Defining the phylogenetics and resistome of the major Clostridioides difficile ribotypes circulating in Australia

Keeley O'Grady; Stacey Hong; Papanin Putsathit; Narelle George; Christine Hemphill; Peter G Huntington; Tony M Korman; Despina Kotsanas; Monica Lahra; Rodney McDougall; Andrew McGlinchey; Avram Levy; Casey V Moore; Graeme Nimmo; Louise Prendergast; Jennifer Robson; David J Speers; Lynette Waring; Michael C Wehrhahn; Gerhard F Weldhagen; Richard M Wilson; Thomas V Riley; Daniel R Knight

doi:10.1099/mgen.0.001232

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Defining the phylogenetics and resistome of the major Clostridioides difficile ribotypes circulating in Australia

Journal article

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Defining the phylogenetics and resistome of the major Clostridioides difficile ribotypes circulating in Australia

Keeley O'Grady, Stacey Hong, Papanin Putsathit, Narelle George, Christine Hemphill, Peter G Huntington, Tony M Korman, Despina Kotsanas, Monica Lahra, Rodney McDougall, …

Microbial genomics, Vol.10(5), 1232

2024

DOI: https://doi.org/10.1099/mgen.0.001232

PMID: 38717815

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Abstract

Anti-Bacterial Agents - pharmacology

Australia - epidemiology

Clostridioides difficile - classification

Clostridioides difficile - drug effects

Clostridioides difficile - genetics

Clostridioides difficile - isolation & purification

Clostridium Infections - epidemiology

Clostridium Infections - microbiology

Clostridium Infections - transmission

Drug Resistance, Bacterial - genetics

Genome, Bacterial

Genotype

Humans

Phylogeny

Polymorphism, Single Nucleotide

Ribotyping

Clostridioides difficile 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 C. difficile ribotypes (RTs) 014/020 (n=169), 002 (n=77) and 056 (n=36), the three most prominent C. difficile 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 MLSB agents in vitro, 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, n=36) to 115.6 (RT002, ST8, n=77) and 315.9 (RT014/020, STs 2, 13, 14, 49, n=169). Just 19 clonal groups (encompassing 40 isolates), defined as isolates differing by ≤2 cgSNPs, were identified across all three RTs (RT014/020, n=14; RT002, n=3; RT056, n=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 C. difficile 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.

Details

Title: Defining the phylogenetics and resistome of the major Clostridioides difficile ribotypes circulating in Australia
Authors/Creators: Keeley O'Grady - Centre for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
Stacey Hong - Government of Western Australia Department of Health
Papanin Putsathit - Edith Cowan University
Narelle George - Royal Brisbane and Women's Hospital
Christine Hemphill - Melbourne Pathology, Collingwood, Victoria, Australia
Peter G Huntington - Department of Microbiology, NSW Health Pathology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
Tony M Korman - Monash Health
Despina Kotsanas - Monash Medical Centre
Monica Lahra - Prince of Wales Hospital
Rodney McDougall - Sullivan Nicolaides Pathology
Andrew McGlinchey - Melbourne Pathology, Collingwood, Victoria, Australia
Avram Levy - Pathwest Laboratory Medicine
Casey V Moore - South Australia Pathology
Graeme Nimmo - Pathology Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
Louise Prendergast - Melbourne Pathology, Collingwood, Victoria, Australia
Jennifer Robson - Sullivan Nicolaides Pathology, Taringa, Queensland, Australia
David J Speers - Pathwest Laboratory Medicine
Lynette Waring - Melbourne Pathology, Collingwood, Victoria, Australia
Michael C Wehrhahn - Douglass Hanly Moir Pathology
Gerhard F Weldhagen - South Australia Pathology
Richard M Wilson - Australian Clinical Labs, Microbiology Department, Wayville, South Australia, Australia
Thomas V Riley - School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
Daniel R Knight - Pathwest Laboratory Medicine
Publication Details: Microbial genomics, Vol.10(5), 1232
Publisher: Microbiology Society
Identifiers: 991005664669407891
Murdoch Affiliation: Centre for Biosecurity and One Health
Language: English
Resource Type: Journal article

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