit, The Gambia (MRCG) played in the early implementation of molecular testing for COVID-19 in The Gambia as part of the national outbreak response. METHODS Laboratory staff members, with experience in molecular biology assays, were identified and trained on COVID-19 testing at the Africa CDC training workshop in Dakar, Senegal. Thereafter risks assessments, drafting of standard operating procedures (SOPs) and inhouse training enabled commencement of testing using commercial RTPCR kits. Subsequently, testing was expanded to the National Public Health Laboratroy and also implemented across field sites for rapid response across the country. RESULTS Capacity for COVID-19 testing at MRCG was developed and can process aproximately 350 tests per day, which can be further scaled up as the demand for testing increases. CONCLUSION The long presence of the Unit in The Gambia and strong collaborative relationship with the National Health Ministry, allowed for a synergistc approach in mounting an effective response that contributed in delaying the establishment of community transmission in the country.
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Affiliation(s)
- Ousman Secka
- Medical Research Council Unit The Gambia at LSHTM, Atlantic Road, Fajara, Gambia
| | - Eniyou C. Oriero
- Medical Research Council Unit The Gambia at LSHTM, Atlantic Road, Fajara, Gambia,Medical Research Council Unit The Gambia at LSHTM Atlantic road, Fajara Box 273 Banjul, The Gambia
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia at LSHTM, Atlantic Road, Fajara, Gambia
| | - Aminata Vilane
- Medical Research Council Unit The Gambia at LSHTM, Atlantic Road, Fajara, Gambia
| | | | - Natalie Hofmann
- Medical Research Council Unit The Gambia at LSHTM, Atlantic Road, Fajara, Gambia
| | - Davis Nwakanma
- Medical Research Council Unit The Gambia at LSHTM, Atlantic Road, Fajara, Gambia
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13
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Costa-Martins AG, Mane K, Lindsey BB, Ogava RLT, Castro IC, Jagne YJ, Sallah HJ, Armitage EP, Jarju S, Ahadzie B, Ellis-Watson R, Tregoning JS, Bingle CD, Bogaert D, Clarke E, Ordovas-Montanes J, Jeffries D, Kampmann B, Nakaya HI, de Silva TI. Erratum: Prior upregulation of interferon pathways in the nasopharynx impacts viral shedding following live attenuated influenza vaccine challenge in children. Cell Rep Med 2022; 3:100516. [PMID: 35243419 PMCID: PMC8861827 DOI: 10.1016/j.xcrm.2022.100516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Jarju S, Senghore E, Brotherton H, Saidykhan A, Jallow S, Krubally E, Sinjanka E, Ndene MN, Bajo F, Sanyang MM, Saidy B, Bah A, Mohammed NI, Forrest K, Clarke E, Dalessandro U, Sesay AK, Usuf E, Cerami C, Roca A, Kampmann B, de Silva TI. Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia. Gates Open Res 2022. [PMID: 36726685 DOI: 10.17605/osf.io/tsf78] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Background: In many countries, non-pharmaceutical interventions to limit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission resulted in significant reductions in other respiratory viruses. However, similar data from Africa are limited. We explored the extent to which viruses such as influenza and rhinovirus co-circulated with SARS-CoV-2 in The Gambia during the COVID-19 pandemic. Methods: Between April 2020 and March 2022, respiratory viruses were detected using RT-PCR in nasopharyngeal swabs from 1397 participants with influenza-like illness. An assay to detect SARS-CoV-2 and a viral multiplex RT-PCR assay was used as previously described to detect influenza A and B, respiratory syncytial virus (RSV) A and B, parainfluenza viruses 1-4, human metapneumovirus (HMPV), adenovirus, seasonal coronaviruses (229E, OC43, NL63) and human rhinovirus. Results: Overall virus positivity was 44.2%, with prevalence higher in children <5 years (80%) compared to children aged 5-17 years (53.1%), adults aged 18-50 (39.5%) and >50 years (39.9%), p<0.0001. After SARS-CoV-2 (18.3%), rhinoviruses (10.5%) and influenza viruses (5.5%) were the most prevalent. SARS-CoV-2 positivity was lower in children <5 (4.3%) and 5-17 years (12.7%) than in adults aged 18-50 (19.3%) and >50 years (24.3%), p<0.0001. In contrast, rhinoviruses were most prevalent in children <5 years (28.7%), followed by children aged 5-17 (15.8%), adults aged 18-50 (8.3%) and >50 years (6.3%), p<0.0001. Four SARS-CoV-2 waves occurred, with 36.1%-52.4% SARS-CoV-2 positivity during peak months. Influenza infections were observed in both 2020 and 2021 during the rainy season as expected (peak positivity 16.4%-23.5%). Peaks of rhinovirus were asynchronous to the months when SARS-CoV-2 and influenza peaked. Conclusion: Our data show that many respiratory viruses continued to circulate during the COVID-19 pandemic in The Gambia, including human rhinoviruses, despite the presence of NPIs during the early stages of the pandemic, and influenza peaks during expected months.
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Affiliation(s)
- Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Elina Senghore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Helen Brotherton
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Saidykhan
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Samba Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Edrissa Krubally
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Edrisa Sinjanka
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Morris Ngor Ndene
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Fabakary Bajo
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Musa M Sanyang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Binta Saidy
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Bah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Nuredin I Mohammed
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Karen Forrest
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ed Clarke
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Umberto Dalessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Abdul K Sesay
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Effua Usuf
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Carla Cerami
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Anna Roca
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Thushan I de Silva
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- 4. Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
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15
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Costa-Martins AG, Mane K, Lindsey BB, Ogava RL, Castro Í, Jagne YJ, Sallah HJ, Armitage EP, Jarju S, Ahadzie B, Ellis-Watson R, Tregoning JS, Bingle CD, Bogaert D, Clarke E, Ordovas-Montanes J, Jeffries D, Kampmann B, Nakaya HI, de Silva TI. Prior upregulation of interferon pathways in the nasopharynx impacts viral shedding following live attenuated influenza vaccine challenge in children. Cell Rep Med 2021; 2:100465. [PMID: 35028607 PMCID: PMC8714852 DOI: 10.1016/j.xcrm.2021.100465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/28/2021] [Accepted: 11/12/2021] [Indexed: 02/06/2023]
Abstract
In children lacking influenza-specific adaptive immunity, upper respiratory tract innate immune responses may influence viral replication and disease outcome. We use trivalent live attenuated influenza vaccine (LAIV) as a surrogate challenge model in children aged 24-59 months to identify pre-infection mucosal transcriptomic signatures associated with subsequent viral shedding. Upregulation of interferon signaling pathways prior to LAIV is significantly associated with lower strain-specific viral loads (VLs) at days 2 and 7. Several interferon-stimulated genes are differentially expressed in children with pre-LAIV asymptomatic respiratory viral infections and negatively correlated with LAIV VLs. Upregulation of genes enriched in macrophages, neutrophils, and eosinophils is associated with lower VLs and found more commonly in children with asymptomatic viral infections. Variability in pre-infection mucosal interferon gene expression in children may impact the course of subsequent influenza infections. This variability may be due to frequent respiratory viral infections, demonstrating the potential importance of mucosal virus-virus interactions in children.
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Affiliation(s)
- André G. Costa-Martins
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Scientific Platform Pasteur, University of São Paulo, São Paulo, Brazil
| | - Karim Mane
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Benjamin B. Lindsey
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK
| | - Rodrigo L.T. Ogava
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ícaro Castro
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ya Jankey Jagne
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Hadijatou J. Sallah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Edwin P. Armitage
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Bankole Ahadzie
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Rebecca Ellis-Watson
- The University of Edinburgh/MRC Centre for Inflammation Research, The Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - John S. Tregoning
- Department of Infectious Disease, Imperial College London, London W2 1NY, UK
| | - Colin D. Bingle
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK
| | - Debby Bogaert
- The University of Edinburgh/MRC Centre for Inflammation Research, The Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Ed Clarke
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - David Jeffries
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
- The Vaccine Centre, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Helder I. Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Scientific Platform Pasteur, University of São Paulo, São Paulo, Brazil
- Corresponding author
| | - Thushan I. de Silva
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK
- Corresponding author
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16
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Peno C, Armitage EP, Clerc M, Balcazar Lopez C, Jagne YJ, Drammeh S, Jarju S, Sallah H, Senghore E, Lindsey BB, Camara J, Bah S, Mohammed NI, Dockrell DH, Kampmann B, Clarke E, Bogaert D, de Silva TI. The effect of live attenuated influenza vaccine on pneumococcal colonisation densities among children aged 24-59 months in The Gambia: a phase 4, open label, randomised, controlled trial. Lancet Microbe 2021; 2:e656-e665. [PMID: 34881370 PMCID: PMC8632704 DOI: 10.1016/s2666-5247(21)00179-8] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND Influenza and other respiratory viruses promote Streptococcus pneumoniae proliferation in the upper respiratory tract. We sought to investigate for what we believe is the first time, the effect of intranasal live attenuated influenza vaccine (LAIV) on nasopharyngeal S pneumoniae density in a low-income to middle-income country population with high pneumococcal carriage rates. METHODS In an open-label, randomised, controlled trial in The Gambia, 330 healthy children aged 24-59 months were randomly assigned 2:1 to receive one trivalent LAIV dose at enrolment (day 0, intervention) or at the end of active follow-up (day 21, control). The investigator team were initially masked to block size and randomisation sequence to avoid allocation bias. Group allocation was later revealed to the investigator team. The primary outcome was PCR-quantified day 7 and 21 pneumococcal density. Asymptomatic respiratory viral infection at baseline and LAIV strain shedding were included as covariates in generalised mixed-effects models, to assess the effect of LAIV and other variables on pneumococcal densities. The study is registered at ClinicalTrials.gov, NCT02972957, and is closed to recruitment. FINDINGS Between Feb 8 and April 12, 2017, and Jan 15 and March 28, 2018, of 343 children assessed for eligibility, 213 in the intervention group and 108 in the control group completed the study and were included in the final analysis. Although no significant differences were seen in pneumococcal carriage or density at each timepoint when comparing groups, changes from baseline were observed in the LAIV group. The baseline S pneumoniae carriage prevalence was high in both LAIV and control groups (75%) and increased by day 21 in the LAIV group (85%, p=0·0037), but not in the control group (79%, p=0·44). An increase in pneumococcal density from day 0 amounts was seen in the LAIV group at day 7 (+0·207 log10 copies per μL, SE 0·105, p=0·050) and day 21 (+0·280 log10 copies per μL, SE 0·105, p=0·0082), but not in the control group. Older age was associated with lower pneumococcal density (-0·015 log10 copies per μL, SE 0·005, p=0·0030), with the presence of asymptomatic respiratory viruses at baseline (+0·259 log10 copies per μL, SE 0·097, p=0·017), and greater LAIV shedding at day 7 (+0·380 log10 copies per μL, SE 0·167, p=0·024) associated with higher pneumococcal density. A significant increase in rhinorrhoea was reported in the LAIV group compared with the control group children during the first 7 days of the study (103 [48%] of 213, compared with 25 [23%] of 108, p<0·0001), and between day 7 and 21 (108 [51%] of 213, compared with 28 [26%] of 108, p<0·0001). INTERPRETATION LAIV was associated with a modest increase in nasopharyngeal pneumococcal carriage and density in the 21 days following vaccination, with the increase in density lower in magnitude than previously described in the UK. This increase was accelerated when LAIV was administered in the presence of pre-existing asymptomatic respiratory viruses, suggesting that nasopharyngeal S pneumoniae proliferation is driven by cumulative mixed-viral co-infections. The effect of LAIV on pneumococcal density is probably similar to other respiratory viral infections in children. Our findings provide reassurance for the use of LAIV to expand influenza vaccine programmes in low-income to middle-income country populations with high pneumococcal carriage. FUNDING Wellcome Trust.
