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Smith AM, Erasmus LK, Tau NP, Smouse SL, Ngomane HM, Disenyeng B, Whitelaw A, Lawrence CA, Sekwadi P, Thomas J. Enteric fever cluster identification in South Africa using genomic surveillance of Salmonella enterica serovar Typhi. Microb Genom 2023; 9. [PMID: 37339282 DOI: 10.1099/mgen.0.001044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023] Open
Abstract
The National Institute for Communicable Diseases in South Africa participates in national laboratory-based surveillance for human isolates of Salmonella species. Laboratory analysis includes whole-genome sequencing (WGS) of isolates. We report on WGS-based surveillance of Salmonella enterica serovar Typhi (Salmonella Typhi) in South Africa from 2020 through 2021. We describe how WGS analysis identified clusters of enteric fever in the Western Cape Province of South Africa and describe the epidemiological investigations associated with these clusters. A total of 206 Salmonella Typhi isolates were received for analysis. Genomic DNA was isolated from bacteria and WGS was performed using Illumina NextSeq technology. WGS data were investigated using multiple bioinformatics tools, including those available at the Centre for Genomic Epidemiology, EnteroBase and Pathogenwatch. Core-genome multilocus sequence typing was used to investigate the phylogeny of isolates and identify clusters. Three major clusters of enteric fever were identified in the Western Cape Province; cluster one (n=11 isolates), cluster two (n=13 isolates), and cluster three (n=14 isolates). To date, no likely source has been identified for any of the clusters. All isolates associated with the clusters, showed the same genotype (4.3.1.1.EA1) and resistome (antimicrobial resistance genes: bla TEM-1B, catA1, sul1, sul2, dfrA7). The implementation of genomic surveillance of Salmonella Typhi in South Africa has enabled rapid detection of clusters indicative of possible outbreaks. Cluster identification allows for targeted epidemiological investigations and a timely, coordinated public health response.
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Affiliation(s)
- Anthony Marius Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Linda Kathleen Erasmus
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nomsa Pauline Tau
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Shannon Lucrecia Smouse
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Hlengiwe Mimmy Ngomane
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Bolele Disenyeng
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Andrew Whitelaw
- Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Charlene Ann Lawrence
- Communicable Disease Control, Service Priorities Coordination, Department of Health, Cape Town, South Africa
| | - Phuti Sekwadi
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Juno Thomas
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
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Quaresma AJPG, Rodrigues YC, Aboim JB, Bezerra MM, Gouveia MIM, Da Costa ARF, de Oliveira Souza C, Bastos FC, Lima LNGC, de Paula Ramos FL, Valéria Batista Lima K. Molecular Epidemiology of Sporadic and Outbreak-Related Salmonella Typhi Isolates in the Brazilian North Region: A Retrospective Analysis from 1995 to 2013. Infect Dis Rep 2022; 14:569-573. [PMID: 36005262 PMCID: PMC9408587 DOI: 10.3390/idr14040060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 02/04/2023] Open
Abstract
Typhoidal salmonellosis is a global public health problem occurring in developing endemic regions. In Brazil, cases are mostly registered in the North and Northeast regions. Molecular characterization of the strains is important to understand the epidemiology of disease infections and to design control strategies. The present study retrospectively evaluates the genotyping features of sporadic and outbreak-related Salmonella Typhi isolates from the Brazilian North region. Bacterial isolates were recovered from blood and a rectal swab of patients in the states of Acre and Pará, Brazilian North region, in the period of 1995 to 2013, and were submitted to genotyping by applying Multilocus sequence typing (MLST) and Pulsed Field Gel Electrophoresis (PFGE) reference methods. MLST genotyping revealed the presence of epidemic clones ST1 and ST2, and 20 pulsotypes were identified by PFGE, including four distinct clusters (A–D), and six subclusters (A1–D1) with indistinguishable strains in different periods and locations. To conclude, the obtained data demonstrates the temporal stability, adaptation, and transmission of outbreak-related and sporadic S. Typhi strains over time, contributing to the transmission chain in the region.
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Affiliation(s)
- Ana Judith Pires Garcia Quaresma
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Health Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (A.J.P.G.Q.); (Y.C.R.); (J.B.A.); (M.M.B.); (M.I.M.G.); (A.R.F.D.C.); (C.d.O.S.); (F.C.B.); (L.N.G.C.L.)
