1887

Abstract

Antimicrobial resistance (AMR) plays an important role in the pathogenesis and spread of infection (CDI), the leading healthcare-related gastrointestinal infection in the world. An association between AMR and CDI outbreaks is well documented, however, data is limited to a few ‘epidemic’ strains in specific geographical regions. Here, through detailed analysis of 10 330 publicly-available genomes from strains isolated worldwide (spanning 270 multilocus sequence types (STs) across all known evolutionary clades), this study provides the first species-wide snapshot of AMR genomic epidemiology in . Of the 10 330 . genomes, 4532 (43.9 %) in 89 STs across clades 1–5 carried at least one genotypic AMR determinant, with 901 genomes (8.7 %) carrying AMR determinants for three or more antimicrobial classes (multidrug-resistant, MDR). No AMR genotype was identified in any strains belonging to the cryptic clades. from Australia/New Zealand had the lowest AMR prevalence compared to strains from Asia, Europe and North America (<0.0001). Based on the phylogenetic clade, AMR prevalence was higher in clades 2 (84.3 %), 4 (81.5 %) and 5 (64.8 %) compared to other clades (collectively 26.9 %) (<0.0001). MDR prevalence was highest in clade 4 (61.6 %) which was over three times higher than in clade 2, the clade with the second-highest MDR prevalence (18.3 %). There was a strong association between specific AMR determinants and three major epidemic STs: ST1 (clade 2) with fluoroquinolone resistance (mainly T82I substitution in GyrA) (<0.0001), ST11 (clade 5) with tetracycline resistance (various -family genes) (<0.0001) and ST37 (clade 4) with macrolide-lincosamide-streptogramin B (MLS) resistance (mainly ) (<0.0001) and MDR (<0.0001). A novel and previously overlooked -positive transposon designated Tn was identified, predominantly among clade 2 strains. This study provides a comprehensive review of AMR in the global population which may aid in the early detection of drug-resistant strains, and prevention of their dissemination worldwide.

Funding
This study was supported by the:
  • Mahidol University
    • Principle Award Recipient: KorakritImwattana
  • National Health and Medical Research Council (Award APP1138257)
    • Principle Award Recipient: DanielR Knight
  • Raine Medical Research Foundation (Award RPG002-19)
    • Principle Award Recipient: DanielR Knight
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
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2021-11-18
2021-12-04
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