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Browne AJ, Chipeta MG, Fell FJ, Haines-Woodhouse G, Kashef Hamadani BH, Kumaran EAP, Robles Aguilar G, McManigal B, Andrews JR, Ashley EA, Audi A, Baker S, Banda HC, Basnyat B, Bigogo G, Ngoun C, Chansamouth V, Chunga A, Clemens JD, Davong V, Dougan G, Dunachie SJ, Feasey NA, Garrett DO, Gordon MA, Hasan R, Haselbeck AH, Henry NJ, Heyderman RS, Holm M, Jeon HJ, Karkey A, Khanam F, Luby SP, Malik FR, Marks F, Mayxay M, Meiring JE, Moore CE, Munywoki PK, Musicha P, Newton PN, Pak G, Phommasone K, Pokharel S, Pollard AJ, Qadri F, Qamar FN, Rattanavong S, Reiner B, Roberts T, Saha S, Saha S, Shakoor S, Shakya M, Simpson AJ, Stanaway J, Turner C, Turner P, Verani JR, Vongsouvath M, Day NPJ, Naghavi M, Hay SI, Sartorius B, Dolecek C. Estimating the subnational prevalence of antimicrobial resistant Salmonella enterica serovars Typhi and Paratyphi A infections in 75 endemic countries, 1990-2019: a modelling study. Lancet Glob Health 2024; 12:e406-e418. [PMID: 38365414 PMCID: PMC10882211 DOI: 10.1016/s2214-109x(23)00585-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 11/19/2023] [Accepted: 12/04/2023] [Indexed: 02/18/2024]
Abstract
BACKGROUND Enteric fever, a systemic infection caused by Salmonella enterica serovars Typhi and Paratyphi A, remains a major cause of morbidity and mortality in low-income and middle-income countries. Enteric fever is preventable through the provision of clean water and adequate sanitation and can be successfully treated with antibiotics. However, high levels of antimicrobial resistance (AMR) compromise the effectiveness of treatment. We provide estimates of the prevalence of AMR S Typhi and S Paratyphi A in 75 endemic countries, including 30 locations without data. METHODS We used a Bayesian spatiotemporal modelling framework to estimate the percentage of multidrug resistance (MDR), fluoroquinolone non-susceptibility (FQNS), and third-generation cephalosporin resistance in S Typhi and S Paratyphi A infections for 1403 administrative level one districts in 75 endemic countries from 1990 to 2019. We incorporated data from a comprehensive systematic review, public health surveillance networks, and large multicountry studies on enteric fever. Estimates of the prevalence of AMR and the number of AMR infections (based on enteric fever incidence estimates by the Global Burden of Diseases study) were produced at the country, super-region, and total endemic area level for each year of the study. FINDINGS We collated data from 601 sources, comprising 184 225 isolates of S Typhi and S Paratyphi A, covering 45 countries over 30 years. We identified a decline of MDR S Typhi in south Asia and southeast Asia, whereas in sub-Saharan Africa, the overall prevalence increased from 6·0% (95% uncertainty interval 4·3-8·0) in 1990 to 72·7% (67·7-77·3) in 2019. Starting from low levels in 1990, the prevalence of FQNS S Typhi increased rapidly, reaching 95·2% (91·4-97·7) in south Asia in 2019. This corresponded to 2·5 million (1·5-3·8) MDR S Typhi infections and 7·4 million (4·7-11·3) FQNS S Typhi infections in endemic countries in 2019. The prevalence of third-generation cephalosporin-resistant S Typhi remained low across the whole endemic area over the study period, except for Pakistan where prevalence of third-generation cephalosporin resistance in S Typhi reached 61·0% (58·0-63·8) in 2019. For S Paratyphi A, we estimated low prevalence of MDR and third-generation cephalosporin resistance in all endemic countries, but a drastic increase of FQNS, which reached 95·0% (93·7-96·1; 3·5 million [2·2-5·6] infections) in 2019. INTERPRETATION This study provides a comprehensive and detailed analysis of the prevalence of MDR, FQNS, and third-generation cephalosporin resistance in S Typhi and S Paratyphi A infections in endemic countries, spanning the last 30 years. Our analysis highlights the increasing levels of AMR in this preventable infection and serves as a resource to guide urgently needed public health interventions, such as improvements in water, sanitation, and hygiene and typhoid fever vaccination campaigns. FUNDING Fleming Fund, UK Department of Health and Social Care; Wellcome Trust; and Bill and Melinda Gates Foundation.
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Carey ME, Dyson ZA, Ingle DJ, Amir A, Aworh MK, Chattaway MA, Chew KL, Crump JA, Feasey NA, Howden BP, Keddy KH, Maes M, Parry CM, Van Puyvelde S, Webb HE, Afolayan AO, Alexander AP, Anandan S, Andrews JR, Ashton PM, Basnyat B, Bavdekar A, Bogoch II, Clemens JD, da Silva KE, De A, de Ligt J, Diaz Guevara PL, Dolecek C, Dutta S, Ehlers MM, Francois Watkins L, Garrett DO, Godbole G, Gordon MA, Greenhill AR, Griffin C, Gupta M, Hendriksen RS, Heyderman RS, Hooda Y, Hormazabal JC, Ikhimiukor OO, Iqbal J, Jacob JJ, Jenkins C, Jinka DR, John J, Kang G, Kanteh A, Kapil A, Karkey A, Kariuki S, Kingsley RA, Koshy RM, Lauer AC, Levine MM, Lingegowda RK, Luby SP, Mackenzie GA, Mashe T, Msefula C, Mutreja A, Nagaraj G, Nagaraj S, Nair S, Naseri TK, Nimarota-Brown S, Njamkepo E, Okeke IN, Perumal SPB, Pollard AJ, Pragasam AK, Qadri F, Qamar FN, Rahman SIA, Rambocus SD, Rasko DA, Ray P, Robins-Browne R, Rongsen-Chandola T, Rutanga JP, Saha SK, Saha S, Saigal K, Sajib MSI, Seidman JC, Shakya J, Shamanna V, Shastri J, Shrestha R, Sia S, Sikorski MJ, Singh A, Smith AM, Tagg KA, Tamrakar D, Tanmoy AM, Thomas M, Thomas MS, Thomsen R, Thomson NR, Tupua S, Vaidya K, Valcanis M, Veeraraghavan B, Weill FX, Wright J, Dougan G, Argimón S, Keane JA, Aanensen DM, Baker S, Holt KE. Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes. eLife 2023; 12:e85867. [PMID: 37697804 PMCID: PMC10506625 DOI: 10.7554/elife.85867] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 08/02/2023] [Indexed: 09/13/2023] Open
Abstract
Background The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). Methods This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. Results Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. Conclusions The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. Funding No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]).
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Affiliation(s)
- Megan E Carey
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- IAVI, Chelsea & Westminster HospitalLondonUnited Kingdom
| | - Zoe A Dyson
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash UniversityMelbourneAustralia
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Danielle J Ingle
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of MelbourneMelbourneAustralia
| | | | - Mabel K Aworh
- Nigeria Field Epidemiology and Laboratory Training ProgrammeAbujaNigeria
- College of Veterinary Medicine, North Carolina State UniversityRaleighUnited States
| | | | - Ka Lip Chew
- National University HospitalSingaporeSingapore
| | - John A Crump
- Centre for International Health, University of OtagoDunedinNew Zealand
| | - Nicholas A Feasey
- Department of Clinical Sciences, Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
- Malawi-Liverpool Wellcome Programme, Kamuzu University of Health SciencesBlantyreMalawi
| | - Benjamin P Howden
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, University of Melbourne at Doherty Institute for Infection and ImmunityMelbourneAustralia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Christopher M Parry
- Department of Clinical Sciences, Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
| | - Sandra Van Puyvelde
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- University of AntwerpAntwerpBelgium
| | - Hattie E Webb
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Ayorinde Oluwatobiloba Afolayan
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | - Shalini Anandan
- Department of Clinical Microbiology, Christian Medical CollegeVelloreIndia
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Philip M Ashton
- Malawi-Liverpool Wellcome ProgrammeBlantyreMalawi
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Buddha Basnyat
- Oxford University Clinical Research Unit NepalKathmanduNepal
| | | | - Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of TorontoTorontoCanada
| | - John D Clemens
- International Vaccine InstituteSeoulRepublic of Korea
- International Centre for Diarrhoeal Disease ResearchDhakaBangladesh
- UCLA Fielding School of Public HealthLos AngelesUnited States
- Korea UniversitySeoulRepublic of Korea
| | - Kesia Esther da Silva
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Anuradha De
- Topiwala National Medical CollegeMumbaiIndia
| | - Joep de Ligt
- ESR, Institute of Environmental Science and Research Ltd., PoriruaWellingtonNew Zealand
| | | | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Shanta Dutta
- ICMR - National Institute of Cholera & Enteric DiseasesKolkataIndia
| | - Marthie M Ehlers
- Department of Medical Microbiology, Faculty of Health Sciences, University of PretoriaPretoriaSouth Africa
- Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory ServicePretoriaSouth Africa
| | | | | | - Gauri Godbole
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | - Melita A Gordon
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Andrew R Greenhill
- Federation University AustraliaChurchillAustralia
- Papua New Guinea Institute of Medical ResearchGorokaPapua New Guinea
| | - Chelsey Griffin
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Madhu Gupta
- Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | | | - Robert S Heyderman
- Research Department of Infection, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | | | - Juan Carlos Hormazabal
- Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomedico, Instituto de Salud Publica de Chile (ISP)SantiagoChile
| | - Odion O Ikhimiukor
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | - Junaid Iqbal
- Department of Pediatrics and Child Health, Aga Khan UniversityKarachiPakistan
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical CollegeVelloreIndia
| | - Claire Jenkins
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | | | - Jacob John
- Department of Community Health, Christian Medical CollegeVelloreIndia
| | - Gagandeep Kang
- Department of Community Health, Christian Medical CollegeVelloreIndia
| | - Abdoulie Kanteh
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical MedicineFajaraGambia
| | - Arti Kapil
- All India Institute of Medical SciencesDelhiIndia
| | | | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research InstituteNairobiKenya
| | | | | | - AC Lauer
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Myron M Levine
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USABaltimoreUnited States
| | | | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Grant Austin Mackenzie
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical MedicineFajaraGambia
| | - Tapfumanei Mashe
- National Microbiology Reference LaboratoryHarareZimbabwe
- World Health OrganizationHarareZimbabwe
| | | | - Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical SciencesBengaluruIndia
| | | | - Satheesh Nair
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | | | | | | | - Iruka N Okeke
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of OxfordOxfordUnited Kingdom
- The NIHR Oxford Biomedical Research CentreOxfordUnited Kingdom
| | | | - Firdausi Qadri
- International Centre for Diarrhoeal Disease ResearchDhakaBangladesh
| | - Farah N Qamar
- Department of Pediatrics and Child Health, Aga Khan UniversityKarachiPakistan
| | | | - Savitra Devi Rambocus
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - David A Rasko
- Department of Microbiology and Immunology, University of Maryland School of MedicineBaltimoreUnited States
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimoreUnited States
| | - Pallab Ray
- Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | - Roy Robins-Browne
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of MelbourneMelbourneAustralia
- Murdoch Children’s Research Institute, Royal Children’s HospitalParkvilleAustralia
| | | | | | | | | | | | - Mohammad Saiful Islam Sajib
- Child Health Research FoundationDhakaBangladesh
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of GlasgowGlasgowUnited Kingdom
