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Mo Y, Ding Y, Cao Y, Hopkins J, Ashley EA, Waithira N, Wannapinij P, Lee SJ, Ling CL, Hamers RL, Roberts T, Lubell Y, Karkey A, Akech S, Lissauer S, Opintan J, Okeke I, Eremin S, Tornimbene B, Hsu LY, Thwaites L, Lam MY, Pham NT, Pham TK, Teo J, Kwa ALH, Marimuthu K, Ng OT, Vasoo S, Kitsaran S, Anunnatsiri S, Kosalaraksa P, Chotiprasitsakul D, Santanirand P, Plongla R, Chua HH, Tiong XT, Wong KJ, Ponnampalavanar SSLS, Sulaiman HB, Mazlan MZ, Salmuna ZN, Rajahram GS, Zaili MZBM, Francis JR, Sarmento N, Guterres H, Oakley T, Yan J, Tilman A, Khalid MOR, Hashmi M, Mahmood SF, Dhiloo AK, Fatima A, Lubis IND, Wijaya H, Abad CL, Roman AD, Lazarte CCM, Mamun GMS, Asli R, Momin MHFBHA, Nyamdavaa K, Gurjav U, Bory S, Varghese GM, Gupta L, Tantia P, Sinto R, Doi Y, Khanal B, Malijan G, Lazaro J, Gunasekara S, Withanage S, Liu PY, Xiao Y, Wang M, Paterson DL, van Doorn HR, Turner P. ACORN (A Clinically-Oriented Antimicrobial Resistance Surveillance Network) II: protocol for case based antimicrobial resistance surveillance. Wellcome Open Res 2023; 8:179. [PMID: 37854055 PMCID: PMC10579854 DOI: 10.12688/wellcomeopenres.19210.2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2023] [Indexed: 10/20/2023] Open
Abstract
Background: Antimicrobial resistance surveillance is essential for empiric antibiotic prescribing, infection prevention and control policies and to drive novel antibiotic discovery. However, most existing surveillance systems are isolate-based without supporting patient-based clinical data, and not widely implemented especially in low- and middle-income countries (LMICs). Methods: A Clinically-Oriented Antimicrobial Resistance Surveillance Network (ACORN) II is a large-scale multicentre protocol which builds on the WHO Global Antimicrobial Resistance and Use Surveillance System to estimate syndromic and pathogen outcomes along with associated health economic costs. ACORN-healthcare associated infection (ACORN-HAI) is an extension study which focuses on healthcare-associated bloodstream infections and ventilator-associated pneumonia. Our main aim is to implement an efficient clinically-oriented antimicrobial resistance surveillance system, which can be incorporated as part of routine workflow in hospitals in LMICs. These surveillance systems include hospitalised patients of any age with clinically compatible acute community-acquired or healthcare-associated bacterial infection syndromes, and who were prescribed parenteral antibiotics. Diagnostic stewardship activities will be implemented to optimise microbiology culture specimen collection practices. Basic patient characteristics, clinician diagnosis, empiric treatment, infection severity and risk factors for HAI are recorded on enrolment and during 28-day follow-up. An R Shiny application can be used offline and online for merging clinical and microbiology data, and generating collated reports to inform local antibiotic stewardship and infection control policies. Discussion: ACORN II is a comprehensive antimicrobial resistance surveillance activity which advocates pragmatic implementation and prioritises improving local diagnostic and antibiotic prescribing practices through patient-centred data collection. These data can be rapidly communicated to local physicians and infection prevention and control teams. Relative ease of data collection promotes sustainability and maximises participation and scalability. With ACORN-HAI as an example, ACORN II has the capacity to accommodate extensions to investigate further specific questions of interest.
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Affiliation(s)
- Yin Mo
- ADVANCE-ID, Saw Swee Hock School Of Public Health, National University of Singapore, Singapore, 117549, Singapore
- Division of Infectious Diseases, National University Hospital, Singapore, Singapore, 119074, Singapore
- Department of Medicine, National University of Singapore, Singapore, 119228, Singapore
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Ying Ding
- ADVANCE-ID, Saw Swee Hock School Of Public Health, National University of Singapore, Singapore, 117549, Singapore
| | - Yang Cao
- Singapore Clinical Research Institute, Singapore, 139234, Singapore
| | - Jill Hopkins
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, 171020, Cambodia
| | - Elizabeth A. Ashley
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Naomi Waithira
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Prapass Wannapinij
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Sue J. Lee
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Claire L. Ling
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, 171020, Cambodia
| | - Raph L. Hamers
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit (OUCRU) Indonesia, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Tamalee Roberts
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Yoel Lubell
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Abhilasha Karkey
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit (OUCRU) Indonesia, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Samuel Akech
- Kenya Medical Research Institute, Nairobi, Kenya
| | - Samantha Lissauer
- Liverpool School of Tropical Medicine (LSTM), University of Liverpool, Liverpool, England, UK
- Malawi-Liverpool-Wellcome Trust (MLW) Clinical Research Programme, Blantyre, Malawi
| | | | | | | | | | - Li Yang Hsu
