Comparative genomic and transmission analysis of Clostridioides difficile between environmental, animal, and clinical sources in China. Issue 1 (1st January 2021)

• Record Type: Journal Article
• Authors: Zhou, Yanzi; Zhou, Wangxiao; Xiao, Tingting; Chen, Yunbo; Lv, Tao; Wang, Yuan; Zhang, Shuntian; Cai, Hongliu; Chi, Xiaohui; Kong, Xiaoyang; Zhou, Kai; Shen, Ping; Shan, Tongling; Xiao, Yonghong
• Is Part Of: Emerging microbes & infections. Volume 10:Issue 1(2021)
• Page Start: 2244
• Page End: 2255
• Publication Date: 2021-01-01
• Subjects: Clostridioides difficile infection -- asymptomatic carrier -- multiple sources -- comparative genome -- transmission; Medical microbiology -- Periodicals; Communicable diseases -- Periodicals; Infection -- Periodicals; 616.9041
• DOI: 10.1080/22221751.2021.2005453
• Languages: English
• ISSNs: 2222-1751

Abstract

ABSTRACT: 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.