Comparative genomic and transmission analysis of Clostridioides difficile between environmental, animal, and clinical sources in China.
Yanzi ZhouWangxiao ZhouTingting XiaoYunbo ChenTao LvYuan WangShuntian ZhangHongliu CaiXiaohui ChiXiaoyang KongKai ZhouPing ShenTongling ShanYong-Hong XiaoPublished in: Emerging microbes & infections (2022)
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.
Keyphrases
- escherichia coli
- clostridium difficile
- end stage renal disease
- drinking water
- chronic kidney disease
- ejection fraction
- newly diagnosed
- healthcare
- genome wide
- biofilm formation
- intensive care unit
- emergency department
- peritoneal dialysis
- prognostic factors
- staphylococcus aureus
- pseudomonas aeruginosa
- gene expression
- cystic fibrosis
- transcription factor
- dna methylation
- risk assessment
- acute care