- Ph.D. Program in Parasitic Biology in the Amazon Region (PPGBPA), State University of Pará (UEPA), Tv. Perebebuí, 2623-Marco, Belém 66087-662, PA, Brazil
| | - Yan Corrêa Rodrigues
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Health Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (A.J.P.G.Q.); (Y.C.R.); (J.B.A.); (M.M.B.); (M.I.M.G.); (A.R.F.D.C.); (C.d.O.S.); (F.C.B.); (L.N.G.C.L.)
| | - Joseline Barbosa Aboim
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Health Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (A.J.P.G.Q.); (Y.C.R.); (J.B.A.); (M.M.B.); (M.I.M.G.); (A.R.F.D.C.); (C.d.O.S.); (F.C.B.); (L.N.G.C.L.)
| | - Mayza Miranda Bezerra
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Health Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (A.J.P.G.Q.); (Y.C.R.); (J.B.A.); (M.M.B.); (M.I.M.G.); (A.R.F.D.C.); (C.d.O.S.); (F.C.B.); (L.N.G.C.L.)
| | - Maria Isabel Montoril Gouveia
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Health Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (A.J.P.G.Q.); (Y.C.R.); (J.B.A.); (M.M.B.); (M.I.M.G.); (A.R.F.D.C.); (C.d.O.S.); (F.C.B.); (L.N.G.C.L.)
| | - Ana Roberta Fusco Da Costa
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Health Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (A.J.P.G.Q.); (Y.C.R.); (J.B.A.); (M.M.B.); (M.I.M.G.); (A.R.F.D.C.); (C.d.O.S.); (F.C.B.); (L.N.G.C.L.)
| | - Cintya de Oliveira Souza
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Health Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (A.J.P.G.Q.); (Y.C.R.); (J.B.A.); (M.M.B.); (M.I.M.G.); (A.R.F.D.C.); (C.d.O.S.); (F.C.B.); (L.N.G.C.L.)
| | - Flávia Corrêa Bastos
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Health Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (A.J.P.G.Q.); (Y.C.R.); (J.B.A.); (M.M.B.); (M.I.M.G.); (A.R.F.D.C.); (C.d.O.S.); (F.C.B.); (L.N.G.C.L.)
| | - Luana Nepomuceno Gondim Costa Lima
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Health Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (A.J.P.G.Q.); (Y.C.R.); (J.B.A.); (M.M.B.); (M.I.M.G.); (A.R.F.D.C.); (C.d.O.S.); (F.C.B.); (L.N.G.C.L.)
- Ph.D. Program in Parasitic Biology in the Amazon Region (PPGBPA), State University of Pará (UEPA), Tv. Perebebuí, 2623-Marco, Belém 66087-662, PA, Brazil
| | - Francisco Lúzio de Paula Ramos
- Evandro Chagas Institute (SABMI/IEC), Health Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil;
| | - Karla Valéria Batista Lima
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Health Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (A.J.P.G.Q.); (Y.C.R.); (J.B.A.); (M.M.B.); (M.I.M.G.); (A.R.F.D.C.); (C.d.O.S.); (F.C.B.); (L.N.G.C.L.)
- Ph.D. Program in Parasitic Biology in the Amazon Region (PPGBPA), State University of Pará (UEPA), Tv. Perebebuí, 2623-Marco, Belém 66087-662, PA, Brazil
- Correspondence:
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Kaewprasert O, Tongsima S, Ong RTH, Faksri K. Optimized analysis parameters of variant calling for whole genome-based phylogeny of Mycobacteroides abscessus. Arch Microbiol 2022; 204:190. [PMID: 35194683 DOI: 10.1007/s00203-022-02792-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/17/2022] [Accepted: 02/04/2022] [Indexed: 02/05/2023]
Abstract
Whole-genome sequence (WGS) analysis provides the best resolution for reconstructing bacterial phylogeny. However, the resulting tree could vary according to parameters used in the WGS pipeline, making it difficult to compare results across multiple studies. This study compares effects on phylogenies when applying different parameter stringencies. We used as the study model to optimize parameters strains of Mycobacteroides abscessus serially isolated at various intervals, isolates known to represent persistent infection (PI) cases or re-infection (RI) cases and isolates from different subspecies. Un-optimized parameters with low stringency provided an excessive number of SNPs (823) compared to the optimized setting (3 SNPs) between paired strains isolated 1 day apart from PI cases, discordant tree topology and misclassification of subspecies and of instances of RI. We demonstrated that using high-quality variants provides more accuracy for recognizing serial isolates of the same clone versus different clones and for phylogenetic analysis of M. abscessus. Our approach might be used as a model for analyses requiring phylogenetic reconstruction of other bacteria.