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Affiliation(s)
- Chikondi Peno
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Edwin P Armitage
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Melanie Clerc
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Carlos Balcazar Lopez
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Ya Jankey Jagne
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Sainabou Drammeh
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Sheikh Jarju
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Hadijatou Sallah
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Elina Senghore
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Benjamin B Lindsey
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
- The Florey Institute & Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, UK
| | - Janko Camara
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Sulayman Bah
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Nuredin I Mohammed
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - David H Dockrell
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, The London School of Hygiene & Tropical Medicine, London, UK
| | - Ed Clarke
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Debby Bogaert
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, The Netherlands
| | - Thushan I de Silva
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
- The Florey Institute & Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, UK
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17
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Nabwera HM, Espinoza JL, Worwui A, Betts M, Okoi C, Sesay AK, Bancroft R, Agbla SC, Jarju S, Bradbury RS, Colley M, Jallow AT, Liu J, Houpt ER, Prentice AM, Antonio M, Bernstein RM, Dupont CL, Kwambana-Adams BA. Interactions between fecal gut microbiome, enteric pathogens, and energy regulating hormones among acutely malnourished rural Gambian children. EBioMedicine 2021; 73:103644. [PMID: 34695658 PMCID: PMC8550991 DOI: 10.1016/j.ebiom.2021.103644] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The specific roles that gut microbiota, known pathogens, and host energy-regulating hormones play in the pathogenesis of non-edematous severe acute malnutrition (marasmus SAM) and moderate acute malnutrition (MAM) during outpatient nutritional rehabilitation are yet to be explored. METHODS We applied an ensemble of sample-specific (intra- and inter-modality) association networks to gain deeper insights into the pathogenesis of acute malnutrition and its severity among children under 5 years of age in rural Gambia, where marasmus SAM is most prevalent. FINDINGS Children with marasmus SAM have distinct microbiome characteristics and biologically-relevant multimodal biomarkers not observed among children with moderate acute malnutrition. Marasmus SAM was characterized by lower microbial richness and biomass, significant enrichments in Enterobacteriaceae, altered interactions between specific Enterobacteriaceae and key energy regulating hormones and their receptors. INTERPRETATION Our findings suggest that marasmus SAM is characterized by the collapse of a complex system with nested interactions and key associations between the gut microbiome, enteric pathogens, and energy regulating hormones. Further exploration of these systems will help inform innovative preventive and therapeutic interventions. FUNDING The work was supported by the UK Medical Research Council (MRC; MC-A760-5QX00) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement; Bill and Melinda Gates Foundation (OPP 1066932) and the National Institute of Medical Research (NIMR), UK. This network analysis was supported by NIH U54GH009824 [CLD] and NSF OCE-1558453 [CLD].
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Affiliation(s)
- Helen M Nabwera
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Josh L Espinoza
- J. Craig Venture Institute, 4120 Capricorn Ln, La Jolla, CA 92037, USA; Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Archibald Worwui
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Modupeh Betts
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Catherine Okoi
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Abdul K Sesay
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Rowan Bancroft
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Schadrac C Agbla
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | | | - Mariama Colley
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Amadou T Jallow
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Jie Liu
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Martin Antonio
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Robin M Bernstein
- Growth and Development Lab, Department of Anthropology, University of Colorado, Boulder, CO, United States of America
| | | | - Brenda A Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, United Kingdom.
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18
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Pavlinac PB, Platts-Mills JA, Tickell KD, Liu J, Juma J, Kabir F, Nkeze J, Okoi C, Operario DJ, Uddin J, Ahmed S, Alonso PL, Antonio M, Becker SM, Breiman RF, Faruque ASG, Fields B, Gratz J, Haque R, Hossain A, Hossain MJ, Jarju S, Qamar F, Iqbal NT, Kwambana B, Mandomando I, McMurry TL, Ochieng C, Ochieng JB, Ochieng M, Onyango C, Panchalingam S, Kalam A, Aziz F, Qureshi S, Ramamurthy T, Roberts JH, Saha D, Sow SO, Stroup SE, Sur D, Tamboura B, Taniuchi M, Tennant SM, Roose A, Toema D, Wu Y, Zaidi A, Nataro JP, Levine MM, Houpt ER, Kotloff KL. The Clinical Presentation of Culture-positive and Culture-negative, Quantitative Polymerase Chain Reaction (qPCR)-Attributable Shigellosis in the Global Enteric Multicenter Study and Derivation of a Shigella Severity Score: Implications for Pediatric Shigella Vaccine Trials. Clin Infect Dis 2021; 73:e569-e579. [PMID: 33044509 PMCID: PMC8326551 DOI: 10.1093/cid/ciaa1545] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 05/13/2020] [Accepted: 10/08/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Shigella is a leading cause of childhood diarrhea and target for vaccine development. Microbiologic and clinical case definitions are needed for pediatric field vaccine efficacy trials. METHODS We compared characteristics of moderate to severe diarrhea (MSD) cases in the Global Enteric Multicenter Study (GEMS) between children with culture positive Shigella to those with culture-negative, quantitative polymerase chain reaction (qPCR)-attributable Shigella (defined by an ipaH gene cycle threshold <27.9). Among Shigella MSD cases, we determined risk factors for death and derived a clinical severity score. RESULTS Compared to culture-positive Shigella MSD cases (n = 745), culture-negative/qPCR-attributable Shigella cases (n = 852) were more likely to be under 12 months, stunted, have a longer duration of diarrhea, and less likely to have high stool frequency or a fever. There was no difference in dehydration, hospitalization, or severe classification from a modified Vesikari score. Twenty-two (1.8%) Shigella MSD cases died within the 14-days after presentation to health facilities, and 59.1% of these deaths were in culture-negative cases. Age <12 months, diarrhea duration prior to presentation, vomiting, stunting, wasting, and hospitalization were associated with mortality. A model-derived score assigned points for dehydration, hospital admission, and longer diarrhea duration but was not significantly better at predicting 14-day mortality than a modified Vesikari score. CONCLUSIONS A composite severity score consistent with severe disease or dysentery may be a pragmatic clinical endpoint for severe shigellosis in vaccine trials. Reliance on culture for microbiologic confirmation may miss a substantial number of Shigella cases but is currently required to measure serotype specific immunity.