| | | | - Jivan Shakya
- Dhulikhel HospitalDhulikhelNepal
- Institute for Research in Science and TechnologyKathmanduNepal
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical SciencesBengaluruIndia
| | - Jayanthi Shastri
- Topiwala National Medical CollegeMumbaiIndia
- Kasturba Hospital for Infectious DiseasesMumbaiIndia
| | - Rajeev Shrestha
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University HospitalDhulikhelNepal
| | - Sonia Sia
- Research Institute for Tropical Medicine, Department of HealthMuntinlupa CityPhilippines
| | - Michael J Sikorski
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USABaltimoreUnited States
- Department of Microbiology and Immunology, University of Maryland School of MedicineBaltimoreUnited States
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimoreUnited States
| | | | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable DiseasesJohannesburgSouth Africa
| | - Kaitlin A Tagg
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Dipesh Tamrakar
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University HospitalDhulikhelNepal
| | | | - Maria Thomas
- Christian Medical College, LudhianaLudhianaIndia
| | | | | | | | - Siaosi Tupua
- Ministry of Health, Government of SamoaApiaSamoa
| | | | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | | | - Jackie Wright
- ESR, Institute of Environmental Science and Research Ltd., PoriruaWellingtonNew Zealand
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Jacqueline A Keane
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- IAVI, Chelsea & Westminster HospitalLondonUnited Kingdom
| | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash UniversityMelbourneAustralia
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Okeke IN, Aboderin AO, Egwuenu A, Underwood A, Afolayan AO, Kekre M, Oaikhena AO, Odih EE, Omotayo HT, Dada-Adegbola H, Ogunleye VO, Ikhimiukor OO, Aanensen DM, Ihekweazu C. Establishing a national reference laboratory for antimicrobial resistance using a whole-genome sequencing framework: Nigeria's experience. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35980376 DOI: 10.1099/mic.0.001208] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Whole-genome sequencing (WGS) is finding important applications in the surveillance of antimicrobial resistance (AMR), providing the most granular data and broadening the scope of niches and locations that can be surveilled. A common but often overlooked application of WGS is to replace or augment reference laboratory services for AMR surveillance. WGS has supplanted traditional strain subtyping in many comprehensive reference laboratories and is now the gold standard for rapidly ruling isolates into or out of suspected outbreak clusters. These and other properties give WGS the potential to serve in AMR reference functioning where a reference laboratory did not hitherto exist. In this perspective, we describe how we have employed a WGS approach, and an academic-public health system collaboration, to provide AMR reference laboratory services in Nigeria, as a model for leapfrogging to national AMR surveillance.
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Affiliation(s)
- Iruka N Okeke
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Aaron O Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | | | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK
| | - Ayorinde O Afolayan
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | - Anderson O Oaikhena
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Erkison Ewomazino Odih
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Hamzat T Omotayo
- World Health Organization, Nigeria Country Office, Abuja, Nigeria
| | - Hannah Dada-Adegbola
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Veronica O Ogunleye
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Odion O Ikhimiukor
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK.,Wellcome Genome Campus, Hinxton, UK
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Davies MR, Duchene S, Valcanis M, Jenkins AP, Jenney A, Rosa V, Hayes AJ, Strobel AG, McIntyre L, Lacey JA, Klemm EJ, Wong VK, Sahukhan A, Thomson H, Page A, Hocking D, Wang N, Tudravu L, Rafai E, Dougan G, Howden BP, Crump JA, Mulholland K, Strugnell RA. Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2022; 24:100488. [PMID: 35769175 PMCID: PMC9234096 DOI: 10.1016/j.lanwpc.2022.100488] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND Typhoid fever is endemic in some Pacific Island Countries including Fiji and Samoa yet genomic surveillance is not routine in such settings. Previous studies suggested imports of the global H58 clade of Salmonella enterica var Typhi (Salmonella Typhi) contribute to disease in these countries which, given the MDR potential of H58, does not auger well for treatment. The objective of the study was to define the genomic epidemiology of Salmonella Typhi in Fiji. METHODS Genomic sequencing approaches were implemented to study the distribution of 255 Salmonella Typhi isolates from the Central Division of Fiji. We augmented epidemiological surveillance and Bayesian phylogenomic approaches with a multi-year typhoid case-control study to define geospatial patterns among typhoid cases. FINDINGS Genomic analyses showed Salmonella Typhi from Fiji resolved into 2 non-H58 genotypes with isolates from the two dominant ethnic groups, the Indigenous (iTaukei) and non-iTaukei genetically indistinguishable. Low rates of international importation of clones was observed and overall, there were very low levels an antibiotic resistance within the endemic Fijian typhoid genotypes. Genomic epidemiological investigations were able to identify previously unlinked case clusters. Bayesian phylodynamic analyses suggested that genomic variation within the larger endemic Salmonella Typhi genotype expanded at discreet times, then contracted. INTERPRETATION Cyclones and flooding drove 'waves' of typhoid outbreaks in Fiji which, through population aggregation, poor sanitation and water safety, and then mobility of the population, spread clones more widely. Minimal international importations of new typhoid clones suggest that targeted local intervention strategies may be useful in controlling endemic typhoid infection. These findings add to our understanding of typhoid transmission networks in an endemic island country with broad implications, particularly across Pacific Island Countries. FUNDING This work was supported by the Coalition Against Typhoid through the Bill and Melinda Gates Foundation [grant number OPP1017518], the Victorian Government, the National Health and Medical Research Council Australia, the Australian Research Council, and the Fiji Ministry of Health and Medical Services.
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Affiliation(s)
- Mark R. Davies
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Aaron P. Jenkins
- Centre for Ecosystem Management, Edith Cowan University, Western Australia
- School of Public Health, University of Sydney, Sydney, NSW, Australia
| | - Adam Jenney
- New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia
- College of Medicine, Nursing and Health Sciences, Fiji National University, Suva, Fiji
| | - Varanisese Rosa
- Fiji Centre for Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Andrew J. Hayes
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Aneley Getahun Strobel
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Liam McIntyre
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Jake A. Lacey
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute of Infection and Immunity, Victoria, Australia
| | - Elizabeth J. Klemm
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Vanessa K. Wong
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Aalisha Sahukhan
- Fiji Centre for Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Helen Thomson
- New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia
| | - Andrew Page
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Quadram Institute Bioscience, Norwich Research Park, Norfolk, United Kingdom
| | - Dianna Hocking
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Nancy Wang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | | | - Eric Rafai
- Fiji Ministry of Health and Medical Services, Suva, Fiji
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - John A. Crump
- Centre for International Health, Otago Medical School, University of Otago, Dunedin, New Zealand
| | - Kim Mulholland
- New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Richard A. Strugnell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
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Maes M, Sikorski MJ, Carey ME, Higginson EE, Dyson ZA, Fernandez A, Araya P, Tennant SM, Baker S, Lagos R, Hormazábal JC, Levine MM, Dougan G. Whole genome sequence analysis of Salmonella Typhi provides evidence of phylogenetic linkage between cases of typhoid fever in Santiago, Chile in the 1980s and 2010-2016. PLoS Negl Trop Dis 2022; 16:e0010178. [PMID: 35767580 PMCID: PMC9275700 DOI: 10.1371/journal.pntd.0010178] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 07/12/2022] [Accepted: 06/08/2022] [Indexed: 11/25/2022] Open
Abstract
Typhoid fever epidemiology was investigated rigorously in Santiago, Chile during the 1980s, when Salmonella enterica serovar Typhi (S. Typhi) caused seasonal, hyperendemic disease. Targeted interventions reduced the annual typhoid incidence rates from 128–220 cases/105 population occurring between 1977–1984 to <8 cases/105 from 1992 onwards. As such, Santiago represents a contemporary example of the epidemiologic transition of an industrialized city from amplified hyperendemic typhoid fever to a period when typhoid is no longer endemic. We used whole genome sequencing (WGS) and phylogenetic analysis to compare the genotypes of S. Typhi cultured from acute cases of typhoid fever occurring in Santiago during the hyperendemic period of the 1980s (n = 74) versus the nonendemic 2010s (n = 80) when typhoid fever was rare. The genotype distribution between “historical” (1980s) isolates and “modern” (2011–2016) isolates was similar, with genotypes 3.5 and 2 comprising the majority of isolations, and 73/80 (91.3%) of modern isolates matching a genotype detected in the 1980s. Additionally, phylogenomically ‘ancient’ genotypes 1.1 and 1.2.1, uncommon in the global collections, were also detected in both eras, with a notable rise amongst the modern isolates. Thus, genotypes of S. Typhi causing acute illness in the modern nonendemic era match the genotypes circulating during the hyperendemic 1980s. The persistence of historical genotypes may be explained by chronic typhoid carriers originally infected during or before the 1980s. Studies of Salmonella Typhi (the cause of typhoid fever) rarely include isolates collected both before and after the interruption of hyperendemic transmission because this typically occurred decades before modern bacteria preservation methods. After substantial reduction in disease, it was assumed that sporadic cases and infrequent outbreaks were due to either chronic biliary carriers or importations, but this was difficult to characterize with low resolution bacterial typing methods. In Santiago, Chile, typhoid fever persisted at hyperendemic levels through the 1980s until organized control efforts in the 1980s and changes to wastewater policy in 1991 caused annual typhoid incidence to plummet. In this study, we used whole genome sequencing (WGS) to investigate whether recent sporadic cases occurring in Santiago in the 2010s were genomically similar to S. Typhi circulating in the 1980s, or dissimilar, possibly representing importations of S. Typhi from outside of Chile. We found concordance amongst S. Typhi genotypes between the 1980s and 2010s, and differences from genotypes circulating in Southeast Asia and Africa where typhoid remains hyperendemic. Our findings suggest that a proportion of modern, rare typhoid cases in Santiago are autochthonous, and that chronic carriers or another unknown reservoir likely contribute. Broadly, our findings corroborate the epidemiologic importance of long-term reservoirs of typhoid fever decades after typhoid elimination.
