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

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.

KEYWORDS:

• Clostridioides difficile infection
• asymptomatic carrier
• multiple sources
• comparative genome
• transmission

Acknowledgments

We thank Jinru Ji, Chaoqun Ying, Zhiying Liu, and Lisi Zheng for providing assistance with bacterial identification, Xu Hao, Dr. Juan Hu, Dr. Jingchen Zhang, and Dr. Jun Xu for providing support for sample collection, Beiwen Zheng and Qixia Luo for providing assistance with manuscript revision, and Dazhi Jin and Xiaojun Song for providing assistance with strains ribotyping.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Disclosure of potential conflicts of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Data availability statement

This whole-genome shotgun project of 98 C. difficile isolates was submitted to GenBank under accession numbers JACFUE000000000-JACFXP000000000 and JAGDLT000000000-JAGDMA000000000 (Table S2). The version described in this paper is the first version.

Additional information

Funding

This study was supported by grants from the National Key Research and Development Program of China (2017YFC1200203), and National Natural Science Foundation of China (81971984 and 31671366).