- ADVANCE-ID, Saw Swee Hock School Of Public Health, National University of Singapore, Singapore, 117549, Singapore
| | - Louise Thwaites
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Minh Yen Lam
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | - Tieu Kieu Pham
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Jeanette Teo
- Department of laboratory Medicine, University Medicine Cluster, National University Hospital, Singapore, Singapore
| | - Andrea Lay-Hoon Kwa
- Pharmacy (Research), Singapore General Hospital, Singapore, Singapore
- Emerging Infectious Diseases Programme, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Kalisvar Marimuthu
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Disease, Tan Tock Seng Hospital, Singapore, Singapore
| | - Oon Tek Ng
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Disease, Tan Tock Seng Hospital, Singapore, Singapore
| | - Shawn Vasoo
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Disease, Tan Tock Seng Hospital, Singapore, Singapore
| | | | - Siriluck Anunnatsiri
- Department of Medicine, Faculty of Medicine, Khon Kaen University, Nai Mueang, Khon Kaen, Thailand
| | - Pope Kosalaraksa
- Department of Pediatrics, Faculty of Medicine, Khon Kaen University, Nai Mueang, Khon Kaen, Thailand
| | | | | | - Rongpong Plongla
- King Chulalongkorn Memorial Hospital, Chulalongkorn University, Bangkok, Thailand
| | | | | | - Ke Juin Wong
- Sabah Women and Children's Hospital, Kota Kinabalu, Malaysia
| | | | | | - Mohd Zulfakar Mazlan
- Department of Anesthesiology and Intensive Care, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Zeti Norfidiyati Salmuna
- Department of Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | | | | | - Joshua R. Francis
- Menzies school of health research, Charles Darwin University, Dili, Timor-Leste
| | - Nevio Sarmento
- Menzies school of health research, Charles Darwin University, Dili, Timor-Leste
- Laboratorio Nacional da Saude, Ministerio da Saude, Dili, Timor-Leste
| | | | - Tessa Oakley
- Menzies school of health research, Charles Darwin University, Dili, Timor-Leste
| | - Jennifer Yan
- Menzies school of health research, Charles Darwin University, Dili, Timor-Leste
| | - Ari Tilman
- Laboratorio Nacional da Saude, Ministerio da Saude, Dili, Timor-Leste
| | | | - Madiha Hashmi
- Dr. Ziauddin Hospital Clifton Campus, Karachi, Pakistan
| | | | | | | | - Inke Nadia D. Lubis
- Faculty of Medicine, Universitas Sumatera Utara, Medan, North Sumatra, Indonesia
| | - Hendri Wijaya
- Faculty of Medicine, Universitas Sumatera Utara, Medan, North Sumatra, Indonesia
- General Hospital H. Adam Malik, Medan, Indonesia
| | | | | | - Cecilia C. Maramba Lazarte
- Philippine General Hospital, Manila, Philippines
- University of the Philippines Manila, Manila, Metro Manila, Philippines
| | | | - Rosmonaliza Asli
- Raja Isteri Pengiran Anak Saleha Hospital, Bandar Seri Begawan, Brunei-Muara District, Brunei
| | | | | | - Ulziijargal Gurjav
- Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | | | | | - Lalit Gupta
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Pratik Tantia
- Ananta Institute of Medical Sciences and Research Center, Siyol, India
| | - Robert Sinto
- Cipto Mangunkusumo National Hospital, Faculty of Medicine, Universitas Indonesia, Depok, West Java, Indonesia
| | - Yohei Doi
- Fujita Health University Hospital, Toyoake, Japan
| | - Basudha Khanal
- B.P. Koirala Institute of Health Sciences, Dharan, Nepal
| | - Greco Malijan
- San Lazaro Hospital, Nagasaki University Collaborative Research Office, Manila, Philippines
| | - Jezreel Lazaro
- Hospital Infection Control Unit, San Lazaro Hospital, Manila, Philippines
| | | | | | - Po Yu Liu
- Taichung Veteran General Hospital, Taichung City, Vietnam
| | - Yonghong Xiao
- The First Affiliated Hospital Of Zhejiang University School Of Medicine, Hangzhou, China
| | - Minggui Wang
- Huashan Hospital, Fudan University, Shanghai, China
| | - David L. Paterson
- ADVANCE-ID, Saw Swee Hock School Of Public Health, National University of Singapore, Singapore, 117549, Singapore
- Department of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - H. Rogier van Doorn
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, 171020, Cambodia
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van Doorn HR, Miliya T, Douangnouvong A, Ta Thi Dieu N, Soputhy C, Lem M, Chommanam D, Keoluangkhot V, Soumphonphakdy B, Rassavong K, Thanadabouth K, Sayarath M, Chansamouth V, Vu MD, Dong PK, Dang VD, Tran VB, Do TKY, Ninh TN, Nguyen HL, Kim NH, Prak S, Vongsouvath M, Van DT, Nguyen TKT, Nguyen HK, Hamers RL, Ling C, Roberts T, Waithira N, Wannapinij P, Vu TVD, Celhay O, Ngoun C, Vongphachanh S, Pham NT, Ashley EA, Turner P. A Clinically Oriented antimicrobial Resistance surveillance Network (ACORN): pilot implementation in three countries in Southeast Asia, 2019-2020. Wellcome Open Res 2022; 7:309. [PMID: 37854668 PMCID: PMC10579863 DOI: 10.12688/wellcomeopenres.18317.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2022] [Indexed: 10/20/2023] Open
Abstract