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Affiliation(s)
- Mailis Maes
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| | - Michael J. Sikorski
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Megan E. Carey
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Ellen E. Higginson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Zoe A. Dyson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Infectious Diseases, Monash University, Melbourne, Australia
- London School of Hygiene & Tropical Medicine, London, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Alda Fernandez
- Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomédico, Instituto de Salud Pública de Chile (ISP), Santiago, Chile
| | - Pamela Araya
- Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomédico, Instituto de Salud Pública de Chile (ISP), Santiago, Chile
| | - Sharon M. Tennant
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Rosanna Lagos
- Centro para Vacunas en Desarollo-Chile (CVD-Chile), Hospital de Niños Roberto del Rio, Santiago, Chile
| | - Juan Carlos Hormazábal
- Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomédico, Instituto de Salud Pública de Chile (ISP), Santiago, Chile
| | - Myron M. Levine
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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Dyson ZA, Malau E, Horwood PF, Ford R, Siba V, Yoannes M, Pomat W, Passey M, Judd LM, Ingle DJ, Williamson DA, Dougan G, Greenhill AR, Holt KE. Whole genome sequence analysis of Salmonella Typhi in Papua New Guinea reveals an established population of genotype 2.1.7 sensitive to antimicrobials. PLoS Negl Trop Dis 2022; 16:e0010306. [PMID: 35344544 PMCID: PMC8989336 DOI: 10.1371/journal.pntd.0010306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 04/07/2022] [Accepted: 03/05/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Typhoid fever, a systemic infection caused by Salmonella enterica serovar Typhi, remains a considerable public health threat in impoverished regions within many low- and middle-income settings. However, we still lack a detailed understanding of the emergence, population structure, molecular mechanisms of antimicrobial resistance (AMR), and transmission dynamics of S. Typhi across many settings, particularly throughout the Asia-Pacific islands. Here we present a comprehensive whole genome sequence (WGS) based overview of S. Typhi populations circulating in Papua New Guinea (PNG) over 30 years. PRINCIPLE FINDINGS Bioinformatic analysis of 86 S. Typhi isolates collected between 1980-2010 demonstrated that the population structure of PNG is dominated by a single genotype (2.1.7) that appears to have emerged in the Indonesian archipelago in the mid-twentieth century with minimal evidence of inter-country transmission. Genotypic and phenotypic data demonstrated that the PNG S. Typhi population appears to be susceptible to former first line drugs for treating typhoid fever (chloramphenicol, ampicillin and co-trimoxazole), as well as fluoroquinolones, third generation cephalosporins, and macrolides. PNG genotype 2.1.7 was genetically conserved, with very few deletions, and no evidence of plasmid or prophage acquisition. Genetic variation among this population was attributed to either single point mutations, or homologous recombination adjacent to repetitive ribosomal RNA operons. SIGNIFICANCE Antimicrobials remain an effective option for the treatment of typhoid fever in PNG, along with other intervention strategies including improvements to water, sanitation and hygiene (WaSH) related infrastructure and potentially the introduction of Vi-conjugate vaccines. However, continued genomic surveillance is warranted to monitor for the emergence of AMR within local populations, or the introduction of AMR associated genotypes of S. Typhi in this setting.
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Affiliation(s)
- Zoe Anne Dyson
- London School of Hygiene & Tropical Medicine, London, United Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Elisheba Malau
- School of Science, Psychology and Sport, Federation University, Churchill, Australia
| | - Paul F. Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| | - Rebecca Ford
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Valentine Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Mition Yoannes
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - William Pomat
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Megan Passey
- University Centre for Rural Health, Faculty of Medicine and Health, University of Sydney, Lismore, Australia
| | - Louise M. Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
| | - Danielle J. Ingle
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Deborah A. Williamson
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Andrew R. Greenhill
- School of Science, Psychology and Sport, Federation University, Churchill, Australia
| | - Kathryn E. Holt
- London School of Hygiene & Tropical Medicine, London, United Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
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7
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Shittu OB, Uzairue LI, Ojo OE, Obuotor TM, Folorunso JB, Raheem-Ademola RR, Olanipekun G, Ajose T, Medugu N, Ebruke B, Obaro SK. Antimicrobial resistance and virulence genes in Salmonella enterica serovars isolated from droppings of layer chicken in two farms in Nigeria. J Appl Microbiol 2022; 132:3891-3906. [PMID: 35129256 DOI: 10.1111/jam.15477] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/26/2022] [Accepted: 02/03/2022] [Indexed: 11/28/2022]
Abstract
AIM This study aimed to investigate the isolation rate, antibiotic resistance, and virulence genes of Salmonella enterica serovar from two commercial farms in Nigeria. METHODS AND RESULTS Salmonella isolation was performed according to the United States Food and Drug Agency (USFDA) method. Serotyping, antimicrobial susceptibility testing, detection of resistance and virulence genes were done using the Kauffman-White Scheme, disc diffusion, minimum inhibitory concentration, and real-time polymerase chain reaction techniques. Salmonella serovars were isolated from only farm A at 22/50 (44.0%) while none were isolated from farm B. Salmonella Typhi, 9 (40.9%); Salmonella Typhimurium, 2 (9.1%), Salmonella Enteritidis, 2 (9.1%), Salmonella Pullorum, 1 (4.5%), Salmonella Kentucky, 4 (18.2%) were identified while 4 (18.2%) were untypable. Sixteen isolates (72.7%) showed multiple drug resistance and 17 different resistance profile types with AMP-CHL-TRM-SXT as the most prevalent pattern. Resistance genes (blaTEM, 12/22 (54.5%) and virulence genes (InvA, sopB, mgtC, and spi4D, 22/22 (100.0%), ssaQ, 16/22 (72.7%), and spvC, 13/22 (59.1%) were found, while blaSHV, blaCTX-M, floR, tetA, tetB, tetG, and LJSGI-1 genes were absent. CONCLUSION Pathogenic Salmonella were isolated from the chicken droppings in this study. Most of these strains were resistant to antibiotics and possessed characteristics of virulence. SIGNIFICANCE AND IMPACT OF THE STUDY Chicken droppings from this study area contained pathogenic strains of Salmonella and a rare occurrence of Salmonella Typhi. The study revealed that the environment and the food chain could be at risk of contamination of highly virulent and antimicrobial-resistant strains of Salmonella. These could affect the profitability of the poultry industry and food consumption. There is a need for caution in indiscriminate disposal of poultry waste and the use of uncomposted chicken droppings in soil amendment.
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Affiliation(s)
- Olufunke B Shittu
- Department of Microbiology, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Leonard I Uzairue
- Department of Microbiology, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria.,International Foundation Against Infectious Disease in Nigeria(IFAIN), Abuja, Nigeria.,Department of Medical Laboratory Sciences, Federal University Oye Ekiti, Ekiti State, Nigeria
| | - Olufemi E Ojo
- Department of Veterinary Microbiology and Parasitology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Tolulope M Obuotor
- Department of Microbiology, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Jamiu B Folorunso
- Department of Microbiology, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria.,Department of Community Medicine, Olabisi Onabanjo Teaching Hospital, Nigeria
| | | | - Grace Olanipekun
- International Foundation Against Infectious Disease in Nigeria(IFAIN), Abuja, Nigeria
| | - Theresa Ajose
- International Foundation Against Infectious Disease in Nigeria(IFAIN), Abuja, Nigeria
| | - Nubwa Medugu
- International Foundation Against Infectious Disease in Nigeria(IFAIN), Abuja, Nigeria.,Department of Microbiology and Parasitology, National Hospital, Abuja, Nigeria
| | - Bernard Ebruke
- International Foundation Against Infectious Disease in Nigeria(IFAIN), Abuja, Nigeria
| | - Stephen K Obaro
- International Foundation Against Infectious Disease in Nigeria(IFAIN), Abuja, Nigeria.,Pediatric Infectious Division, University of Nebraska Medical Center, Omaha, USA
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8
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Zakir M, Khan M, Umar MI, Murtaza G, Ashraf M, Shamim S. Emerging Trends of Multidrug-Resistant (MDR) and Extensively Drug-Resistant (XDR) Salmonella Typhi in a Tertiary Care Hospital of Lahore, Pakistan. Microorganisms 2021; 9:microorganisms9122484. [PMID: 34946085 PMCID: PMC8703728 DOI: 10.3390/microorganisms9122484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 11/23/2022] Open
Abstract
Salmonella Typhi is a Gram-negative pathogen that causes typhoid fever in humans. The use of antibiotics to treat typhoid has considerably mitigated its fatality risk, but rising multidrug-resistant (MDR) and extensively drug-resistant (XDR) resistance in Pakistan threatens effective treatment. This study determined the prevalence of MDR and XDR S. Typhi at a local hospital in Lahore. Blood samples (n = 3000) were obtained and processed for bacterial identification. Antibiotic susceptibility test was performed using VITEK® 2 Compound 30 System. Statistical data analysis was performed using a Mann–Whitney U and Kruskal–Wallis H test, respectively. The results revealed 600 positive cultures, of which the majority were found to be XDR S. Typhi (46.1%) and MDR S. Typhi (24.5%) strains. The disease burden of resistant Salmonella strains was greater in males (60.67%) than females (39.33%), with the most affected age group being 0–10 years old (70.4 %). In both the outpatient department (OPD) and general ward, the prevalence of XDR S. Typhi cases was found to be alarmingly high (48.24%), followed by MDR S. Typhi (25.04 %). The results of the statistical analysis demonstrated that the incidence of resistance in MDR and XDR S. Typhi strains was not affected by the age as well as the gender of patients (p > 0.05). The occurrence of resistant strains against four tested antibiotics (azithromycin, ciprofloxacin, imipenem, and meropenem) was found to be similar in different wards and among hospitalized and OPD patients (p > 0.05). Maximum resistance was observed against chloramphenicol and ampicillin in the OPD and pediatric ward. Piperacillin/Tazobactam was observed to be the most effective antibiotic, followed by co-amoxiclav (p < 0.001). This study is effective in validating the existence of MDR and XDR S. Typhi in Lahore, where stringent methods should be applied for controlling its spread.