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Affiliation(s)
- Patricia B Pavlinac
- Department of Global Health, University of Washington, Seattle, Washington,USA
- Correspondence: Patricia B. Pavlinac, University of Washington, Seattle, WA, United States ()
| | - James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia,USA
| | - Kirkby D Tickell
- Department of Global Health, University of Washington, Seattle, Washington,USA
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia,USA
| | - Jane Juma
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kenya
| | - Furqan Kabir
- Department of Paediatrics and Child Health, Aga Khan University, Karachi,Pakistan
| | - Joseph Nkeze
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland,USA
| | - Catherine Okoi
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul,The Gambia
| | - Darwin J Operario
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia,USA
| | - Jashim Uddin
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia,USA
| | - Shahnawaz Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka,Bangladesh
| | - Pedro L Alonso
- Barcelona Centre for International Health Research (CRESIB), Hospital Clínic, Universitat de Barcelona, Barcelona,Spain
- Centro de Investigação em Saúde da Manhiça, Maputo,Mozambique
| | - Martin Antonio
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul,The Gambia
| | - Stephen M Becker
- Science Applications International Corporation (SAIC), Richmond, Virginia,USA
| | - Robert F Breiman
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Abu S G Faruque
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka,Bangladesh
| | - Barry Fields
- Global Disease Detection Division, Kenya Office of the US Centers for Disease Control and Prevention, Nairobi,Kenya
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia,USA
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka,Bangladesh
| | - Anowar Hossain
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka,Bangladesh
| | - M Jahangir Hossain
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul,The Gambia
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul,The Gambia
| | - Farah Qamar
- Department of Paediatrics and Child Health, Aga Khan University, Karachi,Pakistan
| | - Najeeha Talat Iqbal
- Department of Paediatrics and Child Health, Aga Khan University, Karachi,Pakistan
| | - Brenda Kwambana
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul,The Gambia
| | | | - Timothy L McMurry
- Public Health Sciences, University of Virginia, Charlottesville, Virginia,USA
| | - Caroline Ochieng
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kenya
| | - John B Ochieng
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kenya
| | - Melvin Ochieng
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kenya
| | - Clayton Onyango
- Global Disease Detection Division, Kenya Office of the US Centers for Disease Control and Prevention, Nairobi,Kenya
| | - Sandra Panchalingam
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland,USA
| | - Adil Kalam
- Department of Paediatrics and Child Health, Aga Khan University, Karachi,Pakistan
| | - Fatima Aziz
- Department of Paediatrics and Child Health, Aga Khan University, Karachi,Pakistan
| | - Shahida Qureshi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi,Pakistan
| | | | - James H Roberts
- Public Health Sciences, University of Virginia, Charlottesville, Virginia,USA
| | - Debasish Saha
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul,The Gambia
| | - Samba O Sow
- Centre pour le Développement des Vaccins, Bamako,Mali
| | - Suzanne E Stroup
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia,USA
| | - Dipika Sur
- National Institute of Cholera and Enteric Diseases, Kolkata,India
| | | | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia,USA
| | - Sharon M Tennant
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland,USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland,USA
| | - Anna Roose
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland,USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland,USA
| | - Deanna Toema
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland,USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland,USA
| | - Yukun Wu
- Sanofi Pasteur, Swiftwater, Pennsylvania,USA
| | - Anita Zaidi
- Bill and Melinda Gates Foundation, Seattle, Washington,USA
| | - James P Nataro
- Public Health Sciences, University of Virginia, Charlottesville, Virginia,USA
| | - Myron M Levine
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland,USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland,USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland,USA
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia,USA
| | - Karen L Kotloff
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland,USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland,USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland,USA
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19
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Abatan B, Agboghoroma O, Akemoke F, Antonio M, Awokola B, Bittaye M, Bojang A, Bojang K, Brotherton H, Cerami C, Clarke E, D'Alessandro U, de Silva T, Drammeh M, Forrest K, Hofmann N, Jagne S, Jah H, Jarju S, Jaye A, Jobe M, Kampmann B, Manjang B, Martinez-Alvarez M, Mohammed N, Nadjm B, Ndiath MO, Nkereuwem E, Nwakanma D, Oko F, Okoh E, Okomo U, Olatunji Y, Oriero E, Prentice AM, Roberts C, Roca A, Sabally B, Sambou S, Samateh A, Secka O, Sesay AK, Singhateh Y, Susso B, Usuf E, Vilane A, Wariri O. Intense and Mild First Epidemic Wave of Coronavirus Disease, The Gambia. Emerg Infect Dis 2021; 27:2064-2072. [PMID: 34286683 PMCID: PMC8314844 DOI: 10.3201/eid2708.204954] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is evolving differently in Africa than in other regions. Africa has lower SARS-CoV-2 transmission rates and milder clinical manifestations. Detailed SARS-CoV-2 epidemiologic data are needed in Africa. We used publicly available data to calculate SARS-CoV-2 infections per 1,000 persons in The Gambia. We evaluated transmission rates among 1,366 employees of the Medical Research Council Unit The Gambia (MRCG), where systematic surveillance of symptomatic cases and contact tracing were implemented. By September 30, 2020, The Gambia had identified 3,579 SARS-CoV-2 cases, including 115 deaths; 67% of cases were identified in August. Among infections, MRCG staff accounted for 191 cases; all were asymptomatic or mild. The cumulative incidence rate among nonclinical MRCG staff was 124 infections/1,000 persons, which is >80-fold higher than estimates of diagnosed cases among the population. Systematic surveillance and seroepidemiologic surveys are needed to clarify the extent of SARS-CoV-2 transmission in Africa.
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20
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Senghore M, Tientcheu PE, Worwui AK, Jarju S, Okoi C, Suso SMS, Foster-Nyarko E, Ebruke C, Sonko M, Kourna MH, Agossou J, Tsolenyanu E, Renner LA, Ansong D, Sanneh B, Cisse CB, Boula A, Miwanda B, Lo SW, Gladstone RA, Schwartz S, Hawkins P, McGee L, Klugman KP, Breiman RF, Bentley SD, Mwenda JM, Kwambana-Adams BA, Antonio M. Phylogeography and resistome of pneumococcal meningitis in West Africa before and after vaccine introduction. Microb Genom 2021; 7. [PMID: 34328412 PMCID: PMC8477402 DOI: 10.1099/mgen.0.000506] [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] [Indexed: 11/11/2022] Open
Abstract
Despite contributing to the large disease burden in West Africa, little is known about the genomic epidemiology of Streptococcus pneumoniae which cause meningitis among children under 5 years old in the region. We analysed whole-genome sequencing data from 185 S. pneumoniae isolates recovered from suspected paediatric meningitis cases as part of the World Health Organization (WHO) invasive bacterial diseases surveillance from 2010 to 2016. The phylogeny was reconstructed, accessory genome similarity was computed and antimicrobial-resistance patterns were inferred from the genome data and compared to phenotypic resistance from disc diffusion. We studied the changes in the distribution of serotypes pre- and post-pneumococcal conjugate vaccine (PCV) introduction in the Central and Western sub-regions separately. The overall distribution of non-vaccine, PCV7 (4, 6B, 9V, 14, 18C, 19F and 23F) and additional PCV13 serotypes (1, 3, 5, 6A, 19A and 7F) did not change significantly before and after PCV introduction in the Central region (Fisher's test P value 0.27) despite an increase in the proportion of non-vaccine serotypes to 40 % (n=6) in the post-PCV introduction period compared to 21.9 % (n=14). In the Western sub-region, PCV13 serotypes were more dominant among isolates from The Gambia following the introduction of PCV7, 81 % (n=17), compared to the pre-PCV period in neighbouring Senegal, 51 % (n=27). The phylogeny illustrated the diversity of strains associated with paediatric meningitis in West Africa and highlighted the existence of phylogeographical clustering, with isolates from the same sub-region clustering and sharing similar accessory genome content. Antibiotic-resistance genotypes known to confer resistance to penicillin, chloramphenicol, co-trimoxazole and tetracycline were detected across all sub-regions. However, there was no discernible trend linking the presence of resistance genotypes with the vaccine introduction period or whether the strain was a vaccine or non-vaccine serotype. Resistance genotypes appeared to be conserved within selected sub-clades of the phylogenetic tree, suggesting clonal inheritance. Our data underscore the need for continued surveillance on the emergence of non-vaccine serotypes as well as chloramphenicol and penicillin resistance, as these antibiotics are likely still being used for empirical treatment in low-resource settings. This article contains data hosted by Microreact.
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Affiliation(s)
- Madikay Senghore
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia.,Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
| | - Peggy-Estelle Tientcheu
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Archibald Kwame Worwui
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Sheikh Jarju
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Catherine Okoi
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Sambou M S Suso
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Ebenezer Foster-Nyarko
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Chinelo Ebruke
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Mohamadou Sonko
- Hopital d'Enfants Albert Royer, BP 5297, Fann, Dakar, Senegal
| | | | - Joseph Agossou
- Department of Mother and Child, Faculty of Medicine, University of Parakou, Parakou, Benin.,Borgou Regional University Teaching Hospital, Parakou, Benin
| | - Enyonam Tsolenyanu
- Laboratoire Microbiologie, Centre Hospitalier Universitaire de Tokoin Lomé, BP 57, Lomé, Togo
| | - Lorna Awo Renner
- Central Laboratory Services, Korle-Bu Teaching Hospital, P.O. Box 77, Accra, Ghana
| | - Daniel Ansong
- Komfo Anokye Teaching Hospital, P.O. Box 1934, Kumasi, Ghana
| | - Bakary Sanneh
- Edward Francis Small Teaching Hospital, Banjul, The Gambia
| | - Catherine Boni Cisse
- Laboratoire Central du CHU de Yopougon, Institut Pasteur de Cote d'Ivoire, Abidjan, Ivory Coast
| | - Angeline Boula
- Centre Mere et Enfant de la Fondation, Chantal Biya, Yaounde, Cameroon
| | - Berthe Miwanda
- Institut National de Recherche Biomedicale, Kinshasa, Democratic Republic of Congo
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | | | | | - Paulina Hawkins
- Centers for Disease Control and Prevention, Atlanta, GA, USA.,Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Keith P Klugman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Robert F Breiman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA.,Emory Global Health Institute, Atlanta, GA, USA
| | | | - Jason M Mwenda
- World Health Organization Regional Office for Africa, BP 6, Brazzaville, Republic of Congo
| | - Brenda Anna Kwambana-Adams
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia.,NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
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21
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Mackenzie GA, Hill PC, Jeffries DJ, Ndiaye M, Sahito SM, Hossain I, Uchendu U, Ameh D, Adeyemi O, Pathirana J, Olatunji Y, Abatan B, Muhammad BS, Ahameefula E, Fombah AE, Adeshola B, Lobga BG, Saha D, Mackenzie R, Odutola A, Plumb ID, Akano A, Ebruke BE, Ideh RC, Kuti B, Githua P, Olutunde E, Ofordile O, Green E, Usuf E, Badji H, Ikumapayi UN, Manjang A, Salaudeen R, Nsekpong ED, Jarju S, Antonio M, Sambou S, Ceesay L, Lowe-Jallow Y, Fofana S, Jasseh M, Mulholland K, Knoll M, Levine OS, Howie SR, Adegbola RA, Greenwood BM, Corrah T. Impact of the introduction of pneumococcal conjugate vaccination on invasive pneumococcal disease and pneumonia in The Gambia: 10 years of population-based surveillance. Lancet Infect Dis 2021; 21:1293-1302. [PMID: 34280357 PMCID: PMC8384632 DOI: 10.1016/s1473-3099(20)30880-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 10/01/2020] [Accepted: 11/05/2020] [Indexed: 11/22/2022]
Abstract
Background The Gambia introduced seven-valent pneumococcal conjugate vaccine (PCV7) in August 2009, followed by PCV13 in May, 2011, using a schedule of three primary doses without a booster dose or catch-up immunisation. We aimed to assess the long-term impact of PCV on disease incidence. Methods We did 10 years of population-based surveillance for invasive pneumococcal disease (IPD) and WHO defined radiological pneumonia with consolidation in rural Gambia. The surveillance population included all Basse Health and Demographic Surveillance System residents aged 2 months or older. Nurses screened all outpatients and inpatients at all health facilities using standardised criteria for referral. Clinicians then applied criteria for patient investigation. We defined IPD as a compatible illness with isolation of Streptococcus pneumoniae from a normally sterile site (cerebrospinal fluid, blood, or pleural fluid). We compared disease incidence between baseline (May 12, 2008–May 11, 2010) and post-vaccine years (2016–2017), in children aged 2 months to 14 years, adjusting for changes in case ascertainment over time. Findings We identified 22 728 patients for investigation and detected 342 cases of IPD and 2623 cases of radiological pneumonia. Among children aged 2–59 months, IPD incidence declined from 184 cases per 100 000 person-years to 38 cases per 100 000 person-years, an 80% reduction (95% CI 69–87). Non-pneumococcal bacteraemia incidence did not change significantly over time (incidence rate ratio 0·88; 95% CI, 0·64–1·21). We detected zero cases of vaccine-type IPD in the 2–11 month age group in 2016–17. Incidence of radiological pneumonia decreased by 33% (95% CI 24–40), from 10·5 to 7·0 per 1000 person-years in the 2–59 month age group, while pneumonia hospitalisations declined by 27% (95% CI 22–31). In the 5–14 year age group, IPD incidence declined by 69% (95% CI −28 to 91) and radiological pneumonia by 27% (95% CI −5 to 49). Interpretation Routine introduction of PCV13 substantially reduced the incidence of childhood IPD and pneumonia in rural Gambia, including elimination of vaccine-type IPD in infants. Other low-income countries can expect substantial impact from the introduction of PCV13 using a schedule of three primary doses. Funding Gavi, The Vaccine Alliance; Bill & Melinda Gates Foundation; UK Medical Research Council; Pfizer Ltd.
