Mobility of antimicrobial resistance across serovars and disease presentations in non-typhoidal Salmonella from animals and humans in Vietnam

Bloomfield, Samuel, Duong, Vu Thuy, Tuyen, Ha Thanh, Campbell, James I., Thomson, Nicholas R., Parkhill, Julian, Phuc, Hoang Le, Chau, Tran Thi Hong, Maskell, Duncan J., Perron, Gabriel G., Ngoc, Nguyen Minh, Vi, Lu Lan, Adriaenssens, Evelien M., Baker, Stephen and Mather, Alison E. (2022) Mobility of antimicrobial resistance across serovars and disease presentations in non-typhoidal Salmonella from animals and humans in Vietnam. Microbial Genomics, 8 (5). ISSN 2057-5858

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Abstract

Non-typhoidal Salmonella (NTS) is a major cause of bacterial enterocolitis globally but also causes invasive bloodstream infections. Antimicrobial resistance (AMR) hampers the treatment of these infections and understanding how AMR spreads between NTS may help in developing effective strategies. We investigated NTS isolates associated with invasive disease, diarrhoeal disease and asymptomatic carriage in animals and humans from Vietnam. Isolates included multiple serovars and both common and rare phenotypic AMR profiles; long-and short-read sequencing was used to investigate the genetic mechanisms and genomic backgrounds associated with phenotypic AMR profiles. We demonstrate concordance between most AMR genotypes and phenotypes but identified large genotypic diversity in clinically relevant phenotypes and the high mobility potential of AMR genes (ARGs) in this setting. We found that 84% of ARGs identified were located on plasmids, most commonly those containing IncHI1A_1 and IncHI1B(R27)_1_R27 replicons (33%), and those containing IncHI2_1 and IncHI2A_1 replicons (31%). The vast majority (95%) of ARGS were found within 10 kbp of IS6/IS26 elements, which provide plasmids with a mechanism to exchange ARGs between plasmids and other parts of the genome. Whole genome sequencing with targeted long-read sequencing applied in a One Health context identified a comparatively limited number of insertion sequences and plasmid replicons associated with AMR. Therefore, in the context of NTS from Vietnam and likely for other settings as well, the mechanisms by which ARGs move contribute to a more successful AMR profile than the specific ARGs, facilitating the adaptation of bacteria to different environments or selection pressures.

Item Type: Article
Additional Information: Funding Information: This work was supported by Biotechnology and Biological Sciences Research Council (BBSRC) Anniversary Future Leader fellowship BB/M014088/1 to AEM; SB (at QIB) and AEM are supported by 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); NRT is supported by Wellcome Trust grant 098051; EMA is funded by the BBSRC Institute Strategic Programme Gut Microbes BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356; SB is supported by a Wellcome senior research fellowship (215515/Z/19/Z) and the Sir Henry Dale Fellowship, jointly funded by the Wellcome Trust and the Royal Society (100087/Z/12/Z). The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Uncontrolled Keywords: antimicrobial resistance,chromosome arrangements,insertion sequences,plasmids,salmonella,epidemiology,microbiology,molecular biology,genetics ,/dk/atira/pure/subjectarea/asjc/2700/2713
Faculty \ School:
UEA Research Groups: Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health
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Depositing User: LivePure Connector
Date Deposited: 04 Nov 2022 17:30
Last Modified: 15 Jul 2024 01:14
URI: https://ueaeprints.uea.ac.uk/id/eprint/89632
DOI: 10.1099/mgen.0.000798

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