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ToolsChung The, Hao, Pham, Phuong, Ha Thanh, Tuyen, Phuong, Linh Vo Kim, Yen, Nguyen Phuong, Le, Son Nam H., Vu Thuy, Duong, Chau, Tran Thi Hong, Le Phuc, Hoang, Ngoc, Nguyen Minh, Vi, Lu Lan, Mather, Alison E., Thwaites, Guy E., Thomson, Nicholas R., Baker, Stephen and Pham, Duy Thanh (2023) Multidrug resistance plasmids underlie clonal expansions and international spread of Salmonella enterica serotype 1,4,[5],12:i:- ST34 in Southeast Asia. Communications Biology, 6. ISSN 2399-3642
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Abstract
Salmonella enterica serotype 1,4,[5],12:i:- (Typhimurium monophasic variant) of sequence type (ST) 34 has emerged as the predominant pandemic genotype in recent decades. Despite increasing reports of resistance to antimicrobials in Southeast Asia, Salmonella ST34 population structure and evolution remained understudied in the region. Here we performed detailed genomic investigations on 454 ST34 genomes collected from Vietnam and diverse geographical sources to elucidate the pathogen’s epidemiology, evolution and antimicrobial resistance. We showed that ST34 has been introduced into Vietnam in at least nine occasions since 2000, forming five co-circulating major clones responsible for paediatric diarrhoea and bloodstream infection. Most expansion events were associated with acquisitions of large multidrug resistance plasmids of IncHI2 or IncA/C2. Particularly, the self-conjugative IncA/C2 pST34VN2 (co-transferring bla CTX-M-55, mcr-3.1, and qnrS1) underlies local expansion and intercontinental spread in two separate ST34 clones. At the global scale, Southeast Asia was identified as a potential hub for the emergence and dissemination of multidrug resistant Salmonella ST34, and mutation analysis suggests of selection in antimicrobial responses and key virulence factors.
| Item Type: | Article |
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| Additional Information: | Data availability statement: Raw sequence data are available in the European Nucleotide Archive (ENA) under the project number PRJEB9121. Full-length plasmid sequences generated in this study are deposited in the Genbank repository under the accession numbers OQ658820- OQ658824. Supplementary Data 1 provides the detailed accession numbers and metadata for all genomes used in this study. Supplementary Data 2 provides source data for Figs. 2b, 2c, 3 and 5b. Code availability statement: Source data and R codes used for mutation analysis, phylogeography analysis and visualisation are deposited in Github (https://github.com/Hao-Chung/Salmonella_ST34_SEA). Funding Information: H.C.T. is a Wellcome International Training Fellow (218726/Z/19/Z). A.E.M. is supported by the Biotechnology and Biological Sciences Research Council (BBSRC) through the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10348 (Theme 1, Epidemiology and Evolution of Pathogens in the Food Chain). S.B. is a Wellcome Senior Research Fellow (215515/Z/19/Z). D.T.P. is supported by the Wellcome International Training Fellowship (222983/Z/21/Z). |
| Uncontrolled Keywords: | medicine (miscellaneous),biochemistry, genetics and molecular biology(all),agricultural and biological sciences(all),sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/2700/2701 |
| Faculty \ School: | Faculty of Medicine and Health Sciences > Norwich Medical School |
| UEA Research Groups: | Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 25 Oct 2024 14:30 |
| Last Modified: | 31 Oct 2024 00:52 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97219 |
| DOI: | 10.1038/s42003-023-05365-1 |
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