Background: Case-based surveillance of antimicrobial resistance (AMR) provides more actionable data than isolate- or sample-based surveillance. We developed A Clinically Oriented antimicrobial Resistance surveillance Network (ACORN) as a lightweight but comprehensive platform, in which we combine clinical data collection with diagnostic stewardship, microbiological data collection and visualisation of the linked clinical-microbiology dataset. Data are compatible with WHO GLASS surveillance and can be stratified by syndrome and other metadata. Summary metrics can be visualised and fed back directly for clinical decision-making and to inform local treatment guidelines and national policy. Methods: An ACORN pilot was implemented in three hospitals in Southeast Asia (1 paediatric, 2 general) to collect clinical and microbiological data from patients with community- or hospital-acquired pneumonia, sepsis, or meningitis. The implementation package included tools to capture site and laboratory capacity information, guidelines on diagnostic stewardship, and a web-based data visualisation and analysis platform. Results: Between December 2019 and October 2020, 2294 patients were enrolled with 2464 discrete infection episodes (1786 community-acquired, 518 healthcare-associated and 160 hospital-acquired). Overall, 28-day mortality was 8.7%. Third generation cephalosporin resistance was identified in 54.2% (39/72) of E. coli and 38.7% (12/31) of K. pneumoniae isolates . Almost a quarter of S. aureus isolates were methicillin resistant (23.0%, 14/61). 290/2464 episodes could be linked to a pathogen, highlighting the level of enrolment required to achieve an acceptable volume of isolate data. However, the combination with clinical metadata allowed for more nuanced interpretation and immediate feedback of results. Conclusions: ACORN was technically feasible to implement and acceptable at site level. With minor changes from lessons learned during the pilot ACORN is now being scaled up and implemented in 15 hospitals in 9 low- and middle-income countries to generate sufficient case-based data to determine incidence, outcomes, and susceptibility of target pathogens among patients with infectious syndromes.
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Affiliation(s)
- H. Rogier van Doorn
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Univeristy of Oxford, Oxford, OX3 7LG, UK
- Oxford University Clinical Research Unit, Hanoi, Vietnam
| | - Thyl Miliya
- University of Oxford, Siem Reap, 171202, Cambodia
| | | | | | | | - Meymey Lem
- University of Oxford, Siem Reap, 171202, Cambodia
| | - Danoy Chommanam
- Laos Oxford Mahosot Wellcome Research Unit, Vientiane, Lao People's Democratic Republic
| | | | | | | | | | | | - Vilada Chansamouth
- Laos Oxford Mahosot Wellcome Research Unit, Vientiane, Lao People's Democratic Republic
- Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Minh Dien Vu
- National Hospital for Tropical Diseases, Hanoi, Vietnam
| | | | | | - Van Bac Tran
- National Hospital for Tropical Diseases, Hanoi, Vietnam
| | | | - Thi Ngoc Ninh
- National Hospital for Tropical Diseases, Hanoi, Vietnam
| | | | - Ngoc Hao Kim
- National Hospital for Tropical Diseases, Hanoi, Vietnam
| | - Sothea Prak
- University of Oxford, Siem Reap, 171202, Cambodia
| | - Manivanh Vongsouvath
- Laos Oxford Mahosot Wellcome Research Unit, Vientiane, Lao People's Democratic Republic
- Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | | | | | | | - Raph L. Hamers
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Univeristy of Oxford, Oxford, OX3 7LG, UK
- Oxford University Clinical Research Unit - Indonesia, Jakarta, Indonesia
| | - Clare Ling
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Univeristy of Oxford, Oxford, OX3 7LG, UK
- Shoklo Malaria Research Unit, Mae Sot, 63110, Thailand
| | - Tamalee Roberts
- Laos Oxford Mahosot Wellcome Research Unit, Vientiane, Lao People's Democratic Republic
| | - Naomi Waithira
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Univeristy of Oxford, Oxford, OX3 7LG, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, 10400, Thailand
| | - Prapass Wannapinij
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, 10400, Thailand
| | | | - Olivier Celhay
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, 10400, Thailand
| | | | | | | | - Elizabeth A. Ashley
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Univeristy of Oxford, Oxford, OX3 7LG, UK
- Laos Oxford Mahosot Wellcome Research Unit, Vientiane, Lao People's Democratic Republic
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Univeristy of Oxford, Oxford, OX3 7LG, UK
- University of Oxford, Siem Reap, 171202, Cambodia
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Murray CJL, Ikuta KS, Sharara F, Swetschinski L, Robles Aguilar G, Gray A, Han C, Bisignano C, Rao P, Wool E, Johnson SC, Browne AJ, Chipeta MG, Fell F, Hackett S, Haines-Woodhouse G, Kashef Hamadani BH, Kumaran EAP, McManigal B, Achalapong S, Agarwal R, Akech S, Albertson S, Amuasi J, Andrews J, Aravkin A, Ashley E, Babin FX, Bailey F, Baker S, Basnyat B, Bekker A, Bender R, Berkley JA, Bethou A, Bielicki J, Boonkasidecha S, Bukosia J, Carvalheiro C, Castañeda-Orjuela C, Chansamouth V, Chaurasia S, Chiurchiù S, Chowdhury F, Clotaire Donatien R, Cook AJ, Cooper B, Cressey TR, Criollo-Mora E, Cunningham M, Darboe S, Day NPJ, De Luca M, Dokova K, Dramowski A, Dunachie SJ, Duong Bich T, Eckmanns T, Eibach D, Emami A, Feasey N, Fisher-Pearson N, Forrest K, Garcia C, Garrett D, Gastmeier P, Giref AZ, Greer RC, Gupta V, Haller S, Haselbeck A, Hay SI, Holm M, Hopkins S, Hsia Y, Iregbu KC, Jacobs J, Jarovsky D, Javanmardi F, Jenney AWJ, Khorana M, Khusuwan S, Kissoon N, Kobeissi E, Kostyanev T, Krapp F, Krumkamp R, Kumar A, Kyu HH, Lim C, Lim K, Limmathurotsakul D, Loftus MJ, Lunn M, Ma J, Manoharan A, Marks F, May J, Mayxay M, Mturi N, Munera-Huertas T, Musicha