دورية أكاديمية
Pathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study.
| العنوان: | Pathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study. |
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| المؤلفون: | Dyson ZA; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK. Electronic address: zoe.dyson@lshtm.ac.uk., Ashton PM; Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi; Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK., Khanam F; International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh., Chunga Chirambo A; Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi; Kamuzu University of Health Sciences, Blantyre, Malawi., Shakya M; Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal., Meiring JE; Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK., Tonks S; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK., Karkey A; Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal; Centre for Tropical Medicine and Global Health, Medical Sciences Division, Nuffield Department of Medicine, University of Oxford, Oxford, UK., Msefula C; Kamuzu University of Health Sciences, Blantyre, Malawi., Clemens JD; International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh; International Vaccine Institute, Seoul, South Korea., Dunstan SJ; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia., Baker S; Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK., Dougan G; Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK., Pitzer VE; Department of Epidemiology of Microbial Diseases and the Public Health Modeling Unit, Yale School of Public Health, Yale University, New Haven, CT, USA., Basnyat B; Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal; Centre for Tropical Medicine and Global Health, Medical Sciences Division, Nuffield Department of Medicine, University of Oxford, Oxford, UK., Qadri F; International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh., Heyderman RS; NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK., Gordon MA; Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi; Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK; Kamuzu University of Health Sciences, Blantyre, Malawi; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK., Pollard AJ; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK., Holt KE; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia. |
| مؤلفون مشاركون: | STRATAA Study Group |
| المصدر: | The Lancet. Microbe [Lancet Microbe] 2024 Aug; Vol. 5 (8), pp. 100841. Date of Electronic Publication: 2024 Jul 09. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Elsevier Ltd Country of Publication: England NLM ID: 101769019 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2666-5247 (Electronic) Linking ISSN: 26665247 NLM ISO Abbreviation: Lancet Microbe Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: [Oxford] : Elsevier Ltd., [2020]- |
| مواضيع طبية MeSH: | Typhoid Fever*/epidemiology , Typhoid Fever*/microbiology , Typhoid Fever*/transmission , Typhoid Fever*/drug therapy , Salmonella typhi*/genetics , Salmonella typhi*/drug effects , Anti-Bacterial Agents*/pharmacology , Phylogeny* , Salmonella paratyphi A*/genetics , Salmonella paratyphi A*/drug effects, Humans ; Bangladesh/epidemiology ; Nepal/epidemiology ; Child ; Adult ; Child, Preschool ; Malawi/epidemiology ; Male ; Adolescent ; Drug Resistance, Bacterial/genetics ; Female ; Infant ; Paratyphoid Fever/epidemiology ; Paratyphoid Fever/microbiology ; Paratyphoid Fever/transmission ; Paratyphoid Fever/drug therapy ; Young Adult ; Genotype ; Genome, Bacterial/genetics ; Microbial Sensitivity Tests ; Middle Aged ; Genomics |
| مستخلص: | Background: Enteric fever is a serious public health concern. The causative agents, Salmonella enterica serovars Typhi and Paratyphi A, frequently have antimicrobial resistance (AMR), leading to limited treatment options and poorer clinical outcomes. We investigated the genomic epidemiology, resistance mechanisms, and transmission dynamics of these pathogens at three urban sites in Africa and Asia. Methods: S Typhi and S Paratyphi A bacteria isolated from blood cultures of febrile children and adults at study sites in Dhaka (Bangladesh), Kathmandu (Nepal), and Blantyre (Malawi) during STRATAA surveillance were sequenced. Isolates were charactered in terms of their serotypes, genotypes (according to GenoTyphi and Paratype), molecular determinants of AMR, and population structure. We used phylogenomic analyses incorporating globally representative genomic data from previously published surveillance studies and ancestral state reconstruction to differentiate locally circulating from imported