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Affiliation(s)
- Muhammad Zakir
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Defense Road Campus, Lahore 54000, Pakistan; (M.Z.); (M.K.); (M.A.)
| | - Maryam Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Defense Road Campus, Lahore 54000, Pakistan; (M.Z.); (M.K.); (M.A.)
| | - Muhammad Ihtisham Umar
- Department of Pharmacy, COMSATS University Islamabad, Lahore Campus, Lahore 54000, Pakistan; (M.I.U.); (G.M.)
| | - Ghulam Murtaza
- Department of Pharmacy, COMSATS University Islamabad, Lahore Campus, Lahore 54000, Pakistan; (M.I.U.); (G.M.)
| | - Muhammad Ashraf
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Defense Road Campus, Lahore 54000, Pakistan; (M.Z.); (M.K.); (M.A.)
| | - Saba Shamim
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Defense Road Campus, Lahore 54000, Pakistan; (M.Z.); (M.K.); (M.A.)
- Correspondence: ; Tel.: +92-3218843748
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9
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Patel PD, Patel P, Liang Y, Meiring JE, Misiri T, Mwakiseghile F, Tracy JK, Masesa C, Msuku H, Banda D, Mbewe M, Henrion M, Adetunji F, Simiyu K, Rotrosen E, Birkhold M, Nampota N, Nyirenda OM, Kotloff K, Gmeiner M, Dube Q, Kawalazira G, Laurens MB, Heyderman RS, Gordon MA, Neuzil KM. Safety and Efficacy of a Typhoid Conjugate Vaccine in Malawian Children. N Engl J Med 2021; 385:1104-1115. [PMID: 34525285 PMCID: PMC8202713 DOI: 10.1056/nejmoa2035916] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Typhoid fever caused by multidrug-resistant H58 Salmonella Typhi is an increasing public health threat in sub-Saharan Africa. METHODS We conducted a phase 3, double-blind trial in Blantyre, Malawi, to assess the efficacy of Vi polysaccharide typhoid conjugate vaccine (Vi-TCV). We randomly assigned children who were between 9 months and 12 years of age, in a 1:1 ratio, to receive a single dose of Vi-TCV or meningococcal capsular group A conjugate (MenA) vaccine. The primary outcome was typhoid fever confirmed by blood culture. We report vaccine efficacy and safety outcomes after 18 to 24 months of follow-up. RESULTS The intention-to-treat analysis included 28,130 children, of whom 14,069 were assigned to receive Vi-TCV and 14,061 were assigned to receive the MenA vaccine. Blood culture-confirmed typhoid fever occurred in 12 children in the Vi-TCV group (46.9 cases per 100,000 person-years) and in 62 children in the MenA group (243.2 cases per 100,000 person-years). Overall, the efficacy of Vi-TCV was 80.7% (95% confidence interval [CI], 64.2 to 89.6) in the intention-to-treat analysis and 83.7% (95% CI, 68.1 to 91.6) in the per-protocol analysis. In total, 130 serious adverse events occurred in the first 6 months after vaccination (52 in the Vi-TCV group and 78 in the MenA group), including 6 deaths (all in the MenA group). No serious adverse events were considered by the investigators to be related to vaccination. CONCLUSIONS Among Malawian children 9 months to 12 years of age, administration of Vi-TCV resulted in a lower incidence of blood culture-confirmed typhoid fever than the MenA vaccine. (Funded by the Bill and Melinda Gates Foundation; ClinicalTrials.gov number, NCT03299426.).
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Affiliation(s)
- Priyanka D Patel
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Pratiksha Patel
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Yuanyuan Liang
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - James E Meiring
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Theresa Misiri
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Felistas Mwakiseghile
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - J Kathleen Tracy
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Clemens Masesa
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Harrison Msuku
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - David Banda
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Maurice Mbewe
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Marc Henrion
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Fiyinfolu Adetunji
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Kenneth Simiyu
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Elizabeth Rotrosen
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Megan Birkhold
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Nginache Nampota
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Osward M Nyirenda
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Karen Kotloff
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Markus Gmeiner
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Queen Dube
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Gift Kawalazira
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Matthew B Laurens
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Robert S Heyderman
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Melita A Gordon
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
| | - Kathleen M Neuzil
- From the Malawi-Liverpool-Wellcome Program (P.D.P., P.P., J.E.M., T.M., F.M., C.M., H.M., D.B., M.M., M.H., M.G., M.A.G.), the Blantyre Malaria Project (N.N., O.M.N.), the Department of Paediatrics, Queen Elizabeth Central Hospital (Q.D.), the District Health Office, Blantyre District Council (G.K.), and Kamuzu University of Health Sciences (M.A.G.) - all in Blantyre, Malawi; the Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore (Y.L., J.K.T., F.A., K.S., E.R., M.B., K.K., M.B.L., K.M.N.); and Oxford Vaccine Group, the Department of Paediatrics, Oxford University, Oxford (J.E.M.), Liverpool School of Tropical Medicine (C.M., M.H., M.G.), and the Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool (M.A.G.), and the Division of Infection and Immunity, University College London, London (R.S.H.) - all in the United Kingdom
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10
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Mashe T, Leekitcharoenphon P, Mtapuri-Zinyowera S, Kingsley RA, Robertson V, Tarupiwa A, Kock MM, Makombe EP, Chaibva BV, Manangazira P, Phiri I, Nyadundu S, Chigwena CT, Mufoya LP, Thilliez G, Midzi S, Mwamakamba LW, Hamblion EL, Matheu J, Jensen JD, Aarestrup FM, Hendriksen RS, Ehlers MM. Salmonella enterica serovar Typhi H58 clone has been endemic in Zimbabwe from 2012 to 2019. J Antimicrob Chemother 2021; 76:1160-1167. [PMID: 33347558 DOI: 10.1093/jac/dkaa519] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/11/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Typhoid fever, caused by S. enterica ser. Typhi, continues to be a substantial health burden in developing countries. Little is known of the genotypic diversity of S. enterica ser. Typhi in Zimbabwe, but this is key for understanding the emergence and spread of this pathogen and devising interventions for its control. OBJECTIVES To report the molecular epidemiology of S. enterica ser. Typhi outbreak strains circulating from 2012 to 2019 in Zimbabwe, using comparative genomics. METHODS A review of typhoid cases records from 2012 to 2019 in Zimbabwe was performed. The phylogenetic relationship of outbreak isolates from 2012 to 2019 and emergence of antibiotic resistance was investigated by whole-genome sequence analysis. RESULTS A total 22 479 suspected typhoid cases, 760 confirmed cases were reported from 2012 to 2019 and 29 isolates were sequenced. The majority of the sequenced isolates were predicted to confer resistance to aminoglycosides, β-lactams, phenicols, sulphonamides, tetracycline and fluoroquinolones (including qnrS detection). The qnrS1 gene was associated with an IncN (subtype PST3) plasmid in 79% of the isolates. Whole-genome SNP analysis, SNP-based haplotyping and resistance determinant analysis showed that 93% of the isolates belonged to a single clade represented by multidrug-resistant H58 lineage I (4.3.1.1), with a maximum pair-wise distance of 22 SNPs. CONCLUSIONS This study has provided detailed genotypic characterization of the outbreak strain, identified as S. Typhi 4.3.1.1 (H58). The strain has reduced susceptibility to ciprofloxacin due to qnrS carried by an IncN (subtype PST3) plasmid resulting from ongoing evolution to full resistance.
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Affiliation(s)
- Tapfumanei Mashe
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.,National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Pimlapas Leekitcharoenphon
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens Genomics, FAO Reference Laboratory for Antimicrobial Resistance and European Union Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | | | - Robert A Kingsley
- Quadram Institute Bioscience, Norwich, UK.,University of East Anglia, Norwich, UK
| | - V Robertson
- Medical Microbiology, University of Zimbabwe, Zimbabwe
| | - Andrew Tarupiwa
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Marleen M Kock
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.,National Health Laboratory Service, Tshwane Academic Divisions, Pretoria, South Africa
| | - Evidence P Makombe
- Gweru Provincial Hospital, Ministry of Health and Child Care, Gweru, Zimbabwe
| | | | - Portia Manangazira
- Ministry of Health and Child Care, Epidemiology and Disease Control, Zimbabwe
| | - Isaac Phiri
- Ministry of Health and Child Care, Epidemiology and Disease Control, Zimbabwe
| | - Simon Nyadundu
- Provincial Medical Directorate Offices, Midlands Province, Ministry of Health and Child Care, Gweru, Zimbabwe
| | | | | | | | | | - Lusubilo W Mwamakamba
- World Health Organization Regional Office for Africa, Brazzaville, Republic of Congo
| | - Esther L Hamblion
- World Health Organization Regional Office for Africa, Brazzaville, Republic of Congo
| | | | - Jacob D Jensen
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens Genomics, FAO Reference Laboratory for Antimicrobial Resistance and European Union Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Frank M Aarestrup
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens Genomics, FAO Reference Laboratory for Antimicrobial Resistance and European Union Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Rene S Hendriksen
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens Genomics, FAO Reference Laboratory for Antimicrobial Resistance and European Union Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Marthie M Ehlers
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.,National Health Laboratory Service, Tshwane Academic Divisions, Pretoria, South Africa
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11
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Meiring JE, Laurens MB, Patel P, Patel P, Misiri T, Simiyu K, Mwakiseghile F, Tracy JK, Masesa C, Liang Y, Henrion M, Rotrosen E, Gmeiner M, Heyderman R, Kotloff K, Gordon MA, Neuzil KM. Typhoid Vaccine Acceleration Consortium Malawi: A Phase III, Randomized, Double-blind, Controlled Trial of the Clinical Efficacy of Typhoid Conjugate Vaccine Among Children in Blantyre, Malawi. Clin Infect Dis 2020; 68:S50-S58. [PMID: 30845320 PMCID: PMC6405268 DOI: 10.1093/cid/ciy1103] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Typhoid fever is an acute infection characterized by prolonged fever following the ingestion and subsequent invasion of Salmonella enterica serovar Typhi (S. Typhi), a human-restricted pathogen. The incidence of typhoid fever has been most reported in children 5-15 years of age, but is increasingly recognized in children younger than 5 years old. There has been a recent expansion of multidrug-resistant typhoid fever globally. Prior typhoid vaccines were not suitable for use in the youngest children in countries with a high burden of disease. This study aims to determine the efficacy of a typhoid conjugate vaccine (TCV) that was recently prequalified by the World Health Organization, by testing it in children 9 months through 12 years of age in Blantyre, Malawi. METHODS In this Phase III, individually randomized, controlled, double-blind trial of the clinical efficacy of TCV, 28 000 children 9 months through 12 years of age will be enrolled and randomized in a 1:1 ratio to receive either Vi-TCV or a meningococcal serogroup A conjugate vaccine. A subset of 600 of these children will be further enrolled in an immunogenicity and reactogenicity sub-study to evaluate the safety profile and immune response elicited by Vi-TCV. Recruiting began in February 2018. RESULTS All children will be under passive surveillance for at least 2 years to determine the primary outcome, which is blood culture-confirmed S. Typhi illness. Children enrolled in the immunogenicity and reactogenicity sub-study will have blood drawn before vaccination and at 2 timepoints after vaccination to measure their immune response to vaccination. They will also be followed actively for adverse events and serious adverse events. CONCLUSIONS The introduction of a single-dose, efficacious typhoid vaccine into countries with high burden of disease or significant antimicrobial resistance could have a dramatic impact, protecting children from infection and reducing antimicrobial usage and associated health inequity in the world's poorest places. This trial, the first of a TCV in Africa, seeks to demonstrate the impact and programmatic use of TCVs within an endemic setting. CLINICAL TRIALS REGISTRATION NCT03299426.