P, Musila LA, Mussi-Pinhata MM, Naidu RN, Nakamura T, Nanavati R, Nangia S, Newton P, Ngoun C, Novotney A, Nwakanma D, Obiero CW, Ochoa TJ, Olivas-Martinez A, Olliaro P, Ooko E, Ortiz-Brizuela E, Ounchanum P, Pak GD, Paredes JL, Peleg AY, Perrone C, Phe T, Phommasone K, Plakkal N, Ponce-de-Leon A, Raad M, Ramdin T, Rattanavong S, Riddell A, Roberts T, Robotham JV, Roca A, Rosenthal VD, Rudd KE, Russell N, Sader HS, Saengchan W, Schnall J, Scott JAG, Seekaew S, Sharland M, Shivamallappa M, Sifuentes-Osornio J, Simpson AJ, Steenkeste N, Stewardson AJ, Stoeva T, Tasak N, Thaiprakong A, Thwaites G, Tigoi C, Turner C, Turner P, van Doorn HR, Velaphi S, Vongpradith A, Vongsouvath M, Vu H, Walsh T, Walson JL, Waner S, Wangrangsimakul T, Wannapinij P, Wozniak T, Young Sharma TEMW, Yu KC, Zheng P, Sartorius B, Lopez AD, Stergachis A, Moore C, Dolecek C, Naghavi M. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 2022; 399:629-655. [PMID: 35065702 PMCID: PMC8841637 DOI: 10.1016/s0140-6736(21)02724-0] [Citation(s) in RCA: 3962] [Impact Index Per Article: 1981.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/18/2021] [Accepted: 11/24/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND Antimicrobial resistance (AMR) poses a major threat to human health around the world. Previous publications have estimated the effect of AMR on incidence, deaths, hospital length of stay, and health-care costs for specific pathogen-drug combinations in select locations. To our knowledge, this study presents the most comprehensive estimates of AMR burden to date. METHODS We estimated deaths and disability-adjusted life-years (DALYs) attributable to and associated with bacterial AMR for 23 pathogens and 88 pathogen-drug combinations in 204 countries and territories in 2019. We obtained data from systematic literature reviews, hospital systems, surveillance systems, and other sources, covering 471 million individual records or isolates and 7585 study-location-years. We used predictive statistical modelling to produce estimates of AMR burden for all locations, including for locations with no data. Our approach can be divided into five broad components: number of deaths where infection played a role, proportion of infectious deaths attributable to a given infectious syndrome, proportion of infectious syndrome deaths attributable to a given pathogen, the percentage of a given pathogen resistant to an antibiotic of interest, and the excess risk of death or duration of an infection associated with this resistance. Using these components, we estimated disease burden based on two counterfactuals: deaths attributable to AMR (based on an alternative scenario in which all drug-resistant infections were replaced by drug-susceptible infections), and deaths associated with AMR (based on an alternative scenario in which all drug-resistant infections were replaced by no infection). We generated 95% uncertainty intervals (UIs) for final estimates as the 25th and 975th ordered values across 1000 posterior draws, and models were cross-validated for out-of-sample predictive validity. We present final estimates aggregated to the global and regional level. FINDINGS On the basis of our predictive statistical models, there were an estimated 4·95 million (3·62-6·57) deaths associated with bacterial AMR in 2019, including 1·27 million (95% UI 0·911-1·71) deaths attributable to bacterial AMR. At the regional level, we estimated the all-age death rate attributable to resistance to be highest in western sub-Saharan Africa, at 27·3 deaths per 100 000 (20·9-35·3), and lowest in Australasia, at 6·5 deaths (4·3-9·4) per 100 000. Lower respiratory infections accounted for more than 1·5 million deaths associated with resistance in 2019, making it the most burdensome infectious syndrome. The six leading pathogens for deaths associated with resistance (Escherichia coli, followed by Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa) were responsible for 929 000 (660 000-1 270 000) deaths attributable to AMR and 3·57 million (2·62-4·78) deaths associated with AMR in 2019. One pathogen-drug combination, meticillin-resistant S aureus, caused more than 100 000 deaths attributable to AMR in 2019, while six more each caused 50 000-100 000 deaths: multidrug-resistant excluding extensively drug-resistant tuberculosis, third-generation cephalosporin-resistant E coli, carbapenem-resistant A baumannii, fluoroquinolone-resistant E coli, carbapenem-resistant K pneumoniae, and third-generation cephalosporin-resistant K pneumoniae. INTERPRETATION To our knowledge, this study provides the first comprehensive assessment of the global burden of AMR, as well as an evaluation of the availability of data. AMR is a leading cause of death around the world, with the highest burdens in low-resource settings. Understanding the burden of AMR and the leading pathogen-drug combinations contributing to it is crucial to making informed and location-specific policy decisions, particularly about infection prevention and control programmes, access to essential antibiotics, and research and development of new vaccines and antibiotics. There are serious data gaps in many low-income settings, emphasising the need to expand microbiology laboratory capacity and data collection systems to improve our understanding of this important human health threat. FUNDING Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Health and Social Care using UK aid funding managed by the Fleming Fund.