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Affiliation(s)
| | - Grant A Mackenzie
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia; Murdoch Children's Research Institute, Parkville, Melbourne, VIC, Australia; London School of Hygiene & Tropical Medicine, London, UK; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australi.
| | - Philip C Hill
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - David J Jeffries
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Malick Ndiaye
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Shah M Sahito
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Ilias Hossain
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Uchendu Uchendu
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - David Ameh
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Oyedeji Adeyemi
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Jayani Pathirana
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Yekini Olatunji
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Baderinwa Abatan
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Bilquees S Muhammad
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Ebirim Ahameefula
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Augustin E Fombah
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Banjo Adeshola
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Babila G Lobga
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Debasish Saha
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Roslyn Mackenzie
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Aderonke Odutola
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Ian D Plumb
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Aliu Akano
- The National Hospital, Garki, Abuja, Nigeria
| | - Bernard E Ebruke
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Readon C Ideh
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Bankole Kuti
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Peter Githua
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Emmanuel Olutunde
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Ogochukwu Ofordile
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Edward Green
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Effua Usuf
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Henry Badji
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Usman Na Ikumapayi
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Ahmed Manjang
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Rasheed Salaudeen
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - E David Nsekpong
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Martin Antonio
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia; London School of Hygiene & Tropical Medicine, London, UK; Warwick Medical School, University of Warwick, Coventry, UK
| | - Sana Sambou
- Ministry of Health, Gambia Government, The Gambia
| | - Lamin Ceesay
- Ministry of Health, Gambia Government, The Gambia
| | | | - Sidat Fofana
- Ministry of Health, Gambia Government, The Gambia
| | - Momodou Jasseh
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Kim Mulholland
- Murdoch Children's Research Institute, Parkville, Melbourne, VIC, Australia; London School of Hygiene & Tropical Medicine, London, UK
| | - Maria Knoll
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Orin S Levine
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Stephen R Howie
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia; Centre for International Health, University of Otago, Dunedin, New Zealand; Department of Paediatrics: Child and Youth Health, University of Auckland, Auckland, New Zealand
| | | | | | - Tumani Corrah
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
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22
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Sanyang B, Kanteh A, Usuf E, Nadjm B, Jarju S, Bah A, Bojang A, Grey-Johnson M, Jones JC, Gai A, Sarr C, Sillah F, Wariri O, Oko F, Cerami C, Forrest K, Sey AP, Jallow H, Nwakanma D, Sesay AK, D'Alessandro U, Roca A. COVID-19 reinfections in The Gambia by phylogenetically distinct SARS-CoV-2 variants-first two confirmed events in west Africa. Lancet Glob Health 2021; 9:e905-e907. [PMID: 34090610 PMCID: PMC8175042 DOI: 10.1016/s2214-109x(21)00213-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/09/2021] [Accepted: 04/19/2021] [Indexed: 12/15/2022]
Affiliation(s)
- Bakary Sanyang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | - Abdoulie Kanteh
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | - Effua Usuf
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | - Behzad Nadjm
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | - Alasana Bah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | - Abdoulie Bojang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | - Mary Grey-Johnson
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | - Joquina Chiquita Jones
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | - Abdou Gai
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | - Catherine Sarr
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | - Fatoumata Sillah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | - Oghenebrume Wariri
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | - Francis Oko
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | - Carla Cerami
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | - Karen Forrest
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | | | - Haruna Jallow
- National Public Health Laboratories, Kotu, The Gambia
| | - Davis Nwakanma
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | - Abdul Karim Sesay
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia
| | - Anna Roca
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara 273, The Gambia.
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23
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Gilroy R, Ravi A, Getino M, Pursley I, Horton DL, Alikhan NF, Baker D, Gharbi K, Hall N, Watson M, Adriaenssens EM, Foster-Nyarko E, Jarju S, Secka A, Antonio M, Oren A, Chaudhuri RR, La Ragione R, Hildebrand F, Pallen MJ. Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture. PeerJ 2021; 9:e10941. [PMID: 33868800 PMCID: PMC8035907 DOI: 10.7717/peerj.10941] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/22/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. RESULTS We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces, documenting over forty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii. CONCLUSIONS Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.
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Affiliation(s)
| | | | - Maria Getino
- School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Isabella Pursley
- School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Daniel L. Horton
- School of Veterinary Medicine, University of Surrey, Guildford, UK
| | | | - Dave Baker
- Quadram Institute Bioscience, Norwich, UK
| | - Karim Gharbi
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
| | - Mick Watson
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | - Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Arss Secka
- West Africa Livestock Innovation Centre, Banjul, The Gambia
| | - Martin Antonio
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Roy R. Chaudhuri
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | | | - Falk Hildebrand
- Quadram Institute Bioscience, Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, UK
- University of East Anglia, Norwich, UK
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24
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Foster-Nyarko E, Alikhan NF, Ravi A, Thomson NM, Jarju S, Kwambana-Adams BA, Secka A, O’Grady J, Antonio M, Pallen MJ. Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia. Microb Genom 2021; 7:mgen000484. [PMID: 33253086 PMCID: PMC8115903 DOI: 10.1099/mgen.0.000484] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 11/09/2020] [Indexed: 01/21/2023] Open
Abstract
Chickens and guinea fowl are commonly reared in Gambian homes as affordable sources of protein. Using standard microbiological techniques, we obtained 68 caecal isolates of Escherichia coli from 10 chickens and 9 guinea fowl in rural Gambia. After Illumina whole-genome sequencing, 28 sequence types were detected in the isolates (4 of them novel), of which ST155 was the most common (22/68, 32 %). These strains span four of the eight main phylogroups of E. coli, with phylogroups B1 and A being most prevalent. Nearly a third of the isolates harboured at least one antimicrobial resistance gene, while most of the ST155 isolates (14/22, 64 %) encoded resistance to ≥3 classes of clinically relevant antibiotics, as well as putative virulence factors, suggesting pathogenic potential in humans. Furthermore, hierarchical clustering revealed that several Gambian poultry strains were closely related to isolates from humans. Although the ST155 lineage is common in poultry from Africa and South America, the Gambian ST155 isolates belong to a unique cgMLST cluster comprising closely related (38-39 alleles differences) isolates from poultry and livestock from sub-Saharan Africa - suggesting that strains can be exchanged between poultry and livestock in this setting. Continued surveillance of E. coli and other potential pathogens in rural backyard poultry from sub-Saharan Africa is warranted.
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Affiliation(s)
- Ebenezer Foster-Nyarko
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard Road, Fajara, Gambia
| | | | - Anuradha Ravi
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
| | | | - Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard Road, Fajara, Gambia
| | - Brenda A. Kwambana-Adams
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard Road, Fajara, Gambia
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Arss Secka
- West Africa Livestock Innovation Centre (WALIC), MB 14, Banjul, Gambia
| | - Justin O’Grady
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
| | - Martin Antonio
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard Road, Fajara, Gambia
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Mark John Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
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25
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Boni-Cisse C, Jarju S, Bancroft RE, Lepri NA, Kone H, Kofi N, Britoh-Mlan A, Zaba FS, Usuf E, Ndow PS, Worwui A, Mwenda JM, Biey JN, Ntsama B, Kwambana-Adams BA, Antonio M. Etiology of Bacterial Meningitis Among Children <5 Years Old in Côte d'Ivoire: Findings of Hospital-based Surveillance Before and After Pneumococcal Conjugate Vaccine Introduction. Clin Infect Dis 2020; 69:S114-S120. [PMID: 31505624 PMCID: PMC6761318 DOI: 10.1093/cid/ciz475] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 12/03/2022] Open
Abstract
Background Bacterial meningitis remains a major disease affecting children in Côte d’Ivoire. Thus, with support from the World Health Organization (WHO), Côte d’Ivoire has implemented pediatric bacterial meningitis (PBM) surveillance at 2 sentinel hospitals in Abidjan, targeting the main causes of PBM: Streptococcus pneumoniae (pneumococcus), Haemophilus influenzae, and Neisseria meningitidis (meningococcus). Herein we describe the epidemiological characteristics of PBM observed in Côte d’Ivoire during 2010–2016. Methods Cerebrospinal fluid (CSF) was collected from children aged <5 years admitted to the Abobo General Hospital or University Hospital Center Yopougon with suspected meningitis. Microbiology and polymerase chain reaction (PCR) techniques were used to detect the presence of pathogens in CSF. Where possible, serotyping/grouping was performed to determine the specific causative agents. Results Overall, 2762 cases of suspected meningitis were reported, with CSF from 39.2% (1083/2762) of patients analyzed at the WHO regional reference laboratory in The Gambia. In total, 82 (3.0% [82/2762]) CSF samples were positive for bacterial meningitis. Pneumococcus was the main pathogen responsible for PBM, accounting for 69.5% (52/82) of positive cases. Pneumococcal conjugate vaccine serotypes 5, 18C, 19F, and 6A/B were identified post–vaccine introduction. Emergence of H. influenzae nontypeable meningitis was observed after H. influenzae type b vaccine introduction. Conclusions Despite widespread use and high coverage of conjugate vaccines, pneumococcal vaccine serotypes and H. influenzae type b remain associated with bacterial meningitis among children aged <5 years in Côte d’Ivoire. This reinforces the need for enhanced surveillance for vaccine-preventable diseases to determine the prevalence of bacterial meningitis and vaccine impact across the country.