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Affiliation(s)
- Orawee Kaewprasert
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Sissades Tongsima
- National Biobank of Thailand, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
- National Center for Genetics Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand.
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Fernandes SA, Tavechio AT, Ghilardi ÂCR, Almeida EAD, Silva JMLD, Camargo CH, Tiba-Casas MR. Salmonella enterica serotypes from human and nonhuman sources in Sao Paulo State, Brazil, 2004-2020. Rev Inst Med Trop Sao Paulo 2022; 64:e66. [PMID: 36197427 PMCID: PMC9528755 DOI: 10.1590/s1678-9946202264066] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/09/2022] [Indexed: 11/21/2022] Open
Abstract
Salmonellosis ranks among the most frequently reported zoonosis worldwide and is often associated with foodborne outbreaks. Since the 1950s, the distribution of Salmonella serotypes in Sao Paulo State, Brazil, has been documented and periodically reported. In this study, we updated the data on the distribution of Salmonella serotypes received in our reference laboratory, isolated from human infections and nonhuman sources, from 2004 to 2020. In that period, a total of 9,014 Salmonella isolates were analyzed, of which 3,553 (39.4%) were recovered from human samples, mainly of stool (65%) and blood (25.6%), and 5,461 (60.6%) were isolated from nonhuman origins, such as animals (47.2%), food (27.7%) and animal environments (18.6%). In human isolates, a total of 104 serotypes were identified and the most frequent ones were Enteritidis, Typhimurium, S . I. 4,[5],12:i:-, Dublin and Typhi. A consistent reduction of the Enteritidis proportion was observed over the years. Among the 156 serotypes identified in isolates with nonhuman origins, Enteritidis, Mbandaka, Typhimurium, Agona and Anatum were ranked as the top five Salmonella serotypes; in more recent years, S . Heidelberg has increased in frequency. Although with different proportions, the top 10 prevalent serotypes were identified in both human and nonhuman origins, underscoring the role of animals, food products and environment as reservoirs of Salmonella with potential to cause human salmonellosis.
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Yan S, Zhang W, Li C, Liu X, Zhu L, Chen L, Yang B. Serotyping, MLST, and Core Genome MLST Analysis of Salmonella enterica From Different Sources in China During 2004-2019. Front Microbiol 2021; 12:688614. [PMID: 34603224 PMCID: PMC8481815 DOI: 10.3389/fmicb.2021.688614] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/11/2021] [Indexed: 01/01/2023] Open
Abstract
Salmonella enterica (S. enterica) is an important foodborne pathogen, causing food poisoning and human infection, and critically threatening food safety and public health. Salmonella typing is essential for bacterial identification, tracing, epidemiological investigation, and monitoring. Serotyping and multilocus sequence typing (MLST) analysis are standard bacterial typing methods despite the low resolution. Core genome MLST (cgMLST) is a high-resolution molecular typing method based on whole genomic sequencing for accurate bacterial tracing. We investigated 250 S. enterica isolates from poultry, livestock, food, and human sources in nine provinces of China from 2004 to 2019 using serotyping, MLST, and cgMLST analysis. All S. enterica isolates were divided into 36 serovars using slide agglutination. The major serovars in order were Enteritidis (31 isolates), Typhimurium (29 isolates), Mbandaka (23 isolates), and Indiana (22 isolates). All strains were assigned into 43 sequence types (STs) by MLST. Among them, ST11 (31 isolates) was the primary ST. Besides this, a novel ST, ST8016, was identified, and it was different from ST40 by position 317 C → T in dnaN. Furthermore, these 250 isolates were grouped into 185 cgMLST sequence types (cgSTs) by cgMLST. The major cgST was cgST235530 (11 isolates), and only three cgSTs contained isolates from human and other sources, indicating a possibility of cross-species infection. Phylogenetic analysis indicated that most of the same serovar strains were putatively homologous except Saintpaul and Derby due to their multilineage characteristics. In addition, serovar I 4,[5],12:i:- and Typhimurium isolates have similar genomic relatedness on the phylogenetic tree. In conclusion, we sorted out the phenotyping and genotyping diversity of S. enterica isolates in China during 2004-2019 and clarified the temporal and spatial distribution characteristics of Salmonella from different hosts in China in the recent 16 years. These results greatly supplement Salmonella strain resources, genetic information, and traceability typing data; facilitate the typing, traceability, identification, and genetic evolution analysis of Salmonella; and therefore, improve the level of analysis, monitoring, and controlling of foodborne microorganisms in China.
