Emerging Microbes and Infections (Jan 2021)

Comparative genomic and transmission analysis of Clostridioides difficile between environmental, animal, and clinical sources in China

  • Yanzi Zhou,
  • Wangxiao Zhou,
  • Tingting Xiao,
  • Yunbo Chen,
  • Tao Lv,
  • Yuan Wang,
  • Shuntian Zhang,
  • Hongliu Cai,
  • Xiaohui Chi,
  • Xiaoyang Kong,
  • Kai Zhou,
  • Ping Shen,
  • Tongling Shan,
  • Yonghong Xiao

DOI
https://doi.org/10.1080/22221751.2021.2005453
Journal volume & issue
Vol. 10, no. 1
pp. 2244 – 2255

Abstract

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Clostridioides difficile is the most common pathogen causing antibiotic-associated diarrhea. Previous studies showed that diverse sources, aside from C. difficile infection (CDI) patients, played a major role in C. difficile hospital transmission. This study aimed to investigate relationships and transmission potential of C. difficile strains from different sources. A prospective study was conducted both in the intensive care unit (ICU) and six livestock farms in China in 2018–2019. Ninety-eight strains from CDI patients (10 isolates), asymptomatic hospitalized carriers (55), the ICU environment (12), animals (14), soil (4), and farmers (3) were collected. Sequence type (ST) 3/ribotype (RT) 001, ST35/RT046, and ST48/RT596 were dominant types, distributed widely in multiple sources. Core-genome single-nucleotide polymorphism (cgSNP) analysis showed that hospital and farm strains shared several common clonal groups (CGs, strains separated by ≤ 2 cgSNPs) (CG4/ST3/RT001, CG7/ST35/RT046, CG11/ST48/RT596). CDI patients, asymptomatic carriers, and the ICU environment strains also shared several common CGs. The number of virulence genes was not statistically different between strains from different sources. Multi-source strains in the same CG carried identical virulence gene sequences, including pathogenicity genes at the pathogenicity locus and adhesion-related genes at S-layer cassette. Resistance genes (ermB, tetM, etc.) were widespread in multiple sources, and multi-source strains in the same CG had similar resistance phenotypes and carried consistent transposons and plasmid types. The study indicated that interspecies and cross-regional transmission of C. difficile occurs between animals, the environment, and humans. Community-associated strains from both farms and asymptomatic hospitalized carriers were important reservoirs of CDI in hospitals.

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