Multidrug resistance plasmids underlie clonal expansions and international spread of Salmonella enterica serotype 4,,12,i:- ST34 in Southeast Asia

Chung The, H.; Pham, P.; Thanh Tuyen, H.; Vo Kim Phuong, L.; Phuong Yen, N. T.; Le, S.-N. H.; Duong, V. T.; Chau, T. T. H.; Phuc, H. L.; Ngoc, N. M.; Lan Vi, L.; Mather, A.; Thwaites, G.; Thomson, N. R.; Baker, S.; Pham, D. T.

doi:10.1101/2023.01.10.523379

bioRxiv · 10.1101/2023.01.10.523379

Multidrug resistance plasmids underlie clonal expansions and international spread of Salmonella enterica serotype 4,,12,i:- ST34 in Southeast Asia

Chung The, H.·Pham, P.·Thanh Tuyen, H.·Vo Kim Phuong, L.·Phuong Yen, N. T.·Le, S.-N. H.·Duong, V. T.·Chau, T. T. H.·Phuc, H. L.·Ngoc, N. M.·Lan Vi, L.·Mather, A.·Thwaites, G.·Thomson, N. R.·Baker, S.·Pham, D. T.

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Abstract

Salmonella enterica serotype 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 pathogens 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 blaCTX-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 hotspot for the emergence and dissemination of multidrug resistant Salmonella ST34, and mutation analysis suggests of selection in antimicrobial responses and key virulence factors. Our work enriches the understanding on epidemiology and evolution of this variant in Southeast Asia, and determines that multidrug resistance plasmids have driven its local and potentially global success.

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Chung The, H., Pham, P., Thanh Tuyen, H., Vo Kim Phuong, L., Phuong Yen, N. T., Le, S.-N. H., Duong, V. T., Chau, T. T. H., Phuc, H. L., Ngoc, N. M., Lan Vi, L., Mather, A., Thwaites, G., Thomson, N. R., Baker, S., Pham, D. T.. 2023-01-10. Multidrug resistance plasmids underlie clonal expansions and international spread of Salmonella enterica serotype 4,,12,i:- ST34 in Southeast Asia. https://doi.org/10.1101/2023.01.10.523379

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