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Affiliation(s)
- James E Meiring
- Oxford Vaccine Group, Department of Paediatrics, Oxford University, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Matthew B Laurens
- Center for Vaccine Development and Global Health at the University of Maryland School of Medicine, Baltimore, MD
| | - Pratiksha Patel
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Priyanka Patel
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Theresa Misiri
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Kenneth Simiyu
- Center for Vaccine Development and Global Health at the University of Maryland School of Medicine, Baltimore, MD
| | | | - J Kathleen Tracy
- Center for Vaccine Development and Global Health at the University of Maryland School of Medicine, Baltimore, MD
| | - Clemens Masesa
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Yuanyuan Liang
- Center for Vaccine Development and Global Health at the University of Maryland School of Medicine, Baltimore, MD
| | - Marc Henrion
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Elizabeth Rotrosen
- Center for Vaccine Development and Global Health at the University of Maryland School of Medicine, Baltimore, MD
| | - Markus Gmeiner
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Robert Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Division of Infection and Immunity, University College London, United Kingdom
| | - Karen Kotloff
- Center for Vaccine Development and Global Health at the University of Maryland School of Medicine, Baltimore, MD
| | - Melita A Gordon
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Institute of Infection and Global Health, University of Liverpool, United Kingdom
| | - Kathleen M Neuzil
- Center for Vaccine Development and Global Health at the University of Maryland School of Medicine, Baltimore, MD
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12
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Abstract
Multiple drug (antibiotic) resistance (MDR) has become a major threat to the treatment of typhoid and other infectious diseases. Since the 1970s, this threat has increased in Salmonella enterica serovar Typhi, driven in part by the emergence of successful genetic clades, such as haplotype H58, associated with the MDR phenotype. H58 S. Typhi can express multiple antibiotic resistance determinants while retaining the ability to efficiently transmit and persist within the human population. The recent identification of extensively drug resistant S. Typhi only highlights the dangers of ignoring this threat. Here we discuss the evolution of the S. Typhi MDR phenotype and consider options for management.
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Affiliation(s)
- Zoe A Dyson
- Department of Medicine, University of Cambridge, Hinxton, Cambridge, United Kingdom
| | - Elizabeth J Klemm
- Department of Medicine, University of Cambridge, Hinxton, Cambridge, United Kingdom.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sophie Palmer
- Department of Medicine, University of Cambridge, Hinxton, Cambridge, United Kingdom
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Hinxton, Cambridge, United Kingdom.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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13
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Rahman SIA, Dyson ZA, Klemm EJ, Khanam F, Holt KE, Chowdhury EK, Dougan G, Qadri F. Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016. PLoS Negl Trop Dis 2020; 14:e0008036. [PMID: 32106221 PMCID: PMC7064254 DOI: 10.1371/journal.pntd.0008036] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 03/10/2020] [Accepted: 01/08/2020] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Multi-drug resistant typhoid fever remains an enormous public health threat in low and middle-income countries. However, we still lack a detailed understanding of the epidemiology and genomics of S. Typhi in many regions. Here we have undertaken a detailed genomic analysis of typhoid in urban Dhaka, Bangladesh to unravel the population structure and antimicrobial resistance patterns in S. Typhi isolated between 2004-2016. PRINCIPAL FINDINGS Whole genome sequencing of 202 S. Typhi isolates obtained from three study locations in urban Dhaka revealed a diverse range of S. Typhi genotypes and AMR profiles. The bacterial population within Dhaka were relatively homogenous with little stratification between different healthcare facilities or age groups. We also observed evidence of exchange of Bangladeshi genotypes with neighboring South Asian countries (India, Pakistan and Nepal) suggesting these are circulating throughout the region. This analysis revealed a decline in H58 (genotype 4.3.1) isolates from 2011 onwards, coinciding with a rise in a diverse range of non-H58 genotypes and a simultaneous rise in isolates with reduced susceptibility to fluoroquinolones, potentially reflecting a change in treatment practices. We identified a novel S. Typhi genotype, subclade 3.3.2 (previously defined only to clade level, 3.3), which formed two localized clusters (3.3.2.Bd1 and 3.3.2.Bd2) associated with different mutations in the Quinolone Resistance Determining Region (QRDR) of gene gyrA. SIGNIFICANCE Our analysis of S. Typhi isolates from urban Dhaka, Bangladesh isolated over a twelve year period identified a diverse range of AMR profiles and genotypes. The observed increase in non-H58 genotypes associated with reduced fluoroquinolone susceptibility may reflect a change in treatment practice in this region and highlights the importance of continued molecular surveillance to monitor the ongoing evolution of AMR in Dhaka. We have defined new genotypes and lineages of Bangladeshi S. Typhi which will facilitate the identification of these emerging AMR clones in future surveillance efforts.
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Affiliation(s)
- Sadia Isfat Ara Rahman
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Zoe A. Dyson
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Elizabeth J. Klemm
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Farhana Khanam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Infection Biology, Faculty of Infections and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Emran Kabir Chowdhury
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
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14
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Carey ME, Diaz ZI, Zaidi AKM, Steele AD. A Global Agenda for Typhoid Control-A Perspective from the Bill & Melinda Gates Foundation. Clin Infect Dis 2020; 68:S42-S45. [PMID: 30766999 PMCID: PMC6376097 DOI: 10.1093/cid/ciy928] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recognizing that enteric fever disproportionately affects the poorest and the most vulnerable communities that have limited access to improved sanitation, safe water sources, and optimal medical care, the Bill & Melinda Gates Foundation has funded efforts to augment global understanding of the disease since the foundation’s inception. At the turn of the century, early efforts focused on characterizing the burden of disease in Asia and evaluating use of the available Vi-polysaccharide vaccines through the Diseases of the Most Impoverished projects at the International Vaccine Institute (IVI). More recent efforts have centered on supporting development of typhoid conjugate vaccines and expanding disease surveillance efforts into Africa, as well as generating a greater understanding of the clinical severity and sequelae of enteric fever in Africa, Asia, and India. The Typhoid Vaccine Accelerator Consortium is playing a critical role in coordinating these and other global efforts for the control of typhoid fever. Here, we outline the scope of support and strategic view of the foundation and describe how, by working through strong partnerships, we can realize a radical reduction of the significance of enteric fever as a global public health problem in the next 10 to 15 years.
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Affiliation(s)
- Megan E Carey
- Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, Washington
| | - Zoey I Diaz
- Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, Washington
| | - Anita K M Zaidi
- Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, Washington
| | - A Duncan Steele
- Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, Washington
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15
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Britto CD, John J, Verghese VP, Pollard AJ. A systematic review of antimicrobial resistance of typhoidal Salmonella in India. Indian J Med Res 2019; 149:151-163. [PMID: 31219079 PMCID: PMC6563740 DOI: 10.4103/ijmr.ijmr_830_18] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Background & objectives: The temporal trends in the development of antimicrobial resistance (AMR) among Salmonella Typhi and Salmonella Paratyphi in India have not been systematically reported. We aimed to systematically review the temporal AMR trends (phenotypic and molecular mechanisms) in bacterial isolates from patients with enteric fever over two decades in India. Methods: To identify trends in AMR in India, resistance patterns among 4611 individual S. Typhi isolates and 800 S. Paratyphi A isolates, reported from 1992 to 2017 in 40 publications, were analysed. Molecular resistance determinants were extracted from 22 publications and also reviewed in accordance with the PRISMA guidelines. Articles were sourced using a predefined search strategy from different databases. Results: The analyses suggested that multidrug-resistant (MDR) enteric fever was declining in India and being replaced by fluoroquinolone (FQ) resistance. Mutations in gyrA and parC were key mechanisms responsible for FQ resistance, whereas MDR was largely driven by resistance determinants encoded on mobile genetic elements (plasmids, transposons). Interpretation & conclusions: The results reflect the effect of antimicrobial pressure which has been driving AMR in typhoidal Salmonella in India. Understanding these trends is important in planning future approaches to therapy, which serve as a baseline for assessment of the impact of new typhoid conjugate vaccines against these resistant organisms.