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Affiliation(s)
- Catherine Boni-Cisse
- Département de Microbiologie, Université Félix Houphouët Boigny, Abidjan, Côte d'Ivoire;, UFR des Sciences Médicales.,Sentinel Site Surveillance Laboratory of Paediatric Bacterial Meningitis and Rotavirus Diarrhoea, Centre Hospitalier Universitair de Yopougon, Abidjan, Côte d'Ivoire
| | - Sheikh Jarju
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Rowan E Bancroft
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Nicaise A Lepri
- Département de Microbiologie, Université Félix Houphouët Boigny, Abidjan, Côte d'Ivoire;, UFR des Sciences Médicales
| | - Hamidou Kone
- Département de Microbiologie, Université Félix Houphouët Boigny, Abidjan, Côte d'Ivoire;, UFR des Sciences Médicales
| | - N'zue Kofi
- WHO Country Office, Abidjan, Côte d'Ivoire
| | - Alice Britoh-Mlan
- Sentinel Site Surveillance Laboratory of Paediatric Bacterial Meningitis and Rotavirus Diarrhoea, Centre Hospitalier Universitair de Yopougon, Abidjan, Côte d'Ivoire
| | - Flore Sandrine Zaba
- Sentinel Site Surveillance Laboratory of Paediatric Bacterial Meningitis and Rotavirus Diarrhoea, Centre Hospitalier Universitair de Yopougon, Abidjan, Côte d'Ivoire
| | - Effua Usuf
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Peter Sylvanus Ndow
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Archibald Worwui
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Jason M Mwenda
- WHO Regional Office for Africa, Brazzaville, Republic of Congo
| | - Joseph N Biey
- WHO Intercountry Support Team, Ouagadougou, Burkina Faso
| | - Bernard Ntsama
- WHO Intercountry Support Team, Ouagadougou, Burkina Faso
| | - Brenda A Kwambana-Adams
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Martin Antonio
- World Health Organization (WHO) Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia.,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
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Foster-Nyarko E, Alikhan NF, Ravi A, Thomson N, Jarju S, Secka A, Antonio M, J. Pallen M. Gambian poultry isolates from hyperendemic group of AMR Escherichia coli strains in sub-Saharan Africa. Access Microbiol 2020. [DOI: 10.1099/acmi.ac2020.po0824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chickens and guinea fowl are commonly reared in Gambian homes as affordable sources of protein. Using standard microbiological techniques, we obtained 68 caecal isolates of Escherichia coli from ten chickens and nine guinea fowl in rural Gambia. After Illumina whole-genome sequencing, 28 sequence types were detected in the isolates (four of them novel), of which ST155 was the most common (22/68, 32%). These strains span four of the eight main phylogroups of E. coli, with phylogroups B1 and A being most prevalent. Nearly a third of the isolates harboured at least one antimicrobial resistance gene, while most of the ST155 isolates (14/22, 64%) encoded resistance to ≥3 classes of clinically relevant antibiotics, as well as putative virulence factors, suggesting pathogenic potential in humans. Furthermore, hierarchical clustering revealed that several Gambian poultry strains were closely related to isolates from humans. Although the ST155 lineage is common in poultry from Africa and South America, the Gambian ST155 isolates sit within a tight genomic cluster (100 alleles difference) of strains from poultry and livestock in sub-Saharan Africa (the Gambia, Uganda and Kenya). Continued surveillance of E. coli and other potential pathogens in rural backyard poultry from sub-Saharan Africa is warranted.
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Affiliation(s)
| | | | - Anuradha Ravi
- Quadram Institute Bioscience,Norwich Research Park,Norwich
| | | | - Sheikh Jarju
- Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine,Atlantic Boulevard Road,Fajara
| | - Arss Secka
- West Africa Livestock Innovation Centre,Banjul,Gambia
| | - Martin Antonio
- Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine,Atlantic Boulevard Road,Fajara
| | - Mark J. Pallen
- Quadram Institute Bioscience,Norwich Research Park,Norwich
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27
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Darboe S, Dobreniecki S, Jarju S, Jallow M, Mohammed NI, Wathuo M, Ceesay B, Tweed S, Basu Roy R, Okomo U, Kwambana-Adams B, Antonio M, Bradbury RS, de Silva TI, Forrest K, Roca A, Lawal BJ, Nwakanma D, Secka O. Prevalence of Panton-Valentine Leukocidin (PVL) and Antimicrobial Resistance in Community-Acquired Clinical Staphylococcus aureus in an Urban Gambian Hospital: A 11-Year Period Retrospective Pilot Study. Front Cell Infect Microbiol 2019; 9:170. [PMID: 31192162 PMCID: PMC6540874 DOI: 10.3389/fcimb.2019.00170] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/06/2019] [Indexed: 11/13/2022] Open
Abstract
Background:Staphylococcus aureus is a major human pathogen. Panton-Valentine leukocidin (PVL) is a virulence factor produced by some strains that causes leukocyte lysis and tissue necrosis. PVL-associated S. aureus (PVL-SA) predominantly causes skin and soft-tissue infections (SSTIs) but can also cause invasive infections such as necrotizing pneumonia. It is carried by both community-associated methicillin susceptible S. aureus (CA-MSSA) and methicillin resistant S. aureus (CA-MRSA). This study aims to determine the prevalence of PVL-SA among patients seen at an urban Gambian hospital and associated antibiotic resistance. Methods: Archived clinical S. aureus (70 invasive bacteraemia and 223 non-invasive SSTIs) from 293 patients were retrieved as well as relevant data from clinical records where available. Antibiotic susceptibility was assessed using disc diffusion according to Clinical Laboratory Standards Institute (CLSI) guidelines. Genomic DNA was extracted and the presence of lukF and lukS PVL genes was detected by conventional gel-based PCR. Result: PVL-SA strains accounted for 61.4% (180/293) of S. aureus isolates. PVL prevalence was high in both Gambian bacteraemia and SSTIs S. aureus strains. Antimicrobial resistance was low and included chloramphenicol (4.8%), cefoxitin (2.4%), ciprofloxacin (3.8%), erythromycin (8.9%), gentamicin (5.5%) penicillin (92.5%), tetracycline (41.0%), and sulfamethoxazole-trimethoprim (24.2%). There was no association of PVL with antimicrobial resistance. Conclusion: PVL expression is high among clinical S. aureus strains among Gambian patients. Reporting of PVL-SA clinical infections is necessary to enable the monitoring of the clinical impact of these strains in the population and guide prevention of the spread of virulent PVL-positive CA-MRSA strains. SUMMARY Staphylococcus aureus (S. aureus) is a major human pathogen with several virulence factors. We performed a retrospective analysis to investigate the prevalence of one such virulence factor (PVL) amongst clinical S. aureus samples. We found a high prevalence in our setting but antimicrobial resistance including methicillin resistance was low.
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Affiliation(s)
- Saffiatou Darboe
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | | | - Sheikh Jarju
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Mamadou Jallow
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Nuredin Ibrahim Mohammed
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Miriam Wathuo
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Buntung Ceesay
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Sam Tweed
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Robindra Basu Roy
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Uduak Okomo
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Brenda Kwambana-Adams
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Martin Antonio
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Richard S. Bradbury
- School of Health, Medical and Applied Sciences, Central Queensland University, Rockhampton, QLD, Australia
| | - Thushan I. de Silva
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Karen Forrest
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Anna Roca
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Bolarinde Joseph Lawal
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Davis Nwakanma
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Ousman Secka
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
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28
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Mendy J, Jarju S, Heslop R, Bojang AL, Kampmann B, Sutherland JS. Changes in Mycobacterium tuberculosis-Specific Immunity With Influenza co-infection at Time of TB Diagnosis. Front Immunol 2019; 9:3093. [PMID: 30662443 PMCID: PMC6328457 DOI: 10.3389/fimmu.2018.03093] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 06/27/2018] [Accepted: 12/13/2018] [Indexed: 01/16/2023] Open
Abstract
Background: Prior Influenza A viral (IAV) infection has been shown to increase susceptibility to tuberculosis (TB) and TB has also been shown to be a primary cause of death during pandemics, including the Spanish Influenza outbreak of 1918–1919. The majority of data has been obtained from mouse models, thus the aim of this study was to determine the impact of Flu co-infection on host immunity and disease severity in TB patients at diagnosis. Methods: Sputum from 282 patients with active TB were analyzed for presence of FluA/FluB RNA at presentation using multiplex PCR. Sputum RNA was also analyzed for Mycobacterium tuberculosis (Mtb) load using 16S RNA amplification. Supernatants from digested sputum and Mtb antigen-stimulated whole blood were analyzed using multiplex cytokine arrays and PBMC were analyzed for cytokine production from CD4+ T, CD8+ T and Mucosal Associated Invariant T cells (MAITs). Results: 12 (4.3%) of TB patients were found to have FluA or FluB viral RNA present in their sputum at the time of TB diagnosis. The TB/Flu co-infected patients had a significantly higher bacterial load compared to those with TB mono-infection (p = 0.0026). They had lower levels of IL17A in ex vivo sputum (p = 0.0275) and higher MCP-1 (CCL2) levels in the blood following PPD stimulation (p = 0.0267). TB/Flu co-infected subjects had significantly higher IFN-γ+IL-17+CD4+ and IFN-γ+IL-17-CD8+ cells compared to TB mono-infected subjects. Conclusions: These data show that Flu co-infection at time of TB diagnosis is associated with a higher bacterial load and differential cellular and soluble profiles. These findings show for the first time the impact of TB/Flu co-infection in a human cohort and support the potential benefit of Flu vaccination in TB-endemic settings.
