Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes.

Autor:	Carey ME; Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom.; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom.; IAVI, Chelsea & Westminster Hospital, London, United Kingdom., Dyson ZA; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom.; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia.; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom., Ingle DJ; Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia., Amir A; National Institute of Health, Islamabad, Pakistan., Aworh MK; Nigeria Field Epidemiology and Laboratory Training Programme, Abuja, Nigeria.; College of Veterinary Medicine, North Carolina State University, Raleigh, United States., Chattaway MA; United Kingdom Health Security Agency, London, United Kingdom., Chew KL; National University Hospital, Singapore, Singapore., Crump JA; Centre for International Health, University of Otago, Dunedin, New Zealand., Feasey NA; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.; Malawi-Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi., Howden BP; Centre for Pathogen Genomics, Department of Microbiology and Immunology, University of Melbourne at Doherty Institute for Infection and Immunity, Melbourne, Australia.; Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia., Keddy KH; Independent consultant, Johannesburg, South Africa., Maes M; Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom., Parry CM; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom., Van Puyvelde S; Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom.; University of Antwerp, Antwerp, Belgium., Webb HE; Centers for Disease Control and Prevention, Atlanta, United States., Afolayan AO; Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria., Alexander AP; Lady Willingdon Hospital, Manali, India., Anandan S; Department of Clinical Microbiology, Christian Medical College, Vellore, India., Andrews JR; Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, United States., Ashton PM; Malawi-Liverpool Wellcome Programme, Blantyre, Malawi.; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom., Basnyat B; Oxford University Clinical Research Unit Nepal, Kathmandu, Nepal., Bavdekar A; KEM Hospital Research Centre, Pune, India., Bogoch II; Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Canada., Clemens JD; International Vaccine Institute, Seoul, Republic of Korea.; International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.; UCLA Fielding School of Public Health, Los Angeles, United States.; Korea University, Seoul, Republic of Korea., da Silva KE; Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, United States., De A; Topiwala National Medical College, Mumbai, India., de Ligt J; ESR, Institute of Environmental Science and Research Ltd., Porirua, Wellington, New Zealand., Diaz Guevara PL; Grupo de Microbiologia, Instituto Nacional de Salud, Bogota, Colombia., Dolecek C; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.; Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand., Dutta S; ICMR - National Institute of Cholera & Enteric Diseases, Kolkata, India., Ehlers MM; Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.; Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Pretoria, South Africa., Francois Watkins L; Centers for Disease Control and Prevention, Atlanta, United States., Garrett DO; Sabin Vaccine Institute, Washington DC, United States., Godbole G; United Kingdom Health Security Agency, London, United Kingdom., Gordon MA; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom., Greenhill AR; Federation University Australia, Churchill, Australia.; Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea., Griffin C; Centers for Disease Control and Prevention, Atlanta, United States., Gupta M; Post Graduate Institute of Medical Education and Research, Chandigarh, India., Hendriksen RS; Technical University of Denmark, Copenhagen, Denmark., Heyderman RS; Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom., Hooda Y; Child Health Research Foundation, Dhaka, Bangladesh., Hormazabal JC; Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomedico, Instituto de Salud Publica de Chile (ISP), Santiago, Chile., Ikhimiukor OO; Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria., Iqbal J; Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan., Jacob JJ; Department of Clinical Microbiology, Christian Medical College, Vellore, India., Jenkins C; United Kingdom Health Security Agency, London, United Kingdom., Jinka DR; Rural Development Trust Hospital, Anantapur, India., John J; Department of Community Health, Christian Medical College, Vellore, India., Kang G; Department of Community Health, Christian Medical College, Vellore, India., Kanteh A; Medical Research Council Unit The Gambia at London School Hygiene & Tropical Medicine, Fajara, Gambia., Kapil A; All India Institute of Medical Sciences, Delhi, India., Karkey A; Oxford University Clinical Research Unit Nepal, Kathmandu, Nepal., Kariuki S; Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya., Kingsley RA; Quadram Institute Bioscience, Norwich, United Kingdom., Koshy RM; Makunda Christian Hospital, Assam, India., Lauer AC; Centers for Disease Control and Prevention, Atlanta, United States., Levine MM; Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USA, Baltimore, United States., Lingegowda RK; Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India., Luby SP; Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, United States., Mackenzie GA; Medical Research Council Unit The Gambia at London School Hygiene & Tropical Medicine, Fajara, Gambia., Mashe T; National Microbiology Reference Laboratory, Harare, Zimbabwe.; World Health Organization, Harare, Zimbabwe., Msefula C; Kamuzu University of Health Sciences, Blantyre, Malawi., Mutreja A; Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom., Nagaraj G; Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India., Nagaraj S; Saint Johns Medical College and Hospital, Bengaluru, India., Nair S; United Kingdom Health Security Agency, London, United Kingdom., Naseri TK; Ministry of Health, Government of Samoa, Apia, Samoa., Nimarota-Brown S; Ministry of Health, Government of Samoa, Apia, Samoa., Njamkepo E; Institut Pasteur, Université Paris Cité, Paris, France., Okeke IN; Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria., Perumal SPB; Kanchi Kamakoti CHILDS Trust Hospital, Chennai, India., Pollard AJ; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom.; The NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom., Pragasam AK; Department of Clinical Microbiology, Christian Medical College, Vellore, India., Qadri F; International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh., Qamar FN; Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan., Rahman SIA; International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh., Rambocus SD; Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia., Rasko DA; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, United States.; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, United States., Ray P; Post Graduate Institute of Medical Education and Research, Chandigarh, India., Robins-Browne R; Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia.; Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia., Rongsen-Chandola T; Centre for Health Research and Development, Society for Applied Studies, Delhi, India., Rutanga JP; University of Rwanda, College of Science and Technology, Kigali, Rwanda., Saha SK; Child Health Research Foundation, Dhaka, Bangladesh., Saha S; Child Health Research Foundation, Dhaka, Bangladesh., Saigal K; Chacha Nehru Bal Chikitsalaya, Delhi, India., Sajib MSI; Child Health Research Foundation, Dhaka, Bangladesh.; Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom., Seidman JC; Sabin Vaccine Institute, Washington DC, United States., Shakya J; Dhulikhel Hospital, Dhulikhel, Nepal.; Institute for Research in Science and Technology, Kathmandu, Nepal., Shamanna V; Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India., Shastri J; Topiwala National Medical College, Mumbai, India.; Kasturba Hospital for Infectious Diseases, Mumbai, India., Shrestha R; Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University Hospital, Dhulikhel, Nepal., Sia S; Research Institute for Tropical Medicine, Department of Health, Muntinlupa City, Philippines., Sikorski MJ; Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USA, Baltimore, United States.; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, United States.; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, United States., Singh A; Chinchpada Christian Hospital, Navapur, India., Smith AM; Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa., Tagg KA; Centers for Disease Control and Prevention, Atlanta, United States., Tamrakar D; Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University Hospital, Dhulikhel, Nepal., Tanmoy AM; Child Health Research Foundation, Dhaka, Bangladesh., Thomas M; Christian Medical College, Ludhiana, Ludhiana, India., Thomas MS; Duncan Hospital, Raxaul, India., Thomsen R; Ministry of Health, Government of Samoa, Apia, Samoa., Thomson NR; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom., Tupua S; Ministry of Health, Government of Samoa, Apia, Samoa., Vaidya K; University of California Davis, Davis, United States., Valcanis M; Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia., Veeraraghavan B; Department of Clinical Microbiology, Christian Medical College, Vellore, India., Weill FX; Institut Pasteur, Université Paris Cité, Paris, France., Wright J; ESR, Institute of Environmental Science and Research Ltd., Porirua, Wellington, New Zealand., Dougan G; Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom., Argimón S; Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom., Keane JA; Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom., Aanensen DM; Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom., Baker S; Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom.; IAVI, Chelsea & Westminster Hospital, London, United Kingdom., Holt KE; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom.; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia.
Jazyk:	angličtina
Zdroj:	ELife [Elife] 2023 Sep 12; Vol. 12. Date of Electronic Publication: 2023 Sep 12.
DOI:	10.7554/eLife.85867
Abstrakt:	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]). Competing Interests: MC, ZD, DI, AA, MA, MC, KC, JC, BH, KK, MM, CP, SV, HW, AA, AA, SA, JA, PA, BB, AB, JC, Kd, AD, Jd, PD, CD, SD, ME, LF, DG, GG, MG, AG, CG, MG, RH, RH, YH, JH, OI, JI, JJ, CJ, DJ, JJ, GK, AK, AK, AK, SK, RK, RK, AL, ML, RL, SL, GM, TM, CM, AM, GN, SN, SN, TN, SN, EN, IO, SP, AP, FQ, FQ, SR, SR, DR, PR, RR, TR, JR, SS, SS, KS, MS, JS, JS, VS, JS, RS, SS, MS, AS, AS, KT, DT, AT, MT, MT, RT, NT, ST, KV, MV, BV, FW, JW, GD, SA, JK, DA, SB, KH No competing interests declared, NF NAF chairs the Wellcome Surveillance and Epidemiology of Drug Resistant Infections (SEDRIC) group, which has a focus on antimicrobial resistance. This could be perceived as relevant although not a direct conflict, IB IB has consulted to BlueDot and the NHL Players' Association, AP AJP is chair of the UK Department of Health and Social Care's (DHSC) Joint Committee on Vaccination and Immunisation (JCVI) but does not take part in the JCVI COVID-19 committee. He was a member of WHO SAGE until 2022. AJPs employer, Oxford University has entered into a partnership with AstraZeneca for development of a COVID-19 vaccine. AJP has provided advice to Shionogi & Co., Ltd on development of a COVID19 vaccine (© 2023, Carey et al.)
Databáze:	MEDLINE
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