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Turner P, Ashley EA, Celhay OJ, Douangnouvong A, Hamers RL, Ling CL, Lubell Y, Miliya T, Roberts T, Soputhy C, Ngoc Thach P, Vongsouvath M, Waithira N, Wannapinij P, van Doorn HR. ACORN (A Clinically-Oriented Antimicrobial Resistance Surveillance Network): a pilot protocol for case based antimicrobial resistance surveillance. Wellcome Open Res 2020; 5:13. [PMID: 32509968 PMCID: PMC7250055 DOI: 10.12688/wellcomeopenres.15681.2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2020] [Indexed: 11/20/2022] Open
Abstract
Background: Antimicrobial resistance (AMR) / drug resistant infections (DRIs) are a major global health priority. Surveillance data is critical to inform infection treatment guidelines, monitor trends, and to assess interventions. However, most existing AMR / DRI surveillance systems are passive and pathogen-based with many potential biases. Addition of clinical and patient outcome data would provide considerable added value to pathogen-based surveillance. Methods: The aim of the ACORN project is to develop an efficient clinically-oriented AMR surveillance system, implemented alongside routine clinical care in hospitals in low- and middle-income country settings. In an initial pilot phase, clinical and microbiology data will be collected from patients presenting with clinically suspected meningitis, pneumonia, or sepsis. Community-acquired infections will be identified by daily review of new admissions, and hospital-acquired infections will be enrolled during weekly point prevalence surveys, on surveillance wards. Clinical variables will be collected at enrolment, hospital discharge, and at day 28 post-enrolment using an electronic questionnaire on a mobile device. These data will be merged with laboratory data onsite using a flexible automated computer script. Specific target pathogens will be
Streptococcus pneumoniae, Staphylococcus aureus, Salmonella spp
., Klebsiella pneumoniae, Escherichia coli, and
Acinetobacter baumannii. A bespoke browser-based app will provide sites with fully interactive data visualisation, analysis, and reporting tools. Discussion: ACORN will generate data on the burden of DRI which can be used to inform local treatment guidelines / national policy and serve as indicators to measure the impact of interventions. Following development, testing and iteration of the surveillance tools during an initial six-month pilot phase, a wider rollout is planned.
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Affiliation(s)
- Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elizabeth A Ashley
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Olivier J Celhay
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Anousone Douangnouvong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Raph L Hamers
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Eijkman-Oxford Clinical Research Unit, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Clare L Ling
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Yoel Lubell
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Thyl Miliya
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Tamalee Roberts
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Chansovannara Soputhy
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | | | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Naomi Waithira
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Prapass Wannapinij
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - H Rogier van Doorn
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Clinical Research Unit, National Hospital for Tropical Diseases, Hanoi, Vietnam
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5
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Turner P, Ashley EA, Celhay OJ, Douangnouvong A, Hamers RL, Ling CL, Lubell Y, Miliya T, Roberts T, Soputhy C, Ngoc Thach P, Vongsouvath M, Waithira N, Wannapinij P, van Doorn HR. ACORN (A Clinically-Oriented Antimicrobial Resistance Surveillance Network): a pilot protocol for case based antimicrobial resistance surveillance. Wellcome Open Res 2020; 5:13. [PMID: 32509968 DOI: 10.12688/wellcomeopenres.15681.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2020] [Indexed: 12/13/2022] Open
Abstract
Background: Antimicrobial resistance (AMR) / drug resistant infections (DRIs) are a major global health priority. Surveillance data is critical to inform infection treatment guidelines, monitor trends, and to assess interventions. However, most existing AMR / DRI surveillance systems are passive and pathogen-based with many potential biases. Addition of clinical and patient outcome data would provide considerable added value to pathogen-based surveillance. Methods: The aim of the ACORN project is to develop an efficient clinically-oriented AMR surveillance system, implemented alongside routine clinical care in hospitals in low- and middle-income country settings. In an initial pilot phase, clinical and microbiology data will be collected from patients presenting with clinically suspected meningitis, pneumonia, or sepsis. Community-acquired infections will be identified by daily review of new admissions, and hospital-acquired infections will be enrolled during weekly point prevalence surveys, on surveillance wards. Clinical variables will be collected at enrolment, hospital discharge, and at day 28 post-enrolment using an electronic questionnaire on a mobile device. These data will be merged with laboratory data onsite using a flexible automated computer script. Specific target pathogens will be Streptococcus pneumoniae, Staphylococcus aureus, Salmonella spp ., Klebsiella pneumoniae, Escherichia coli, and Acinetobacter baumannii. A bespoke browser-based app will provide sites with fully interactive data visualisation, analysis, and reporting tools. Discussion: ACORN will generate data on the burden of DRI which can be used to inform local treatment guidelines / national policy and serve as indicators to measure the impact of interventions. Following development, testing and iteration of the surveillance tools during an initial six-month pilot phase, a wider rollout is planned.