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Affiliation(s)
- Joseph Mendy
- Vaccines & Immunity Theme, MRC Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Sheikh Jarju
- Vaccines & Immunity Theme, MRC Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Rhiannon Heslop
- Vaccines & Immunity Theme, MRC Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia.,Faculty of Biosciences, The University of Manchester, Manchester, United Kingdom
| | - Adama L Bojang
- Vaccines & Immunity Theme, MRC Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Beate Kampmann
- Vaccines & Immunity Theme, MRC Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Jayne S Sutherland
- Vaccines & Immunity Theme, MRC Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, Gambia
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29
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Mackenzie GA, Hill PC, Sahito SM, Jeffries DJ, Hossain I, Bottomley C, Uchendu U, Ameh D, Ndiaye M, Osuorah CD, Adeyemi O, Pathirana J, Olatunji Y, Abatan B, Ahameefula E, Muhammad BS, Fombah AE, Saha D, Mackenzie R, Plumb I, Akano A, Ebruke B, Ideh RC, Kuti B, Githua P, Olutunde E, Ofordile O, Green E, Usuf E, Badji H, Ikumapayi UNA, Manjang A, Salaudeen R, Nsekpong ED, Jarju S, Antonio M, Sambou S, Ceesay L, Lowe-Jallow Y, Sowe D, Jasseh M, Mulholland K, Knoll M, Levine OS, Howie SR, Adegbola RA, Greenwood BM, Corrah T. Impact of the introduction of pneumococcal conjugate vaccination on pneumonia in The Gambia: population-based surveillance and case-control studies. Lancet Infect Dis 2017; 17:965-973. [PMID: 28601421 PMCID: PMC5589209 DOI: 10.1016/s1473-3099(17)30321-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/11/2017] [Accepted: 04/25/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND Pneumococcal conjugate vaccines (PCVs) are used in many low-income countries but their impact on the incidence of pneumonia is unclear. The Gambia introduced PCV7 in August, 2009, and PCV13 in May, 2011. We aimed to measure the impact of the introduction of these vaccines on pneumonia incidence. METHODS We did population-based surveillance and case-control studies. The primary endpoint was WHO-defined radiological pneumonia with pulmonary consolidation. Population-based surveillance was for suspected pneumonia in children aged 2-59 months (minimum age 3 months in the case-control study) between May 12, 2008, and Dec 31, 2015. Surveillance for the impact study was limited to the Basse Health and Demographic Surveillance System (BHDSS), whereas surveillance for the case-control study included both the BHDSS and Fuladu West Health and Demographic Surveillance System. Nurses screened all outpatients and inpatients at all health facilities in the surveillance area using standardised criteria for referral to clinicians in Basse and Bansang. These clinicians recorded clinical findings and applied standardised criteria to identify patients with suspected pneumonia. We compared the incidence of pneumonia during the baseline period (May 12, 2008, to May 11, 2010) and the PCV13 period (Jan 1, 2014, to Dec 31, 2015). We also investigated the effectiveness of PCV13 using case-control methods between Sept 12, 2011, and Sept 31, 2014. Controls were aged 90 days or older, and were eligible to have received at least one dose of PCV13; cases had the same eligibility criteria with the addition of having WHO-defined radiological pneumonia. FINDINGS We investigated 18 833 children with clinical pneumonia and identified 2156 cases of radiological pneumonia. Among children aged 2-11 months, the incidence of radiological pneumonia fell from 21·0 cases per 1000 person-years in the baseline period to 16·2 cases per 1000 person-years (23% decline, 95% CI 7-36) in 2014-15. In the 12-23 month age group, radiological pneumonia decreased from 15·3 to 10·9 cases per 1000 person-years (29% decline, 12-42). In children aged 2-4 years, incidence fell from 5·2 to 4·1 cases per 1000 person-years (22% decline, 1-39). Incidence of all clinical pneumonia increased by 4% (-1 to 8), but hospitalised cases declined by 8% (3-13). Pneumococcal pneumonia declined from 2·9 to 1·2 cases per 1000 person-years (58% decline, 22-77) in children aged 2-11 months and from 2·6 to 0·7 cases per 1000 person-years (75% decline, 47-88) in children aged 12-23 months. Hypoxic pneumonia fell from 13·1 to 5·7 cases per 1000 person-years (57% decline, 42-67) in children aged 2-11 months and from 6·8 to 1·9 cases per 1000 person-years (72% decline, 58-82) in children aged 12-23 months. In the case-control study, the best estimate of the effectiveness of three doses of PCV13 against radiological pneumonia was an adjusted odds ratio of 0·57 (0·30-1·08) in children aged 3-11 months and vaccine effectiveness increased with greater numbers of doses (p=0·026). The analysis in children aged 12 months and older was underpowered because there were few unvaccinated cases and controls. INTERPRETATION The introduction of PCV in The Gambia was associated with a moderate impact on the incidence of radiological pneumonia, a small reduction in cases of hospitalised pneumonia, and substantial reductions of pneumococcal and hypoxic pneumonia in young children. Low-income countries that introduce PCV13 with reasonable coverage can expect modest reductions in hospitalised cases of pneumonia and a marked impact on the incidence of severe childhood pneumonia. FUNDING GAVI's Pneumococcal vaccines Accelerated Development and Introduction Plan, Bill & Melinda Gates Foundation, and UK Medical Research Council.
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Affiliation(s)
- Grant A Mackenzie
- Medical Research Council Unit, The Gambia, Fajara, The Gambia,Murdoch Childrens Research Institute, Melbourne, VIC, Australia,London School of Hygiene & Tropical Medicine, London, UK,Correspondence to: Dr Grant A Mackenzie, Basse Field Station, MRC The Gambia Unit, PO Box 273, Banjul, The GambiaCorrespondence to: Dr Grant A MackenzieBasse Field StationMRC The Gambia UnitPO Box 273BanjulThe Gambia
| | - Philip C Hill
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Shah M Sahito
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | | | - Ilias Hossain
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | | | - Uchendu Uchendu
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | - David Ameh
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | - Malick Ndiaye
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | | | - Oyedeji Adeyemi
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | | | - Yekini Olatunji
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | - Bade Abatan
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | | | | | | | - Debasish Saha
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | | | - Ian Plumb
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | | | - Bernard Ebruke
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | - Readon C Ideh
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | - Bankole Kuti
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | - Peter Githua
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | | | | | - Edward Green
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | - Effua Usuf
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | - Henry Badji
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | | | - Ahmad Manjang
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | | | | | - Sheikh Jarju
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | - Martin Antonio
- Medical Research Council Unit, The Gambia, Fajara, The Gambia,Microbiology and Infection Unit, Warwick Medical School, Coventry, UK
| | - Sana Sambou
- Ministry of Health and Social Welfare, Gambia Government, Kotu, The Gambia
| | - Lamin Ceesay
- Ministry of Health and Social Welfare, Gambia Government, Kotu, The Gambia
| | | | - Dawda Sowe
- Ministry of Health and Social Welfare, Gambia Government, Kotu, The Gambia
| | - Momodou Jasseh
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
| | - Kim Mulholland
- Murdoch Childrens Research Institute, Melbourne, VIC, Australia,London School of Hygiene & Tropical Medicine, London, UK
| | - Maria Knoll
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Orin S Levine
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Stephen R Howie
- Medical Research Council Unit, The Gambia, Fajara, The Gambia,Centre for International Health, University of Otago, Dunedin, New Zealand,Department of Paediatrics: Child and Youth Health, University of Auckland, Auckland, New Zealand
| | | | | | - Tumani Corrah
- Medical Research Council Unit, The Gambia, Fajara, The Gambia
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30
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Odutola A, Ota MOC, Antonio M, Ogundare EO, Saidu Y, Foster-Nyarko E, Owiafe PK, Ceesay F, Worwui A, Idoko OT, Owolabi O, Bojang A, Jarju S, Drammeh I, Kampmann B, Greenwood BM, Alderson M, Traskine M, Devos N, Schoonbroodt S, Swinnen K, Verlant V, Dobbelaere K, Borys D. Efficacy of a novel, protein-based pneumococcal vaccine against nasopharyngeal carriage of Streptococcus pneumoniae in infants: A phase 2, randomized, controlled, observer-blind study. Vaccine 2017; 35:2531-2542. [PMID: 28389097 DOI: 10.1016/j.vaccine.2017.03.071] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 01/30/2023]
Abstract
BACKGROUND Conserved pneumococcal proteins are potential candidates for inclusion in vaccines against pneumococcal diseases. In the first part of a two-part study, an investigational vaccine (PHiD-CV/dPly/PhtD-30) containing 10 pneumococcal serotype-specific polysaccharide conjugates (10VT) combined with pneumolysin toxoid and pneumococcal histidine triad protein D (30μg each) was well tolerated by Gambian children. Part two, presented here, assessed the efficacy of two PHiD-CV/dPly/PhtD formulations against pneumococcal nasopharyngeal carriage (NPC) prevalence in infants. METHODS In this phase 2, randomized, controlled, observer-blind trial, healthy infants aged 8-10weeks, recruited from a peri-urban health center, were randomized (1:1:1:1:1:1) into six groups. Four groups received PHiD-CV/dPly/PhtD (10 or 30μg of each protein), PHiD-CV, or 13-valent pneumococcal conjugate vaccine at ages 2-3-4months (3+0 infant schedule) and two groups PHiD-CV/dPly/PhtD-30 or PHiD-CV at 2-4-9months (2+1 infant schedule). The primary objective was impact on non-10VT NPC at ages 5-9-12months. Secondary objectives included confirmatory analysis of protein dose superiority and safety/reactogenicity. Impact on pneumococcal NPC acquisition, bacterial load, and ply and phtD gene sequencing were explored. RESULTS 1200 infants were enrolled between June 2011 and May 2012. Prevalences of pneumococcal (60-67%) and non-10VT (55-61%) NPC were high at baseline. Across all post-vaccination time points, efficacy of PHiD-CV/dPly/PhtD-10 and PHiD-CV/dPly/PhtD-30 against non-10VT NPC (3+0 schedule) was 1.1% (95% CI -21.5, 19.5) and 2.1% (-20.3, 20.3), respectively; efficacy of PHiD-CV/dPly/PhtD-30 (2+1 schedule) was 0.5% (-22.1, 18.9) versus PHiD-CV. No differences were observed in pneumococcal NPC acquisition, clearance, or bacterial load. Both protein-based vaccines elicited immune responses to pneumococcal proteins. CONCLUSIONS In this high carriage prevalence setting, inclusion of pneumococcal proteins in the PHiD-CV/dPly/PhtD investigational vaccine had no impact on pneumococcal NPC in infants, regardless of protein dose or schedule. Future evaluations will assess its impact against pneumococcal disease endpoints. FUNDING PATH, GlaxoSmithKline Biologicals SA. ClinicalTrials.gov identifier NCT01262872.
