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Volume 10, Issue 5

Defining the phylogenetics and resistome of the major ribotypes circulating in Australia Open Access

Abstract

infection (CDI) remains a significant public health threat globally. New interventions to treat CDI rely on an understanding of the evolution and epidemiology of circulating strains. Here we provide longitudinal genomic data on strain diversity, transmission dynamics and antimicrobial resistance (AMR) of ribotypes (RTs) 014/020 (=169), 002 (=77) and 056 (=36), the three most prominent strains causing CDI in Australia. Genome scrutiny showed that AMR was uncommon in these lineages, with resistance-conferring alleles present in only 15/169 RT014/020 strains (8.9 %), 1/36 RT056 strains (2.78 %) and none of 77 RT002 strains. Notably, ~90 % of strains were resistant to MLS agents , but only ~5.9 % harboured known resistance alleles, highlighting an incongruence between AMR genotype and phenotype. Core genome analyses revealed all three RTs contained genetically heterogeneous strain populations with limited evidence of clonal transmission between CDI cases. The average number of pairwise core genome SNP (cgSNP) differences within each RT group ranged from 23.3 (RT056, ST34, =36) to 115.6 (RT002, ST8, =77) and 315.9 (RT014/020, STs 2, 13, 14, 49, =169). Just 19 clonal groups (encompassing 40 isolates), defined as isolates differing by ≤2 cgSNPs, were identified across all three RTs (RT014/020, =14; RT002, =3; RT056, =2). Of these clonal groups, 63 % (12/19) comprised isolates from the same Australian State and 37 % (7/19) comprised isolates from different States. The low number of plausible transmission events found for these major RTs (and previously documented populations in animal and environmental sources/reservoirs) points to widespread and persistent community sources of diverse strains as opposed to ongoing nationwide healthcare outbreaks dominated by a single clone. Together, these data provide new insights into the evolution of major lineages causing CDI in Australia and highlight the urgent need for enhanced surveillance, and for public health interventions to move beyond the healthcare setting and into a One Health paradigm to effectively combat this complex pathogen.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): AMR , Clostridioides difficile , epidemiology , microbial genomics and WGS
Funding
This study was supported by the:
  • Raine Medical Research Foundation (Award RPG002-19)
    • Principle Award Recipient: DanielR Knight
  • National Health and Medical Research Council (Award APP1138257)
    • Principle Award Recipient: DanielR Knight
© 2024 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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2024-05-08
2024-05-19
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Defining the phylogenetics and resistome of the major Clostridioides difficile ribotypes circulating in Australia
M Gen 10, 001232 (2024); https://doi.org/10.1099/mgen.0.001232
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