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Affiliation(s)
- Carl D Britto
- Department of Paediatrics, University of Oxford & NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Jacob John
- Department of Community Medicine, Christian Medical College, Vellore, India
| | - Valsan P Verghese
- Department of Paediatrics, Christian Medical College, Vellore, India
| | - Andrew J Pollard
- Department of Paediatrics, University of Oxford & NIHR Oxford Biomedical Research Centre, Oxford, UK
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16
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Acheampong G, Owusu M, Owusu-Ofori A, Osei I, Sarpong N, Sylverken A, Kung HJ, Cho ST, Kuo CH, Park SE, Marks F, Adu-Sarkodie Y, Owusu-Dabo E. Chromosomal and plasmid-mediated fluoroquinolone resistance in human Salmonella enterica infection in Ghana. BMC Infect Dis 2019; 19:898. [PMID: 31660876 PMCID: PMC6819380 DOI: 10.1186/s12879-019-4522-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/30/2019] [Indexed: 11/19/2022] Open
Abstract
Background Salmonella infection poses significant public health threat globally, especially in resource-limited countries. Emergence and spread of antibiotic resistant strains to fluoroquinolones have led to treatment failures and increased mortality in Salmonella infection. However, there is dearth of information regarding mechanisms of resistance to fluoroquinolones in Ghana. This study therefore sought to identify chromosomal mutations and plasmid-mediated resistance as possible mechanisms of fluoroquinolone resistance from clinical isolates in Ghana. Methods This was a retrospective study of archived isolates biobanked at Kumasi Centre for Collaborative Research in Tropical Medicine, Ghana. Isolates were obtained from blood, stool and oropharynx samples at two hospitals, between May, 2016 and January, 2018. Salmonella identification was done using standard microbiological protocols and antibiotic susceptibility testing performed by Kirby-Bauer disc diffusion method. Isolates with intermediate susceptibility and/or resistance to nalidixic acid and/or ciprofloxacin were selected and examined for chromosomal mutations by Sanger sequencing and plasmid-mediated resistance by PCR. Results Of 133 biobanked isolates cultured, 68 (51.1%) and 16 (12%) were identified as Salmonella Typhi and non-typhoidal Salmonella (NTS), respectively. Sequence analysis of gyrA gene revealed the presence of 5 different nonsynonymous mutations, with the most frequent mutation (Ile203Ser) occurring in 12 out of 13 isolates tested. Gyrase B (gyrB) gene had 1 nonsynonymous mutation in 3 out of 13 isolates, substituting phenylalanine with leucine at codon 601 (Phe601Leu). No mutation was observed in parC and parE genes. Two NTS isolates were found to harbour qnrS plasmid-mediated resistant gene of molecular size 550 bp with high ciprofloxacin MIC of 0.5 μg/ml. Conclusion This study reports for the first time in Ghana plasmid-mediated fluoroquinolone resistant gene qnrS in Salmonella clinical isolates. Nonsynonymous mutations of gyrA and gyrB genes likely to confer Salmonella reduced susceptibility to ciprofloxacin were also reported.
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Affiliation(s)
- Godfred Acheampong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Michael Owusu
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana.,Department of Medical Laboratory Technology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Alex Owusu-Ofori
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Isaac Osei
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | | | - Augustina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana.,Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Hung-Jui Kung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Se Eun Park
- Department of Epidemiology, International Vaccine Institute, Seoul, South Korea.,Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, 764 Vo Van Kiet, Quant 5, Ho Chi Minh City, Vietnam
| | - Florian Marks
- Department of Epidemiology, International Vaccine Institute, Seoul, South Korea
| | - Yaw Adu-Sarkodie
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Ellis Owusu-Dabo
- Department of Global and International Health, School of Public Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.
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17
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Abstract
We combine methodology from history and genetics to reconstruct the biosocial history of antimicrobial resistance (AMR) in the bacterium Salmonella enterica serovar Typhi (S. Typhi). We show how evolutionary divergence in S. Typhi was driven by rising global antibiotic use and by the neglect of typhoid outside of high-income countries. Although high-income countries pioneered 1960s precautionary antibiotic regulations to prevent selection for multidrug resistance, new antibiotic classes, typhoid's cultural status as a supposedly ancient disease of "undeveloped" countries, limited international funding, and narrow biosecurity agendas helped fragment effective global collective action for typhoid control. Antibiotic-intensive compensation for weak water and healthcare systems subsequently fueled AMR selection in low- and middle-income countries but often remained invisible due to lacking surveillance capabilities. The recent rise of extensively drug-resistant typhoid bears the biosocial footprint of more than half a century of antibiotic-intensive international neglect.
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Affiliation(s)
- Claas Kirchhelle
- Wellcome Unit for the History of Medicine/Oxford Martin School, University of Oxford, Addenbrooke’s Hospital, United Kingdom
| | - Zoe Anne Dyson
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, United Kingdom
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, United Kingdom
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18
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Ingle DJ, Nair S, Hartman H, Ashton PM, Dyson ZA, Day M, Freedman J, Chattaway MA, Holt KE, Dallman TJ. Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers. PLoS Negl Trop Dis 2019; 13:e0007620. [PMID: 31513580 PMCID: PMC6741848 DOI: 10.1371/journal.pntd.0007620] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 07/09/2019] [Indexed: 11/30/2022] Open
Abstract
Salmonella enterica serovar Typhi (S. Typhi) is the causative agent of typhoid fever, a systemic human infection with a burden exceeding 20 million cases each year that occurs disproportionately among children in low and middle income countries. Antimicrobial therapy is the mainstay for treatment, but resistance to multiple agents is common. Here we report genotypes and antimicrobial resistance (AMR) determinants detected from routine whole-genome sequencing (WGS) of 533 S. Typhi isolates referred to Public Health England between April 2014 and March 2017, 488 (92%) of which had accompanying patient travel information obtained via an enhanced surveillance questionnaire. The majority of cases involved S. Typhi 4.3.1 (H58) linked with travel to South Asia (59%). Travel to East and West Africa were associated with genotypes 4.3.1 and 3.3.1, respectively. Point mutations in the quinolone resistance determining region (QRDR), associated with reduced susceptibility to fluoroquinolones, were very common (85% of all cases) but the frequency varied significantly by region of travel: 95% in South Asia, 43% in East Africa, 27% in West Africa. QRDR triple mutants, resistant to ciprofloxacin, were restricted to 4.3.1 lineage II and associated with travel to India, accounting for 23% of cases reporting travel to the country. Overall 24% of isolates were MDR, however the frequency varied significantly by region and country of travel: 27% in West Africa, 52% in East Africa, 55% in Pakistan, 24% in Bangladesh, 3% in India. MDR determinants were plasmid-borne (IncHI1 PST2 plasmids) in S. Typhi 3.1.1 linked to West Africa, but in all other regions MDR was chromosomally integrated in 4.3.1 lineage I. We propose that routine WGS data from travel-associated cases in industrialised countries could serve as informal sentinel AMR genomic surveillance data for countries where WGS is not available or routinely performed. Our data demonstrate how routine WGS data produced by Public Health England can be further mined for informal passive surveillance of Salmonella Typhi circulating in different geographical regions where typhoid is endemic. We have shown the public health utility of a simplified approach to WGS reporting based on the GenoTyphi genotyping framework and nomenclature, which doesn’t require the generation of a phylogenetic tree or other phylogenetic analysis. These approaches yielded results consistent with previously reported antimicrobial resistance (AMR) patterns of S. Typhi, including prevalence of multi-drug resistant (MDR) and fluoroquinolone resistance in different regions in association with different pathogen variants. These data provide a rationale and framework for the extraction and reporting of geographically stratified genotype and AMR data from public health labs in non-endemic countries. Prospective analysis and reporting of such data could potentially detect shifts in regional S. Typhi populations, such as replacement or spread of different subclades and the emergence and dissemination of MDR, fluoroquinolone resistant and/or extensively drug resistant S. Typhi, providing valuable data to inform typhoid control measures in low and middle income countries that are still building their genomics capacity.
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Affiliation(s)
- Danielle J. Ingle
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- * E-mail:
| | - Satheesh Nair
- Gastrointestinal Bacteria Reference Unit, Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kingdom
| | - Hassan Hartman
- Gastrointestinal Bacteria Reference Unit, Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kingdom
| | - Philip M. Ashton
- Gastrointestinal Bacteria Reference Unit, Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kingdom
| | - Zoe A. Dyson
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Martin Day
- Gastrointestinal Bacteria Reference Unit, Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kingdom
| | - Joanne Freedman
- Travel Migrant and Health Department, Public Health England, 61 Colindale Avenue, London, United Kingdom
| | - Marie A. Chattaway
- Gastrointestinal Bacteria Reference Unit, Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kingdom
| | - Kathryn E. Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Timothy J. Dallman
- Gastrointestinal Bacteria Reference Unit, Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kingdom
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19
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Abstract
Purpose of review Enteric fever remains a major global-health concern, estimated to be responsible for between 11.9 and 26.9 million cases annually. Long-term prevention of enteric fever will require improved access to safe drinking water combined with investment in sanitation and hygiene interventions. In the short-to-medium term, new control strategies for typhoid fever have arrived in the form of typhoid Vi-conjugate vaccines (TCVs), offering hope that disease control can be achieved in the near future. Recent findings The diagnosis of enteric fever is complicated by its nonspecific clinical presentation, coupled with the low sensitivity of commonly used diagnostics. Investment in diagnostics has the potential to improve management, to refine estimates of disease burden and to facilitate vaccine impact studies. A new generation of reliable, diagnostic tests is needed that are simultaneously accessible, cost-effective, sensitive, and specific. The emergence and global dissemination of multidrug-resistant, fluoroquinolone-resistant, and extensively drug-resistant (XDR) strains of Salmonella Typhi emphasizes the importance of continued surveillance and appropriate antibiotic stewardship, integrated into a global strategy to address antimicrobial resistance (AMR). Current empirical treatment guidelines are out of date and should be updated to respond to local trends in AMR, so as to guide treatment choices in the absence of robust diagnostics and laboratory facilities. In September 2017, the WHO Strategic Advisory Group of Experts (SAGE) immunization recommended the programmatic use of TCVs in high burden countries. Ongoing and future studies should aim to study the impact of these vaccines in a diverse range of setting and to support the deployment of TCVs in high-burden countries. Summary The advent of new generation TCVs offers us a practical and affordable public-health tool that – for the first time – can be integrated into routine childhood immunization programmes. In this review, we advocate for the deployment of TCVs in line with WHO recommendations, to improve child health and limit the spread of antibiotic-resistant S. Typhi.
