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Genomic diversity of antimicrobial resistance in non-typhoidal Salmonella in Victoria, Australia

Non-typhoidal Salmonella (NTS) is the second most common cause of foodborne bacterial gastroenteritis in Australia with antimicrobial resistance (AMR) increasing in recent years. Whole-genome sequencing (WGS) provides opportunities for in silico detection of AMR determinants. The objectives of this...

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Autores principales: Sia, Cheryll M., Baines, Sarah L., Valcanis, Mary, Lee, Darren Y. J., Gonçalves da Silva, Anders, Ballard, Susan A., Easton, Marion, Seemann, Torsten, Howden, Benjamin P., Ingle, Danielle J., Williamson, Deborah A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Microbiology Society 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8767345/
https://www.ncbi.nlm.nih.gov/pubmed/34907895
http://dx.doi.org/10.1099/mgen.0.000725
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author Sia, Cheryll M.
Baines, Sarah L.
Valcanis, Mary
Lee, Darren Y. J.
Gonçalves da Silva, Anders
Ballard, Susan A.
Easton, Marion
Seemann, Torsten
Howden, Benjamin P.
Ingle, Danielle J.
Williamson, Deborah A.
author_facet Sia, Cheryll M.
Baines, Sarah L.
Valcanis, Mary
Lee, Darren Y. J.
Gonçalves da Silva, Anders
Ballard, Susan A.
Easton, Marion
Seemann, Torsten
Howden, Benjamin P.
Ingle, Danielle J.
Williamson, Deborah A.
author_sort Sia, Cheryll M.
collection PubMed
description Non-typhoidal Salmonella (NTS) is the second most common cause of foodborne bacterial gastroenteritis in Australia with antimicrobial resistance (AMR) increasing in recent years. Whole-genome sequencing (WGS) provides opportunities for in silico detection of AMR determinants. The objectives of this study were two-fold: (1) establish the utility of WGS analyses for inferring phenotypic resistance in NTS, and (2) explore clinically relevant genotypic AMR profiles to third generation cephalosporins (3GC) in NTS lineages. The concordance of 2490 NTS isolates with matched WGS and phenotypic susceptibility data against 13 clinically relevant antimicrobials was explored. In silico serovar prediction and typing was performed on assembled reads and interrogated for known AMR determinants. The surrounding genomic context, plasmid determinants and co-occurring AMR patterns were further investigated for multidrug resistant serovars harbouring bla (CMY-2), bla (CTX-M-55) or bla (CTX-M-65). Our data demonstrated a high correlation between WGS and phenotypic susceptibility testing. Phenotypic-genotypic concordance was observed between 2440/2490 (98.0 %) isolates, with overall sensitivity and specificity rates >98 % and positive and negative predictive values >97 %. The most common AMR determinants were bla (TEM-1), sul2, tet(A), strA-strB and floR. Phenotypic resistance to cefotaxime and azithromycin was low and observed in 6.2 % (151/2486) and 0.9 % (16/1834) of the isolates, respectively. Several multi-drug resistant NTS lineages were resistant to 3GC due to different genetic mechanisms including bla (CMY-2), bla (CTX-M-55) or bla (CTX-M-65). This study shows WGS can enhance existing AMR surveillance in NTS datasets routinely produced in public health laboratories to identify emerging AMR in NTS. These approaches will be critical for developing capacity to detect emerging public health threats such as resistance to 3GC.
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spelling pubmed-87673452022-01-19 Genomic diversity of antimicrobial resistance in non-typhoidal Salmonella in Victoria, Australia Sia, Cheryll M. Baines, Sarah L. Valcanis, Mary Lee, Darren Y. J. Gonçalves da Silva, Anders Ballard, Susan A. Easton, Marion Seemann, Torsten Howden, Benjamin P. Ingle, Danielle J. Williamson, Deborah A. Microb Genom Research Articles Non-typhoidal Salmonella (NTS) is the second most common cause of foodborne bacterial gastroenteritis in Australia with antimicrobial resistance (AMR) increasing in recent years. Whole-genome sequencing (WGS) provides opportunities for in silico detection of AMR determinants. The objectives of this study were two-fold: (1) establish the utility of WGS analyses for inferring phenotypic resistance in NTS, and (2) explore clinically relevant genotypic AMR profiles to third generation cephalosporins (3GC) in NTS lineages. The concordance of 2490 NTS isolates with matched WGS and phenotypic susceptibility data against 13 clinically relevant antimicrobials was explored. In silico serovar prediction and typing was performed on assembled reads and interrogated for known AMR determinants. The surrounding genomic context, plasmid determinants and co-occurring AMR patterns were further investigated for multidrug resistant serovars harbouring bla (CMY-2), bla (CTX-M-55) or bla (CTX-M-65). Our data demonstrated a high correlation between WGS and phenotypic susceptibility testing. Phenotypic-genotypic concordance was observed between 2440/2490 (98.0 %) isolates, with overall sensitivity and specificity rates >98 % and positive and negative predictive values >97 %. The most common AMR determinants were bla (TEM-1), sul2, tet(A), strA-strB and floR. Phenotypic resistance to cefotaxime and azithromycin was low and observed in 6.2 % (151/2486) and 0.9 % (16/1834) of the isolates, respectively. Several multi-drug resistant NTS lineages were resistant to 3GC due to different genetic mechanisms including bla (CMY-2), bla (CTX-M-55) or bla (CTX-M-65). This study shows WGS can enhance existing AMR surveillance in NTS datasets routinely produced in public health laboratories to identify emerging AMR in NTS. These approaches will be critical for developing capacity to detect emerging public health threats such as resistance to 3GC. Microbiology Society 2021-12-15 /pmc/articles/PMC8767345/ /pubmed/34907895 http://dx.doi.org/10.1099/mgen.0.000725 Text en © 2021 The Authors https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
spellingShingle Research Articles
Sia, Cheryll M.
Baines, Sarah L.
Valcanis, Mary
Lee, Darren Y. J.
Gonçalves da Silva, Anders
Ballard, Susan A.
Easton, Marion
Seemann, Torsten
Howden, Benjamin P.
Ingle, Danielle J.
Williamson, Deborah A.
Genomic diversity of antimicrobial resistance in non-typhoidal Salmonella in Victoria, Australia
title Genomic diversity of antimicrobial resistance in non-typhoidal Salmonella in Victoria, Australia
title_full Genomic diversity of antimicrobial resistance in non-typhoidal Salmonella in Victoria, Australia
title_fullStr Genomic diversity of antimicrobial resistance in non-typhoidal Salmonella in Victoria, Australia
title_full_unstemmed Genomic diversity of antimicrobial resistance in non-typhoidal Salmonella in Victoria, Australia
title_short Genomic diversity of antimicrobial resistance in non-typhoidal Salmonella in Victoria, Australia
title_sort genomic diversity of antimicrobial resistance in non-typhoidal salmonella in victoria, australia
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8767345/
https://www.ncbi.nlm.nih.gov/pubmed/34907895
http://dx.doi.org/10.1099/mgen.0.000725
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