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Volume 7, Issue 12

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

Abstract

Non-typhoidal (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 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. 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 , or . 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 , , (A), and . 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 , or . 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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antimicrobial resistance , public health surveillance , Salmonella and whole genome sequencing
Funding
This study was supported by the:
  • National Health and Medical Research Council (Award GNT1196103)
    • Principle Award Recipient: BenjaminP Howden
  • National Health and Medical Research Council (Award GNT1195210)
    • Principle Award Recipient: DanielleJ Ingle
  • National Health and Medical Research Council (Award GNT1174555)
    • Principle Award Recipient: DeborahA Williamson
  • National Health and Medical Research Council (Award APP1149991)
    • Principle Award Recipient: BenjaminP Howden
  • National Health and Medical Research Council (Award APP1129770)
    • Principle Award Recipient: BenjaminP Howden
© 2021 The Authors
  • 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.
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2021-12-15
2024-04-25
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Genomic diversity of antimicrobial resistance in non-typhoidal Salmonella in Victoria, Australia
M Gen 7, 000725 (2021); https://doi.org/10.1099/mgen.0.000725
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