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20
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Smith AM. Review of molecular subtyping methodologies used to investigate outbreaks due to multidrug-resistant enteric bacterial pathogens in sub-Saharan Africa. Afr J Lab Med 2019; 8:760. [PMID: 31205868 PMCID: PMC6556818 DOI: 10.4102/ajlm.v8i1.760] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 09/25/2018] [Indexed: 01/05/2023] Open
Abstract
Background In sub-Saharan Africa, molecular epidemiological investigation of outbreaks caused by antimicrobial-resistant enteric bacterial pathogens have mostly been described for Salmonella species, Vibrio cholerae, Shigella species and Escherichia coli. For these organisms, I reviewed all publications describing the use of molecular subtyping methodologies to investigate outbreaks caused by multidrug-resistant (MDR) enteric bacterial infections. Objectives To describe the use of molecular subtyping methodologies to investigate outbreaks caused by MDR enteric bacterial pathogens in sub-Saharan Africa and to describe the current status of molecular subtyping capabilities in the region. Methods A PubMed database literature search (English language only) was performed using the search strings: ‘Africa outbreak MDR’, ‘Africa outbreak multi’, ‘Africa outbreak multidrug’, ‘Africa outbreak multi drug’, ‘Africa outbreak resistance’, ‘Africa outbreak resistant’, ‘Africa outbreak drug’, ‘Africa outbreak antibiotic’, ‘Africa outbreak antimicrobial’. These search strings were used in combination with genus and species names of the organisms listed above. All results were included in the review. Results The year 1991 saw one of the first reports describing the use of molecular subtyping methodologies in sub-Saharan Africa; this included the use of plasmid profiling to characterise Salmonella Enteritidis. To date, several methodologies have been used; pulsed-field gel electrophoresis analysis and multilocus sequence typing have been the most commonly used methodologies. Investigations have particularly highlighted the emergence and spread of MDR clones; these include Salmonella Typhi H58 and Salmonella Typhimurium ST313 clones. In recent times, whole-genome sequencing (WGS) analysis approaches have increasingly been used. Conclusion Traditional molecular subtyping methodologies are still commonly used and still have their place in investigations; however, WGS approaches have increasingly been used and are slowly gaining a stronghold. African laboratories need to start adapting their molecular surveillance methodologies to include WGS, as it is foreseen that WGS analysis will eventually replace all traditional methodologies.
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Affiliation(s)
- Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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21
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Abstract
Typhoid fever is a continuing public health problem in many low- and middle-income countries; however, routine vaccination as a recommended control strategy has not been implemented in the past in most countries. Greater understanding of the typhoid fever burden, the increasing threat of antimicrobial resistance, and licensure of a new generation of typhoid conjugate vaccines (TCVs) were instrumental in paving the way for the World Health Organization (WHO) to issue a revised global policy on typhoid vaccines in March 2018. The new policy follows evidence-based recommendations by the WHO Strategic Advisory Group of Experts on immunization for routine and catch-up vaccination with TCVs and highlights considerations for universal, risk-based, or phased vaccination strategies in different settings. Further, the first WHO-prequalified TCV and Gavi funding for eligible countries make vaccination a realistic control strategy for many affected countries, especially if combined with improved water and sanitation services, strengthened surveillance systems, and appropriate antimicrobial treatment.
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Affiliation(s)
- Adwoa D Bentsi-Enchill
- Department of Immunization, Vaccines and Biologicals, World Health Organization, Geneva, Switzerland
| | - Joachim Hombach
- Department of Immunization, Vaccines and Biologicals, World Health Organization, Geneva, Switzerland
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The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa. Nat Commun 2018; 9:5094. [PMID: 30504848 PMCID: PMC6269545 DOI: 10.1038/s41467-018-07370-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/18/2018] [Indexed: 11/18/2022] Open
Abstract
There is paucity of data regarding the geographical distribution, incidence, and phylogenetics of multi-drug resistant (MDR) Salmonella Typhi in sub-Saharan Africa. Here we present a phylogenetic reconstruction of whole genome sequenced 249 contemporaneous S. Typhi isolated between 2008-2015 in 11 sub-Saharan African countries, in context of the 2,057 global S. Typhi genomic framework. Despite the broad genetic diversity, the majority of organisms (225/249; 90%) belong to only three genotypes, 4.3.1 (H58) (99/249; 40%), 3.1.1 (97/249; 39%), and 2.3.2 (29/249; 12%). Genotypes 4.3.1 and 3.1.1 are confined within East and West Africa, respectively. MDR phenotype is found in over 50% of organisms restricted within these dominant genotypes. High incidences of MDR S. Typhi are calculated in locations with a high burden of typhoid, specifically in children aged <15 years. Antimicrobial stewardship, MDR surveillance, and the introduction of typhoid conjugate vaccines will be critical for the control of MDR typhoid in Africa. Typhoid fever is caused by the bacterium Salmonella Typhi. Here, Park et al. analyse the genomes of 249 S. Typhi isolates from 11 sub-Saharan African countries, identifying genes and plasmids associated with antibiotic resistance and showing that multi-drug resistance is highly pervasive in sub-Saharan Africa.
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Salmonella enterica Serovar Typhi in Bangladesh: Exploration of Genomic Diversity and Antimicrobial Resistance. mBio 2018; 9:mBio.02112-18. [PMID: 30425150 PMCID: PMC6234861 DOI: 10.1128/mbio.02112-18] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Typhoid fever, caused by Salmonella enterica serovar Typhi, is a global public health concern due to increasing antimicrobial resistance (AMR). Characterization of S Typhi genomes for AMR and the evolution of different lineages, especially in countries where typhoid fever is endemic such as Bangladesh, will help public health professionals to better design and implement appropriate preventive measures. We studied whole-genome sequences (WGS) of 536 S Typhi isolates collected in Bangladesh during 1999 to 2013 and compared those sequences with data from a recent outbreak in Pakistan reported previously by E. J. Klemm, S. Shakoor, A. J. Page, F. N. Qamar, et al. (mBio 9:e00105-18, 2018, https://doi.org/10.1128/mBio.00105-18), and a laboratory surveillance in Nepal reported previously by C. D. Britto, Z. A. Dyson, S. Duchene, M. J. Carter, et al. [PLoS Negl. Trop. Dis. 12(4):e0006408, 2018, https://doi.org/10.1371/journal.pntd.0006408]. WGS had high sensitivity and specificity for prediction of ampicillin, chloramphenicol, co-trimoxazole, and ceftriaxone AMR phenotypes but needs further improvement for prediction of ciprofloxacin resistance. We detected a new local lineage of genotype 4.3.1 (named lineage Bd) which recently diverged into a sublineage (named Bdq) containing qnr genes associated with high-level ciprofloxacin resistance. We found a ceftriaxone-resistant isolate with the bla CTX-M-15 gene and a genotype distinct from the genotypes of extensively drug-resistant (XDR) isolates from Pakistan. This result suggests a different source and geographical origin of AMR. Genotype 4.3.1 was dominant in all three countries but formed country-specific clusters in the maximum likelihood phylogenetic tree. Thus, multiple independent genetic events leading to ciprofloxacin and ceftriaxone resistance took place in these neighboring regions of Pakistan, Nepal, and Bangladesh. These independent mutational events may enhance the risk of global spread of these highly resistant clones. A short-term global intervention plan is urgently needed.IMPORTANCE Typhoid fever, caused by Salmonella enterica serovar Typhi, is responsible for an estimated burden of approximately 17 million new episodes per year worldwide. Adequate and timely antimicrobial treatment invariably cures typhoid fever. The increasing antimicrobial resistance (AMR) of S Typhi severely limits the treatment options. We studied whole-genome sequences (WGS) of 536 S Typhi isolates collected in Bangladesh between 1999 and 2013 and compared those sequences with data from a recent outbreak in Pakistan and a laboratory surveillance in Nepal. The analysis suggests that multiple ancestral origins of resistance against ciprofloxacin and ceftriaxone are present in three countries. Such independent genetic events and subsequent dissemination could enhance the risk of a rapid global spread of these highly resistant clones. Given the current treatment challenges, vaccination seems to be the most appropriate short-term intervention to reduce the disease burden of typhoid fever at a time of increasing AMR.
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Britto CD, Wong VK, Dougan G, Pollard AJ. A systematic review of antimicrobial resistance in Salmonella enterica serovar Typhi, the etiological agent of typhoid. PLoS Negl Trop Dis 2018; 12:e0006779. [PMID: 30307935 PMCID: PMC6198998 DOI: 10.1371/journal.pntd.0006779] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 10/23/2018] [Accepted: 08/23/2018] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The temporal and spatial change in trends of antimicrobial resistance (AMR) in typhoid have not been systematically studied, and such information will be critical for defining intervention, as well as planning sustainable prevention strategies. METHODOLOGY AND FINDINGS To identify the phenotypic trends in AMR, 13,833 individual S. Typhi isolates, reported from 1973 to 2018 in 62 publications, were analysed to determine the AMR preponderance over time. Separate analyses of molecular resistance determinants present in over 4,000 isolates reported in 61 publications were also conducted. Multi-drug resistant (MDR) typhoid is in decline in Asia in a setting of high fluoroquinolone resistance while it is on the increase in Africa. Mutations in QRDRs in gyrA (S83F, D87N) and parC (S80I) are the most common mechanisms responsible for fluoroquinolone resistance. Cephalosporin resistant S. Typhi, dubbed extensively drug-resistant (XDR) is a real threat and underscores the urgency in deploying the Vi-conjugate vaccines. CONCLUSION From these observations, it appears that AMR in S. Typhi will continue to emerge leading to treatment failure, changes in antimicrobial policy and further resistance developing in S. Typhi isolates and other Gram-negative bacteria in endemic regions. The deployment of typhoid conjugate vaccines to control the disease in endemic regions may be the best defence.
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Affiliation(s)
- Carl D. Britto
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Vanessa K. Wong
- Wellcome Trust Sanger Institute and the Department of Medicine, Cambridge University, Cambridge, United Kingdom
| | - Gordan Dougan
- Wellcome Trust Sanger Institute and the Department of Medicine, Cambridge University, Cambridge, United Kingdom
| | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
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Pérez-Losada M, Arenas M, Castro-Nallar E. Microbial sequence typing in the genomic era. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 63:346-359. [PMID: 28943406 PMCID: PMC5908768 DOI: 10.1016/j.meegid.2017.09.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 12/18/2022]
Abstract
Next-generation sequencing (NGS), also known as high-throughput sequencing, is changing the field of microbial genomics research. NGS allows for a more comprehensive analysis of the diversity, structure and composition of microbial genes and genomes compared to the traditional automated Sanger capillary sequencing at a lower cost. NGS strategies have expanded the versatility of standard and widely used typing approaches based on nucleotide variation in several hundred DNA sequences and a few gene fragments (MLST, MLVA, rMLST and cgMLST). NGS can now accommodate variation in thousands or millions of sequences from selected amplicons to full genomes (WGS, NGMLST and HiMLST). To extract signals from high-dimensional NGS data and make valid statistical inferences, novel analytic and statistical techniques are needed. In this review, we describe standard and new approaches for microbial sequence typing at gene and genome levels and guidelines for subsequent analysis, including methods and computational frameworks. We also present several applications of these approaches to some disciplines, namely genotyping, phylogenetics and molecular epidemiology.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA 20147, USA; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal; Children's National Medical Center, Washington, DC 20010, USA.