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Affiliation(s)
- Aderonke Odutola
- Medical Research Council Unit, Vaccines & Immunity Theme, Banjul, Gambia.
| | - Martin O C Ota
- Medical Research Council Unit, Vaccines & Immunity Theme, Banjul, Gambia.
| | - Martin Antonio
- Medical Research Council Unit, Vaccines & Immunity Theme, Banjul, Gambia.
| | - Ezra O Ogundare
- Medical Research Council Unit, Vaccines & Immunity Theme, Banjul, Gambia.
| | - Yauba Saidu
- Medical Research Council Unit, Vaccines & Immunity Theme, Banjul, Gambia.
| | | | - Patrick K Owiafe
- Medical Research Council Unit, Vaccines & Immunity Theme, Banjul, Gambia.
| | - Fatima Ceesay
- Medical Research Council Unit, Vaccines & Immunity Theme, Banjul, Gambia.
| | - Archibald Worwui
- Medical Research Council Unit, Vaccines & Immunity Theme, Banjul, Gambia.
| | - Olubukola T Idoko
- Medical Research Council Unit, Vaccines & Immunity Theme, Banjul, Gambia.
| | - Olumuyiwa Owolabi
- Medical Research Council Unit, Vaccines & Immunity Theme, Banjul, Gambia.
| | - Abdoulie Bojang
- Medical Research Council Unit, Vaccines & Immunity Theme, Banjul, Gambia.
| | - Sheikh Jarju
- Medical Research Council Unit, Vaccines & Immunity Theme, Banjul, Gambia.
| | - Isatou Drammeh
- Medical Research Council Unit, Vaccines & Immunity Theme, Banjul, Gambia.
| | - Beate Kampmann
- Medical Research Council Unit, Vaccines & Immunity Theme, Banjul, Gambia.
| | - Brian M Greenwood
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
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Heslop R, Bojang AL, Jarju S, Mendy J, Mulwa S, Secka O, Mendy FS, Owolabi O, Kampmann B, Sutherland JS. Changes in Host Cytokine Patterns of TB Patients with Different Bacterial Loads Detected Using 16S rRNA Analysis. PLoS One 2016; 11:e0168272. [PMID: 27992487 PMCID: PMC5161358 DOI: 10.1371/journal.pone.0168272] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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: 09/20/2016] [Accepted: 11/29/2016] [Indexed: 12/23/2022] Open
Abstract
Background Tuberculosis (TB) has overtaken HIV as the biggest infectious disease killer, with the majority of deaths occurring in sub-Saharan Africa. However it is unknown how differences in bacterial load alter host immune profiles in the sputum and blood of TB patients. Methods 16S ribosomal RNA analysis was used to determine bacterial load in sputum samples obtained from 173 patients with active TB (57 pre-treatment and 116 post-treatment). Host analyte concentrations in sputum and Mycobacterium tuberculosis (Mtb) antigen stimulated whole blood assay supernatants were analysed using multiplex cytokine arrays. Results Multiple logistic regression adjusting for age, sex and HIV status showed highly significant correlation of bacterial load with IL1β, IL2, IL1RA, IL4, IL6, IL8, IL9, IL15, IL17, EOTAX, FGF, IFN-γ, GCSF, MCP1, M1P1α, M1P1β, PDGF, TNFα, VEGF in sputum. With increasing time on treatment, FGF levels in sputum displayed the most significant inverse correlation with reduction in bacterial load. Conclusions We show that differences in bacterial load correlates with changes in several host biomarkers. These findings have implications for development of tests for TB diagnosis and treatment response.
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Affiliation(s)
- Rhiannon Heslop
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Banjul, The Gambia
- The University of Manchester, Oxford Rd, Manchester, United Kingdom
| | - Adama L. Bojang
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Banjul, The Gambia
| | - Sheikh Jarju
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Banjul, The Gambia
| | - Joseph Mendy
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Banjul, The Gambia
| | - Sarah Mulwa
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Banjul, The Gambia
| | - Ousman Secka
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Banjul, The Gambia
| | - Francis S. Mendy
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Banjul, The Gambia
| | - Olumuyiwa Owolabi
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Banjul, The Gambia
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Banjul, The Gambia
| | - Jayne S. Sutherland
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Banjul, The Gambia
- * E-mail:
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Liu J, Platts-Mills JA, Juma J, Kabir F, Nkeze J, Okoi C, Operario DJ, Uddin J, Ahmed S, Alonso PL, Antonio M, Becker SM, Blackwelder WC, Breiman RF, Faruque ASG, Fields B, Gratz J, Haque R, Hossain A, Hossain MJ, Jarju S, Qamar F, Iqbal NT, Kwambana B, Mandomando I, McMurry TL, Ochieng C, Ochieng JB, Ochieng M, Onyango C, Panchalingam S, Kalam A, Aziz F, Qureshi S, Ramamurthy T, Roberts JH, Saha D, Sow SO, Stroup SE, Sur D, Tamboura B, Taniuchi M, Tennant SM, Toema D, Wu Y, Zaidi A, Nataro JP, Kotloff KL, Levine MM, Houpt ER. Use of quantitative molecular diagnostic methods to identify causes of diarrhoea in children: a reanalysis of the GEMS case-control study. Lancet 2016; 388:1291-301. [PMID: 27673470 PMCID: PMC5471845 DOI: 10.1016/s0140-6736(16)31529-x] [Citation(s) in RCA: 539] [Impact Index Per Article: 67.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Diarrhoea is the second leading cause of mortality in children worldwide, but establishing the cause can be complicated by diverse diagnostic approaches and varying test characteristics. We used quantitative molecular diagnostic methods to reassess causes of diarrhoea in the Global Enteric Multicenter Study (GEMS). METHODS GEMS was a study of moderate to severe diarrhoea in children younger than 5 years in Africa and Asia. We used quantitative real-time PCR (qPCR) to test for 32 enteropathogens in stool samples from cases and matched asymptomatic controls from GEMS, and compared pathogen-specific attributable incidences with those found with the original GEMS microbiological methods, including culture, EIA, and reverse-transcriptase PCR. We calculated revised pathogen-specific burdens of disease and assessed causes in individual children. FINDINGS We analysed 5304 sample pairs. For most pathogens, incidence was greater with qPCR than with the original methods, particularly for adenovirus 40/41 (around five times), Shigella spp or enteroinvasive Escherichia coli (EIEC) and Campylobactor jejuni o C coli (around two times), and heat-stable enterotoxin-producing E coli ([ST-ETEC] around 1·5 times). The six most attributable pathogens became, in descending order, Shigella spp, rotavirus, adenovirus 40/41, ST-ETEC, Cryptosporidium spp, and Campylobacter spp. Pathogen-attributable diarrhoeal burden was 89·3% (95% CI 83·2-96·0) at the population level, compared with 51·5% (48·0-55·0) in the original GEMS analysis. The top six pathogens accounted for 77·8% (74·6-80·9) of all attributable diarrhoea. With use of model-derived quantitative cutoffs to assess individual diarrhoeal cases, 2254 (42·5%) of 5304 cases had one diarrhoea-associated pathogen detected and 2063 (38·9%) had two or more, with Shigella spp and rotavirus being the pathogens most strongly associated with diarrhoea in children with mixed infections. INTERPRETATION A quantitative molecular diagnostic approach improved population-level and case-level characterisation of the causes of diarrhoea and indicated a high burden of disease associated with six pathogens, for which targeted treatment should be prioritised. FUNDING Bill & Melinda Gates Foundation.
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Affiliation(s)
- Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Jane Juma
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Furqan Kabir
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Joseph Nkeze
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Darwin J Operario
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Jashim Uddin
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Shahnawaz Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Pedro L Alonso
- Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique; Barcelona Centre for International Health Research (CRESIB, Hospital Clinic-Universitat de Barcelona), Barcelona, Spain
| | | | - Stephen M Becker
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - William C Blackwelder
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Robert F Breiman
- Global Disease Detection Division, Kenya Office of the US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Abu S G Faruque
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Barry Fields
- Global Disease Detection Division, Kenya Office of the US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Anowar Hossain
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | | | - Sheikh Jarju
- Medical Research Council Unit, Banjul, The Gambia
| | - Farah Qamar
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Najeeha Talat Iqbal
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | | | - Timothy L McMurry
- Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Caroline Ochieng
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - John B Ochieng
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Melvin Ochieng
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Clayton Onyango
- Global Disease Detection Division, Kenya Office of the US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Sandra Panchalingam
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Adil Kalam
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Fatima Aziz
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Shahida Qureshi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - James H Roberts
- Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | | | - Samba O Sow
- Centre pour le Développement des Vaccins, Bamako, Mali
| | - Suzanne E Stroup
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Dipika Sur
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Sharon M Tennant
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Deanna Toema
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yukun Wu
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Anita Zaidi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - James P Nataro
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Karen L Kotloff
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Myron M Levine
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
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Foster-Nyarko E, Kwambana B, Aderonke O, Ceesay F, Jarju S, Bojang A, McLellan J, Jafali J, Kampmann B, Ota MO, Adetifa I, Antonio M. Associations between nasopharyngeal carriage of Group B Streptococcus and other respiratory pathogens during early infancy. BMC Microbiol 2016; 16:97. [PMID: 27230066 PMCID: PMC4882866 DOI: 10.1186/s12866-016-0714-7] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 05/19/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In West Africa, the carriage of Group B Streptococcus (GBS), among infants is poorly characterised. We investigated co-carriage of GBS with other respiratory pathogens in the infants' nasopharynx in The Gambia. METHODS We assessed the carriage, serotypes and antibiotic susceptibility of Beta-haemolytic Streptococci (BHS) groups A-G; along with the carriage of Streptococcus pneumoniae; Haemophilus influenzae; Staphylococcus aureus and Moraxella catarrhalis in 1200 two-month old infants. RESULTS The BHS prevalence was 20.0 % and GBS dominated (13.8 %), particularly serotypes V and II; serotype V being negatively associated with H. Influenzae carriage (OR 0.41 [95 % CI: 0.18-0.93], p = 0.033). Although co-colonization of GBS and other BHS was not seen, colonization with GBS was positively associated with S. aureus (OR 1.89 [95 % CI: 1.33-2.69], P < 0.001) and negatively associated with S. pneumoniae (OR 0.47 [95 % CI: 0.33-0.67], p < 0.001) and M. catarrhalis (OR 0.61 [95 % CI: 0.40-0.92], p = 0.017). ≥ 89 % of GBS isolates were susceptible to most antibiotics tested, except for tetracycline resistance, which was 89 %. CONCLUSION This study provides baseline data on the carriage of GBS in two month old infants from West Africa. The dominant serotypes of GBS in this setting are serotypes V and II. This may be important for future GBS vaccine development for the West African sub-region.