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Affiliation(s)
- Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elizabeth A Ashley
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Olivier J Celhay
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Anousone Douangnouvong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Raph L Hamers
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Eijkman-Oxford Clinical Research Unit, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Clare L Ling
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Yoel Lubell
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Thyl Miliya
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Tamalee Roberts
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Chansovannara Soputhy
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | | | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Naomi Waithira
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Prapass Wannapinij
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - H Rogier van Doorn
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Clinical Research Unit, National Hospital for Tropical Diseases, Hanoi, Vietnam
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6
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Greer RC, Intralawan D, Mukaka M, Wannapinij P, Day NPJ, Nedsuwan S, Lubell Y. Retrospective review of the management of acute infections and the indications for antibiotic prescription in primary care in northern Thailand. BMJ Open 2018; 8:e022250. [PMID: 30061442 PMCID: PMC6067334 DOI: 10.1136/bmjopen-2018-022250] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
INTRODUCTION Antibiotic use in low-income and middle-income countries continues to rise despite the knowledge that antibiotic overuse can lead to antimicrobial resistance. There is a paucity of detailed data on the use of antibiotics in primary care in low-resource settings. OBJECTIVE To describe the presentation of acute infections and the indications for antibiotic prescription. DESIGN A 2-year retrospective review of routinely collected data. SETTING All 32 primary care units in one district in northern Thailand. PARTICIPANTS Patients attending primary care with a history of fever, documented temperature, International Statistical Classification of Diseases 10 code for infection or prescribed a systemic antibiotic. Patients attending after the initiation of a study on C-reactive protein testing in four centres were excluded. OUTCOME MEASURES The proportion of patients prescribed an antibiotic and the frequency of clinical presentations. RESULTS 762 868 patients attended the health centres, of whom 103 196 met the inclusion criteria, 5966 were excluded resulting in 97 230 attendances consisting of 83 661 illness episodes.46.9% (39 242) of the patients were prescribed an antibiotic during their illness. Indications for antibiotic prescription in the multivariable logistic regression analysis included male sex (adjusted OR (aOR) 1.21 (95% CI 1.16 to 1.28), p<0.001), adults (aOR 1.77 (95% CI 1.57 to 2), p<0.001) and a temperature >37.5°C (aOR 1.24 (95% CI 1.03 to 1.48), p=0.020). 77.9% of the presentations were for respiratory-related problems, of which 98.6% were upper respiratory tract infections. The leading infection diagnoses were common cold (50%), acute pharyngitis (18.9%) and acute tonsillitis (5%) which were prescribed antibiotics in 10.5%, 88.7% and 87.1% of cases, respectively. Amoxicillin was the most commonly prescribed antibiotic. CONCLUSIONS Nearly half of the patients received an antibiotic, the majority of whom had a respiratory infection. The results can be used to plan interventions to improve the rational use of antibiotics. Further studies in private facilities, pharmacies and dental clinics are required.
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Affiliation(s)
- Rachel C Greer
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daranee Intralawan
- Social and Preventive Medicine Department, Chiang Rai Regional Hospital, Chiang Rai, Thailand
| | - Mavuto Mukaka
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Prapass Wannapinij
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nicholas P J Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Supalert Nedsuwan
- Social and Preventive Medicine Department, Chiang Rai Regional Hospital, Chiang Rai, Thailand
| | - Yoel Lubell
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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7
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Hinjoy S, Hantrakun V, Kongyu S, Kaewrakmuk J, Wangrangsimakul T, Jitsuronk S, Saengchun W, Bhengsri S, Akarachotpong T, Thamthitiwat S, Sangwichian O, Anunnatsiri S, Sermswan RW, Lertmemongkolchai G, Sitthidet Tharinjaroen C, Preechasuth K, Udpaun R, Chuensombut P, Waranyasirikul N, Anudit C, Narenpitak S, Jutrakul Y, Teparrukkul P, Teerawattanasook N, Thanvisej K, Suphan A, Sukbut P, Ploddi K, Sirichotirat P, Chiewchanyon B, Rukseree K, Hongsuwan M, Wongsuwan G, Sunthornsut P, Wuthiekanun V, Sachaphimukh S, Wannapinij P, Chierakul W, Chewapreecha C, Thaipadungpanit J, Chantratita N, Korbsrisate S, Taunyok A, Dunachie S, Palittapongarnpim P, Sirisinha S, Kitphati R, Iamsirithaworn S, Chaowagul W, Chetchotisak P, Whistler T, Wongratanacheewin S, Limmathurotsakul D. Melioidosis in Thailand: Present and Future. Trop Med Infect Dis 2018; 3:38. [PMID: 29725623 PMCID: PMC5928800 DOI: 10.3390/tropicalmed3020038] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [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: 01/31/2018] [Accepted: 03/21/2018] [Indexed: 12/29/2022] Open
Abstract
A recent modelling study estimated that there are 2800 deaths due to melioidosis in Thailand yearly. The Thailand Melioidosis Network (formed in 2012) has been working closely with the Ministry of Public Health (MoPH) to investigate and reduce the burden of this disease. Based on updated data, the incidence of melioidosis is still high in Northeast Thailand. More than 2000 culture-confirmed cases of melioidosis are diagnosed in general hospitals with microbiology laboratories in this region each year. The mortality rate is around 35%. Melioidosis is endemic throughout Thailand, but it is still not uncommon that microbiological facilities misidentify Burkholderia pseudomallei as a contaminant or another organism. Disease awareness is low, and people in rural areas neither wear boots nor boil water before drinking to protect themselves from acquiring B. pseudomallei. Previously, about 10 melioidosis deaths were formally reported to the National Notifiable Disease Surveillance System (Report 506) each year, thus limiting priority setting by the MoPH. In 2015, the formally reported number of melioidosis deaths rose to 112, solely because Sunpasithiprasong Hospital, Ubon Ratchathani province, reported its own data (n = 107). Melioidosis is truly an important cause of death in Thailand, and currently reported cases (Report 506) and cases diagnosed at research centers reflect the tip of the iceberg. Laboratory training and communication between clinicians and laboratory personnel are required to improve diagnosis and treatment of melioidosis countrywide. Implementation of rapid diagnostic tests, such as a lateral flow antigen detection assay, with high accuracy even in melioidosis-endemic countries such as Thailand, is critically needed. Reporting of all culture-confirmed melioidosis cases from every hospital with a microbiology laboratory, together with final outcome data, is mandated under the Communicable Diseases Act B.E.2558. By enforcing this legislation, the MoPH could raise the priority of this disease, and should consider implementing a campaign to raise awareness and melioidosis prevention countrywide.