pathogen AMR variants. Clusters of sequences without any single-nucleotide variants in their core genome were identified and used to explore spatiotemporal patterns and transmission dynamics. Findings: We sequenced 731 genomes from isolates obtained during surveillance across the three sites between Oct 1, 2016, and Aug 31, 2019 (24 months in Dhaka and Kathmandu and 34 months in Blantyre). S Paratyphi A was present in Dhaka and Kathmandu but not Blantyre. S Typhi genotype 4.3.1 (H58) was common in all sites, but with different dominant variants (4.3.1.1.EA1 in Blantyre, 4.3.1.1 in Dhaka, and 4.3.1.2 in Kathmandu). Multidrug resistance (ie, resistance to chloramphenicol, co-trimoxazole, and ampicillin) was common in Blantyre (138 [98%] of 141 cases) and Dhaka (143 [32%] of 452), but absent from Kathmandu. Quinolone-resistance mutations were common in Dhaka (451 [>99%] of 452) and Kathmandu (123 [89%] of 138), but not in Blantyre (three [2%] of 141). Azithromycin-resistance mutations in acrB were rare, appearing only in Dhaka (five [1%] of 452). Phylogenetic analyses showed that most cases derived from pre-existing, locally established pathogen variants; 702 (98%) of 713 drug-resistant infections resulted from local circulation of AMR variants, not imported variants or recent de novo emergence; and pathogen variants circulated across age groups. 479 (66%) of 731 cases clustered with others that were indistinguishable by point mutations; individual clusters included multiple age groups and persisted for up to 2·3 years, and AMR determinants were invariant within clusters. Interpretation: Enteric fever was associated with locally established pathogen variants that circulate across age groups. AMR infections resulted from local transmission of resistant strains. These results form a baseline against which to monitor the impacts of control measures. Funding: Wellcome Trust, Bill & Melinda Gates Foundation, EU Horizon 2020, and UK National Institute for Health and Care Research. Competing Interests: Declaration of interests AJP is Chair of the UK Government Department of Health and Social Care’s Joint Committee on Vaccination and Immunisation (unpaid) and was a member of WHO's SAGE until 2022 (unpaid). VEP has received travel reimbursement from Merck and Pfizer for attending scientific input engagements unrelated to the topic of the manuscript, and is a member of the WHO Immunization and Vaccine-related Implementation Research Advisory Committee. All other authors declare no competing interests. (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.) |
| فهرسة مساهمة: | Investigator: HC Banda, Malawi-Liverpool Wellcome Programme, Blantyre, Malawi.; PK Biswas, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.; MAI Bhuiyan, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.; C Blohmke, Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.; TC Darton, Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.; C Dolecek, Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.; S Dongol, Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal.; YF Mujadidi, Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.; J Hill, Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.; NT Hoang, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.; TM Jere, Malawi-Liverpool Wellcome Programme, Blantyre, Malawi.; M Mbewe, Malawi-Liverpool Wellcome Programme, Blantyre, Malawi.; H Msuku, Malawi-Liverpool Wellcome Programme, Blantyre, Malawi.; TVT Nga, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.; R Nkhata, Malawi-Liverpool Wellcome Programme, Blantyre, Malawi.; SI Rahman, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.; N Rahman, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.; NJ Saad, Department of Epidemiology of Microbial Diseases and the Public Health Modeling Unit, Yale School of Public Health, Yale University, New Haven, CT, USA.; TV Tan, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.; D Thindwa, Malawi-Liverpool Wellcome Programme, Blantyre, Malawi.; M Voysey, Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.; R Wachepa, Malawi-Liverpool Wellcome Programme, Blantyre, Malawi. |
| المشرفين على المادة: | 0 (Anti-Bacterial Agents) |
| تواريخ الأحداث: | Date Created: 20240712 Date Completed: 20240808 Latest Revision: 20240808 |
| رمز التحديث: | 20240809 |
| مُعرف محوري في PubMed: | PMC11300424 |
| DOI: | 10.1016/S2666-5247(24)00047-8 |
| PMID: | 38996496 |
| قاعدة البيانات: | MEDLINE |
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Full Text Finder | تدمد: | 2666-5247 |
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| DOI: | 10.1016/S2666-5247(24)00047-8 |