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Affiliation(s)
| | - Brenda Kwambana
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, The Gambia
| | - Odutola Aderonke
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, The Gambia
| | - Fatima Ceesay
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, The Gambia
| | - Sheikh Jarju
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, The Gambia
| | - Abdoulie Bojang
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, The Gambia
| | - Jessica McLellan
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, The Gambia
| | - James Jafali
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, The Gambia
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, The Gambia
| | - Martin O Ota
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, The Gambia
- Current Address: WHO Regional Office for Africa, Brazzaville, Congo
| | - Ifedayo Adetifa
- Disease Control and Elimination Theme, Medical Research Council Unit, Banjul, The Gambia
- Current Address: Infectious Diseases Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council Unit, Banjul, The Gambia.
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, UK.
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Sarr I, Jarju S, kebbeh N, Sey G, Saidykhan M, Thomas G, Secka F, Antonio M, Bojang K. The impact of pre-hospital antibiotics on blood culture yields in a low resource setting. Int J Infect Dis 2016. [DOI: 10.1016/j.ijid.2016.02.206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Ashu EE, Jarju S, Dione M, Mackenzie G, Ikumapayi UN, Manjang A, Azuine R, Antonio M. Population structure, epidemiology and antibiotic resistance patterns of Streptococcus pneumoniae serotype 5: prior to PCV-13 vaccine introduction in Eastern Gambia. BMC Infect Dis 2016; 16:33. [PMID: 26822883 PMCID: PMC4731921 DOI: 10.1186/s12879-016-1370-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 05/11/2015] [Accepted: 01/22/2016] [Indexed: 11/25/2022] Open
Abstract
Background Streptococcus pneumoniae serotype 5 is among the most common serotypes causing invasive pneumococcal disease (IPD) in The Gambia. We anticipate that introduction of the 13-valent pneumococcal conjugate vaccine (PCV-13) into routine vaccination in The Gambia will reduce serotype 5 IPD. However, the emergence of new clones that have altered their genetic repertoire through capsular switching or genetic recombination after vaccination with PCV-13 poses a threat to this public health effort. In order to monitor for potential genetic changes post-PCV-13 vaccination, we established the baseline population structure, epidemiology, and antibiotic resistance patterns of serotype 5 before the introduction of PCV-13. Methods Fifty-five invasive S. pneumoniae serotype 5 isolates were recovered from January 2009 to August 2011 in a population-based study in the Upper River Region of The Gambia. Serotyping was done by latex agglutination and confirmed by serotype-specific Polymerase Chain Reaction (PCR). Genotyping was undertaken using Multilocus Sequence Typing (MLST). Antimicrobial sensitivity was done using disc diffusion. Contingency table analyses were conducted using Pearson’s Chi2 and Fisher’s exact test. Clustering was performed using Bionumerics version 6.5. Results MLST resolved S. pneumoniae serotype 5 isolates into 3 sequence types (ST), namely ST 289(6/55), ST 3339(19/55) and ST 3404(30/55). ST 289 was identified as the major clonal complex. ST 3339, the prevalent genotype in 2009 [84.6 % (11/13)], was replaced by ST 3404 [70.4 % (19/27)] in 2010 as the dominant ST. Interestingly, ST 3404 showed lower resistance to tetracycline and oxacillin (P < 0.001), an empirical surrogate to penicillin in The Gambia. Conclusions There has been an emergence of ST 3404 in The Gambia prior to the introduction of PCV-13. Our findings provide important background data for future assessment of the impact of PCV-13 into routine immunization in developing countries, such as The Gambia.
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Affiliation(s)
- Eta E Ashu
- Department of Biology, McMaster University, 1280 Main St. W, Hamilton, ON, L8S 4 K1, Canada. .,Medical Research Council Unit, P. O. Box 273, Fajara, The Gambia.
| | - Sheikh Jarju
- Medical Research Council Unit, P. O. Box 273, Fajara, The Gambia
| | - Michel Dione
- Medical Research Council Unit, P. O. Box 273, Fajara, The Gambia
| | - Grant Mackenzie
- Medical Research Council Unit, P. O. Box 273, Fajara, The Gambia
| | | | - Ahmed Manjang
- Medical Research Council Unit, P. O. Box 273, Fajara, The Gambia.,King Fahad Medical City, Central, 11525, Saudi Arabia
| | - Romuladus Azuine
- Center for Global Health and Health Policy, Global Health and Education Projects, P. O. BOX 234, Riverdale, MD, 20738, USA
| | - Martin Antonio
- Medical Research Council Unit, P. O. Box 273, Fajara, The Gambia
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Usuf E, Badji H, Bojang A, Jarju S, Ikumapayi UN, Antonio M, Mackenzie G, Bottomley C. Pneumococcal carriage in rural Gambia prior to the introduction of pneumococcal conjugate vaccine: a population-based survey. Trop Med Int Health 2015; 20:871-9. [PMID: 25778937 DOI: 10.1111/tmi.12505] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To evaluate pneumococcal colonisation before and after the introduction of pneumococcal conjugate vaccine (PCV) in eastern Gambia. METHODS Population-based cross-sectional survey of pneumococcal carriage between May and August 2009 before the introduction of PCV into the Expanded Program on Immunization. Nasopharyngeal swabs were collected from all household members, but in selected households, only children aged 6-10 years were swabbed. This age group participated in an earlier trial of a nine-valent PCV between 2000 and 2004. RESULTS The prevalence of nasopharyngeal pneumococcal carriage in 2933 individuals was 72.0% in underfives (N = 515), 41.6% in children aged 5-17 (N = 1508) and 13.0% in adults ≥18 (N = 910) years. The age-specific prevalence of serotypes included in PCV7, PCV10 and PCV13 was 24.7%, 26.6% and 46.8% among children <5 years of age; 8.5%, 9.2% and 17.7% among children 5-17 years; and 2.5%, 3.3% and 5.5% among adults ≥18 years. The most common serotypes were 6A (13.1%), 23F (7.6%), 3 (7.3%), 19F (7.1%) and 34 (4.6%). There was no difference in the overall carriage of pneumococci between vaccinated and unvaccinated children 8 years after the primary vaccination with three doses of PCV (48.3% vs. 41.1%). CONCLUSION Before the introduction of PCV, serotypes included in PCV13 accounted for about half the pneumococcal serotypes in nasopharyngeal carriage. Thus, the potential impact of PCV13 on pneumococcal disease in the Gambia is substantial.
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Affiliation(s)
- Effua Usuf
- Medical Research Council Unit, Fajara, The Gambia
| | - Henry Badji
- Medical Research Council Unit, Fajara, The Gambia
| | | | - Sheikh Jarju
- Medical Research Council Unit, Fajara, The Gambia
| | | | - Martin Antonio
- Medical Research Council Unit, Fajara, The Gambia.,Microbiology and Infection Unit, University of Warwick, Coventry, UK.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Grant Mackenzie
- Medical Research Council Unit, Fajara, The Gambia.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.,Murdoch Children's Research Institute, Melbourne, Vic., Australia
| | - Christian Bottomley
- Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK
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van Tienen C, de Silva TI, Alcantara LCJ, Onyango CO, Jarju S, Gonçalves N, Vincent T, Aaby P, Whittle H, Schim van der Loeff M, Cotten M. Molecular epidemiology of endemic human T-lymphotropic virus type 1 in a rural community in Guinea-Bissau. PLoS Negl Trop Dis 2012; 6:e1690. [PMID: 22720106 PMCID: PMC3373628 DOI: 10.1371/journal.pntd.0001690] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [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: 08/29/2011] [Accepted: 05/01/2012] [Indexed: 11/19/2022] Open
Abstract
Background Human T-Lymphotropic Virus Type 1 (HTLV-1) infection causes lethal adult T-cell leukemia (ATL) and severely debilitating HTLV-associated myelopathy/tropical spastic paraparesis (HAM/TSP) in up to 5% of infected adults. HTLV-1 is endemic in parts of Africa and the highest prevalence in West Africa (5%) has been reported in Caio, a rural area in the North-West of Guinea-Bissau. It is not known which HTLV-1 variants are present in this community. Sequence data can provide insights in the molecular epidemiology and help to understand the origin and spread of HTLV-1. Objective To gain insight into the molecular diversity of HTLV-1 in West Africa. Methods HTLV-1 infected individuals were identified in community surveys between 1990–2007. The complete Long Terminal Repeat (LTR) and p24 coding region of HTLV-1 was sequenced from infected subjects. Socio-demographic data were obtained from community census and from interviews performed by fieldworkers. Phylogenetic analyses were performed to characterize the relationship between the Caio HTLV-1 and HTLV-1 from other parts of the world. Results LTR and p24 sequences were obtained from 72 individuals (36 LTR, 24 p24 only and 12 both). Consistent with the low evolutionary change of HTLV-1, many of the sequences from unrelated individuals showed 100% nucleotide identity. Most (45 of 46) of the LTR sequences clustered with the Cosmopolitan HTLV-1 subtype 1a, subgroup D (1aD). LTR and p24 sequences from two subjects were divergent and formed a significant cluster with HTLV-1 subtype 1g, and with the most divergent African Simian T-cell Lymphotropic Virus, Tan90. Conclusions The Cosmopolitan HTLV-1 1aD predominates in this rural West African community. However, HTLV-1 subtype 1g is also present. This subtype has not been described before in West Africa and may be more widespread than previously thought. These data are in line with the hypothesis that multiple monkey-to-man zoonotic events are contributing to HTLV-1 diversity. Human T-Lymphotropic Virus type 1 (HTLV-1) affects millions of people worldwide. It is very similar to Simian T-Lymphotropic Virus, a virus that circulates in monkeys. HTLV-1 causes a lethal form of leukemia (Adult T-cell Leukemia) and a debilitating neurological syndrome (HTLV-associated myelopathy/tropical spastic paraparesis) in approximately 5% of infected people. Based on sequence variation, HTLV-1 can be divided into 7 subtypes (1a–1g) with the Cosmopolitan subtype 1a further subdivided into subgroups (A–E). We examined HTLV-1 diversity in a rural area in Guinea-Bissau, a country in West Africa with a high HTLV-1 prevalence (5%). We found that most viruses belong to the Cosmopolitan subtype 1a, subgroup D, but 2 viruses belonged to subtype 1g. This subtype had thus far only been found in monkey hunters in Cameroon, who were probably recently infected by monkeys. Our findings indicate that this subtype has spread beyond Central Africa. An important, unresolved question is whether persons with this subtype were infected by monkeys or through human-to-human transmission.
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