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Affiliation(s)
- Soawapak Hinjoy
- Bureau of Epidemiology, Department of Disease Control, Ministry of Public Health, Nonthaburi 11000, Thailand; (S.H.); (S.K.)
| | - Viriya Hantrakun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (V.H.); (T.W.); (M.H.); (G.W.); (P.S.); (V.W.); (S.S.); (P.W.); (W.C.); (C.C.); (J.T.); (N.C)
| | - Somkid Kongyu
- Bureau of Epidemiology, Department of Disease Control, Ministry of Public Health, Nonthaburi 11000, Thailand; (S.H.); (S.K.)
| | - Jedsada Kaewrakmuk
- Faculty of Science, Prince of Songkla University, Songkla 90110, Thailand;
| | - Tri Wangrangsimakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (V.H.); (T.W.); (M.H.); (G.W.); (P.S.); (V.W.); (S.S.); (P.W.); (W.C.); (C.C.); (J.T.); (N.C)
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK;
| | - Siroj Jitsuronk
- Faculty of Medicine, Prince of Songkla University, Songkla, 90110, Thailand;
| | - Weerawut Saengchun
- Department of Clinical Pathology, Chiang Rai Prachanukroh Hospital, Chiang Rai 57000, Thailand;
| | - Saithip Bhengsri
- Division of Global Health Protection, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi 11000, Thailand; (S.B.); (T.A.); (S.T.); (O.S.); (T.W.)
| | - Thantapat Akarachotpong
- Division of Global Health Protection, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi 11000, Thailand; (S.B.); (T.A.); (S.T.); (O.S.); (T.W.)
| | - Somsak Thamthitiwat
- Division of Global Health Protection, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi 11000, Thailand; (S.B.); (T.A.); (S.T.); (O.S.); (T.W.)
| | - Ornuma Sangwichian
- Division of Global Health Protection, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi 11000, Thailand; (S.B.); (T.A.); (S.T.); (O.S.); (T.W.)
| | - Siriluck Anunnatsiri
- Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (S.A.); (R.W.S.); (P.C.); (S.W.)
| | - Rasana W Sermswan
- Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (S.A.); (R.W.S.); (P.C.); (S.W.)
| | - Ganjana Lertmemongkolchai
- The Centre for Research & Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Chayada Sitthidet Tharinjaroen
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (C.S.T.); (K.P.); (R.U.)
| | - Kanya Preechasuth
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (C.S.T.); (K.P.); (R.U.)
| | - Ratchadaporn Udpaun
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (C.S.T.); (K.P.); (R.U.)
| | - Poomin Chuensombut
- Department of Clinical Pathology, Chiangkham Hospital, Phayao, 56110 Thailand;
| | - Nisarat Waranyasirikul
- Department of Clinical Pathology, Somdejphrajaotaksin Maharaj Hospital, Tak 63000, Thailand;
| | - Chanihcha Anudit
- Department of Clinical Pathology, Uthai Thani Hospital, Uthai Thani 61000, Thailand;
| | - Surapong Narenpitak
- Department of Internal Medicine, Udon Thani Hospital, Udon Thani 41000, Thailand;
| | - Yaowaruk Jutrakul
- Department of Clinical Pathology, Udon Thani Hospital, Udon Thani 41000, Thailand;
| | - Prapit Teparrukkul
- Department of Internal Medicine, Sunpasitthiprasong Hospital, Ubon Ratchathani 34000, Thailand; (P.T.); (W.C)
| | - Nittaya Teerawattanasook
- Department of Clinical Pathology, Sunpasitthiprasong Hospital, Ubon Ratchathani 34000, Thailand;
| | - Kittisak Thanvisej
- Department of Internal Medicine, Nakhon Panom Hospital, Nakhon Panom 48000, Thailand;
| | - Alisa Suphan
- Ubon Ratchathani Provincial Public Health Office, Ubon Ratchathani 34000, Thailand;
| | - Punchawee Sukbut
- Mukdahan Provincial Public Health Office, Mukdahan 49000, Thailand;
| | - Kritchavat Ploddi
- The Office of Disease Prevention and Control 8, Udon Thani 41000, Thailand;
| | - Poolsri Sirichotirat
- The Office of Disease Prevention and Control 10, Ubon Ratchathani 34000, Thailand;
| | | | | | - Maliwan Hongsuwan
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (V.H.); (T.W.); (M.H.); (G.W.); (P.S.); (V.W.); (S.S.); (P.W.); (W.C.); (C.C.); (J.T.); (N.C)
| | - Gumphol Wongsuwan
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (V.H.); (T.W.); (M.H.); (G.W.); (P.S.); (V.W.); (S.S.); (P.W.); (W.C.); (C.C.); (J.T.); (N.C)
| | - Pornpan Sunthornsut
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (V.H.); (T.W.); (M.H.); (G.W.); (P.S.); (V.W.); (S.S.); (P.W.); (W.C.); (C.C.); (J.T.); (N.C)
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (V.H.); (T.W.); (M.H.); (G.W.); (P.S.); (V.W.); (S.S.); (P.W.); (W.C.); (C.C.); (J.T.); (N.C)
| | - Sandy Sachaphimukh
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (V.H.); (T.W.); (M.H.); (G.W.); (P.S.); (V.W.); (S.S.); (P.W.); (W.C.); (C.C.); (J.T.); (N.C)
| | - Prapass Wannapinij
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (V.H.); (T.W.); (M.H.); (G.W.); (P.S.); (V.W.); (S.S.); (P.W.); (W.C.); (C.C.); (J.T.); (N.C)