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago 8370146, Chile
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Keddy KH, Smith AM, Sooka A, Tau NP, Ngomane HMP, Radhakrishnan A, Als D, Benson FG. The Burden of Typhoid Fever in South Africa: The Potential Impact of Selected Interventions. Am J Trop Med Hyg 2018; 99:55-63. [PMID: 30047360 PMCID: PMC6128358 DOI: 10.4269/ajtmh.18-0182] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Typhoid fever is notifiable in South Africa but clinical notification is notoriously poor. South Africa has an estimated annual incidence rate of 0.1 cases per 100,000 population of culture-confirmed typhoid fever, decreased from 17 cases per 100,000 population in the 1980s. This work was undertaken to identify the reasons for this decrease and identify potential weaknesses that may result in an increase of observed cases. Culture-confirmed cases, with additional demographic and clinical data have been collected from selected sentinel sites since 2003. Data on contextual factors (gross domestic product [GDP], sanitation, female education, and childhood diarrhea mortality) were collected. National incidence rates of culture-confirmed typhoid fever have remained constant for the past 13 years, with the exception of an outbreak in 2005: incidence was 0.4 per 100,000 population. Paratyphoid fever remains a rare disease. Antimicrobial susceptibility data suggest resistance to ciprofloxacin and azithromycin is emerging. The South African population increased from 27.5 million in 1980 to 55.0 million in 2015: urbanization increased from 50% to 65%, GDP increased from United States Dollar (USD) $2,910 to USD $6,167, access to sanitation improved from 64.4% to 70.0% in the urban population and 26.4% to 60.5% in rural areas. Female literacy levels improved from 74.8% to 92.6% over the period. Improved socioeconomic circumstances in South Africa have been temporally associated with decreasing incidence rates of typhoid fever over a 35-year period. Ongoing challenges remain including potential for large outbreaks, a large immigrant population, and emerging antimicrobial resistance. Continued active surveillance is mandatory.
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Affiliation(s)
- Karen H Keddy
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Anthony M Smith
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Arvinda Sooka
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Nomsa P Tau
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Hlengiwe M P Ngomane
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | | | - Daina Als
- Centre for Global Child Health, The Hospital for Sick Children, Toronto, Canada
| | - Frew G Benson
- Gauteng Provincial Health Department, Johannesburg, South Africa
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Meiring JE, Patel P, Patel P, Gordon MA. Typhoid conjugate vaccines: making vaccine history in Africa. Expert Rev Vaccines 2018; 17:673-676. [PMID: 29972655 DOI: 10.1080/14760584.2018.1496825] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- James E Meiring
- a Oxford Vaccine Group, Department of Paediatrics , Oxford University , Oxford , UK.,b Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine , Blantyre , Malawi
| | - Pratiksha Patel
- b Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine , Blantyre , Malawi
| | - Priyanka Patel
- b Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine , Blantyre , Malawi
| | - Melita A Gordon
- b Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine , Blantyre , Malawi
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Cuypers WL, Jacobs J, Wong V, Klemm EJ, Deborggraeve S, Van Puyvelde S. Fluoroquinolone resistance in Salmonella: insights by whole-genome sequencing. Microb Genom 2018; 4. [PMID: 29975627 PMCID: PMC6113872 DOI: 10.1099/mgen.0.000195] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Fluoroquinolone (FQ)-resistant Salmonella spp. were listed by the WHO in 2017 as priority pathogens for which new antibiotics were urgently needed. The overall global burden of Salmonella infections is high, but differs per region. Whereas typhoid fever is most prevalent in South and South-East Asia, non-typhoidal salmonellosis is prevalent across the globe and associated with a mild gastroenteritis. By contrast, invasive non-typhoidal Salmonella cause bloodstream infections associated with high mortality, particularly in sub-Saharan Africa. Most Salmonella strains from clinical sources are resistant to first-line antibiotics, with FQs now being the antibiotic of choice for treatment of invasive Salmonella infections. However, FQ resistance is increasingly being reported in Salmonella, and multiple molecular mechanisms are already described. Whole-genome sequencing (WGS) is becoming more frequently used to analyse bacterial genomes for antibiotic-resistance markers, and to understand the phylogeny of bacteria in relation to their antibiotic-resistance profiles. This mini-review provides an overview of FQ resistance in Salmonella, guided by WGS studies that demonstrate that WGS is a valuable tool for global surveillance.
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Affiliation(s)
- Wim L Cuypers
- 1Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium.,2Department of Mathematics and Computer Science, University of Antwerp, Antwerpen, Belgium
| | - Jan Jacobs
- 3Department of Clinical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium.,4Department of Microbiology and Immunology, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Vanessa Wong
- 5Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.,6Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Stijn Deborggraeve
- 1Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
| | - Sandra Van Puyvelde
- 6Wellcome Trust Sanger Institute, Hinxton, UK.,1Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
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Tadesse G, Tessema TS, Beyene G, Aseffa A. Molecular epidemiology of fluoroquinolone resistant Salmonella in Africa: A systematic review and meta-analysis. PLoS One 2018; 13:e0192575. [PMID: 29432492 PMCID: PMC5809059 DOI: 10.1371/journal.pone.0192575] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 01/25/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Wide-ranging evidence on the occurrence of fluoroquinolone (FQ) resistance genetic determinants in African Salmonella strains is not available. The main objectives of this study were to assess the heterogeneity, estimate pooled proportions and describe the preponderance of FQ-resistance determinants in typhoidal and non-typhoidal Salmonella (NTS) isolates of Africa. METHODS Genetic and phenotypic data on 6103 Salmonella isolates were considered. Meta- and frequency analyses were performed depending on the number of studies by category, number of isolates and risks of bias. A random effects model was used to assess heterogeneity and estimate pooled proportions. Relative and cumulative frequencies were calculated to describe the overall preponderance of FQ-resistance determinants in quinolone resistant isolates. RESULTS The pooled proportion of gyrA mutants (Salmonella enterica serovar Typhi, Salmonella enterica serovar Typhimurium, and Salmonella enterica serovar Enteritidis) was estimated at 5.7% (95% Confidence interval (CI) = 2.6, 9.8; Tau squared (T2) = 0.1105), and was higher in S. Typhi than in S. Typhimurium (odds ratio (OR) = 3.3, 95%CI = 2, 5.7). The proportions of each of gyrB and parC mutants, and strains with Plasmid Mediated Quinolone Resistance genes (qnrA, qnrB and qnrS) were low (≤ 0.3%). Overall, 23 mutant serotypes were identified, and most strains had mutations at codons encoding Ser83 and Asp87 of gyrA (82%, 95%CI = 78, 86). CONCLUSIONS Mutations at gyrA appear to account for ciprofloxacin non-susceptibility in most clinical Salmonella strains in Africa. The estimates could be harnessed to develop a mismatch-amplification mutation-assay for the detection of FQ-resistant strains in Africa.
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Affiliation(s)
- Getachew Tadesse
- Department of Biomedical Sciences, College of Veterinary Medicine and Agriculture, Addis Ababa University, Debre Zeit, Ethiopia
| | - Tesfaye S. Tessema
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Getenet Beyene
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute (AHRI), ALERT Campus, Addis Ababa, Ethiopia
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Dyson ZA, Thanh DP, Bodhidatta L, Mason CJ, Srijan A, Rabaa MA, Vinh PV, Thanh TH, Thwaites GE, Baker S, Holt KE. Whole Genome Sequence Analysis of Salmonella Typhi Isolated in Thailand before and after the Introduction of a National Immunization Program. PLoS Negl Trop Dis 2017; 11:e0005274. [PMID: 28060810 PMCID: PMC5245908 DOI: 10.1371/journal.pntd.0005274] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/19/2017] [Accepted: 12/20/2016] [Indexed: 12/31/2022] Open
Abstract
Vaccines against Salmonella Typhi, the causative agent of typhoid fever, are commonly used by travellers, however, there are few examples of national immunization programs in endemic areas. There is therefore a paucity of data on the impact of typhoid immunization programs on localised populations of S. Typhi. Here we have used whole genome sequencing (WGS) to characterise 44 historical bacterial isolates collected before and after a national typhoid immunization program that was implemented in Thailand in 1977 in response to a large outbreak; the program was highly effective in reducing typhoid case numbers. Thai isolates were highly diverse, including 10 distinct phylogenetic lineages or genotypes. Novel prophage and plasmids were also detected, including examples that were previously only reported in Shigella sonnei and Escherichia coli. The majority of S. Typhi genotypes observed prior to the immunization program were not observed following it. Post-vaccine era isolates were more closely related to S. Typhi isolated from neighbouring countries than to earlier Thai isolates, providing no evidence for the local persistence of endemic S. Typhi following the national immunization program. Rather, later cases of typhoid appeared to be caused by the occasional importation of common genotypes from neighbouring Vietnam, Laos, and Cambodia. These data show the value of WGS in understanding the impacts of vaccination on pathogen populations and provide support for the proposal that large-scale typhoid immunization programs in endemic areas could result in lasting local disease elimination, although larger prospective studies are needed to test this directly. Typhoid fever is a systemic infection caused by the bacterium Salmonella Typhi. Typhoid fever is associated with inadequate hygiene in low-income settings and a lack of sanitation infrastructure. A sustained outbreak of typhoid fever occurred in Thailand in the 1970s, which peaked in 1975–1976. In response to this typhoid fever outbreak the government of Thailand initiated an immunization program, which resulted in a dramatic reduction in the number of typhoid cases in Thailand. To better understand the population of S. Typhi circulating in Thailand at this time, as well as the impact of the immunization program on the pathogen population, we sequenced the genomes of 44 S. Typhi obtained from hospitals in Thailand before and after the immunization program. The genome sequences showed that isolates of S. Typhi bacteria isolated from post-immunization era typhoid cases were likely imported from neighbouring countries, rather than strains that have persisted in Thailand throughout the immunization period. Our work provides the first historical insights into S. Typhi in Thailand during the 1970s, and provides a model for the impact of immunization on S. Typhi populations.
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Affiliation(s)
- Zoe A. Dyson
- Centre for Systems Genomics, University of Melbourne, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (KEH); (ZAD)
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ladaporn Bodhidatta
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Carl Jeffries Mason
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Apichai Srijan
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Maia A. Rabaa
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
| | - Phat Voong Vinh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tuyen Ha Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Guy E. Thwaites
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kathryn E. Holt
- Centre for Systems Genomics, University of Melbourne, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (KEH); (ZAD)
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