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Affiliation(s)
- Shigan Yan
- Shandong Provincial Key Laboratory of Bioengineering, School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Wencheng Zhang
- Shandong Provincial Key Laboratory of Bioengineering, School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Chengyu Li
- Shandong Provincial Key Laboratory of Bioengineering, School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Xu Liu
- Shandong Provincial Key Laboratory of Bioengineering, School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Liping Zhu
- Shandong Provincial Key Laboratory of Bioengineering, School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Leilei Chen
- Institute of Agro-Food Sciences and Technology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Baowei Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
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Guevara PD, Maes M, Thanh DP, Duarte C, Rodriguez EC, Montaño LA, Dan THN, Nguyen TNT, Carey ME, Campos J, Chinen I, Perez E, Baker S. A genomic snapshot of Salmonella enterica serovar Typhi in Colombia. PLoS Negl Trop Dis 2021; 15:e0009755. [PMID: 34529660 PMCID: PMC8478212 DOI: 10.1371/journal.pntd.0009755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 09/28/2021] [Accepted: 08/24/2021] [Indexed: 11/23/2022] Open
Abstract
Little is known about the genetic diversity of Salmonella enterica serovar Typhi (S. Typhi) circulating in Latin America. It has been observed that typhoid fever is still endemic in this part of the world; however, a lack of standardized blood culture surveillance across Latin American makes estimating the true disease burden problematic. The Colombian National Health Service established a surveillance system for tracking bacterial pathogens, including S. Typhi, in 2006. Here, we characterized 77 representative Colombian S. Typhi isolates collected between 1997 and 2018 using pulse field gel electrophoresis (PFGE; the accepted genotyping method in Latin America) and whole genome sequencing (WGS). We found that the main S. Typhi clades circulating in Colombia were clades 2.5 and 3.5. Notably, the sequenced S. Typhi isolates from Colombia were closely related in a global phylogeny. Consequently, these data suggest that these are endemic clades circulating in Colombia. We found that AMR in S. Typhi in Colombia was uncommon, with a small subset of organisms exhibiting mutations associated with reduced susceptibility to fluoroquinolones. This is the first time that S. Typhi isolated from Colombia have been characterized by WGS, and after comparing these data with those generated using PFGE, we conclude that PFGE is unsuitable for tracking S. Typhi clones and mapping transmission. The genetic diversity of pathogens such as S. Typhi is limited in Latin America and should be targeted for future surveillance studies incorporating WGS.
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Affiliation(s)
| | - Mailis Maes
- University of Cambridge School of Clinical Medicine Department of Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Level 5 Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, United Kingdom
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Carolina Duarte
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | | | | | - Thanh Ho Ngoc Dan
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - To Nguyen Thi Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Megan E. Carey
- University of Cambridge School of Clinical Medicine Department of Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Level 5 Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, United Kingdom
| | - Josefina Campos
- Red Pulsenet Latinoamérica y el Caribe, INEI-ANLIS “Dr Carlos Malbran, Buenos Aires, Argentina
| | - Isabel Chinen
- Red Pulsenet Latinoamérica y el Caribe, INEI-ANLIS “Dr Carlos Malbran, Buenos Aires, Argentina
| | - Enrique Perez
- Health Emergencies Department, Pan American Health Organization/World Health Organization, PAHO/WHO, Washington DC, United States of America
| | - Stephen Baker
- University of Cambridge School of Clinical Medicine Department of Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Level 5 Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, United Kingdom
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