| | - Wirongrong Chierakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (V.H.); (T.W.); (M.H.); (G.W.); (P.S.); (V.W.); (S.S.); (P.W.); (W.C.); (C.C.); (J.T.); (N.C)
| | - Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (V.H.); (T.W.); (M.H.); (G.W.); (P.S.); (V.W.); (S.S.); (P.W.); (W.C.); (C.C.); (J.T.); (N.C)
| | - Janjira Thaipadungpanit
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (V.H.); (T.W.); (M.H.); (G.W.); (P.S.); (V.W.); (S.S.); (P.W.); (W.C.); (C.C.); (J.T.); (N.C)
| | - Narisara Chantratita
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (V.H.); (T.W.); (M.H.); (G.W.); (P.S.); (V.W.); (S.S.); (P.W.); (W.C.); (C.C.); (J.T.); (N.C)
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Apichai Taunyok
- Department of Infectious Diseases & Immunology, Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA;
| | - Susanna Dunachie
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK;
| | - Prasit Palittapongarnpim
- National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand;
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
| | - Stitaya Sirisinha
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
| | - Rungrueng Kitphati
- Institute for Urban Disease Control and Prevention, Department of Disease Control, Ministry of Public Health, Bangkok 10220, Thailand;
| | - Sopon Iamsirithaworn
- Bureau of General Communicable Diseases, Department of Disease Control, Ministry of Public Health, Nonthaburi 11000, Thailand;
| | - Wipada Chaowagul
- Department of Internal Medicine, Sunpasitthiprasong Hospital, Ubon Ratchathani 34000, Thailand; (P.T.); (W.C)
| | - Ploenchan Chetchotisak
- Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (S.A.); (R.W.S.); (P.C.); (S.W.)
| | - Toni Whistler
- Division of Global Health Protection, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi 11000, Thailand; (S.B.); (T.A.); (S.T.); (O.S.); (T.W.)
| | | | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (V.H.); (T.W.); (M.H.); (G.W.); (P.S.); (V.W.); (S.S.); (P.W.); (W.C.); (C.C.); (J.T.); (N.C)
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK;
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8
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Lim C, Wannapinij P, White L, Day NPJ, Cooper BS, Peacock SJ, Limmathurotsakul D. Using a web-based application to define the accuracy of diagnostic tests when the gold standard is imperfect. PLoS One 2013; 8:e79489. [PMID: 24265775 PMCID: PMC3827152 DOI: 10.1371/journal.pone.0079489] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [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: 05/29/2013] [Accepted: 09/21/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Estimates of the sensitivity and specificity for new diagnostic tests based on evaluation against a known gold standard are imprecise when the accuracy of the gold standard is imperfect. Bayesian latent class models (LCMs) can be helpful under these circumstances, but the necessary analysis requires expertise in computational programming. Here, we describe open-access web-based applications that allow non-experts to apply Bayesian LCMs to their own data sets via a user-friendly interface. METHODS/PRINCIPAL FINDINGS Applications for Bayesian LCMs were constructed on a web server using R and WinBUGS programs. The models provided (http://mice.tropmedres.ac) include two Bayesian LCMs: the two-tests in two-population model (Hui and Walter model) and the three-tests in one-population model (Walter and Irwig model). Both models are available with simplified and advanced interfaces. In the former, all settings for Bayesian statistics are fixed as defaults. Users input their data set into a table provided on the webpage. Disease prevalence and accuracy of diagnostic tests are then estimated using the Bayesian LCM, and provided on the web page within a few minutes. With the advanced interfaces, experienced researchers can modify all settings in the models as needed. These settings include correlation among diagnostic test results and prior distributions for all unknown parameters. The web pages provide worked examples with both models using the original data sets presented by Hui and Walter in 1980, and by Walter and Irwig in 1988. We also illustrate the utility of the advanced interface using the Walter and Irwig model on a data set from a recent melioidosis study. The results obtained from the web-based applications were comparable to those published previously. CONCLUSIONS The newly developed web-based applications are open-access and provide an important new resource for researchers worldwide to evaluate new diagnostic tests.
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Affiliation(s)
- Cherry Lim
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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