Changing patterns and biological features of community-acquired <i>Clostridioides difficile</i> infection in Southwest China: 7 years of surveillance data

The molecular epidemiological features of community-acquired <i>Clostridioides difficile</i> infection in Southwest China from 7 years of surveillance data were analyzed. Four representative <i>C. difficile</i> strains were selected for RNA-seq, biofilm formation, toxin expression, and cytotoxicity assays. Overall, 5.04% of the <i>C. difficile</i> strains were isolated within 7 years, 85.51% of which were toxigenic <i>C. difficile</i> (both <i>tcdA</i>+/<i>tcdB</i>+). Multilocus sequence typing (ST) and genomic sequencing divided all the isolates into two clusters, namely, clade 1 and clade 4, respectively. ST37 of <i>C. difficile</i> gradually replaced the ST3, ST35, and ST54 genotypes and became the dominant genotype in this area. The antibiotic resistance rate of strains in clade 4 was higher than that in clade 1, especially for the ST37 genotype strains, which were resistant to quinolones. Four <i>C. difficile</i> strains, R20291 (RT027), CD21062 (RT078), CD279 (ST54), and CD413 (ST37), were selected as representative isolates for subsequent biological investigations. RNA-seq revealed that the DEGs of <i>C. difficile</i> ST54 were enriched mainly in ABC transporters, two-component systems, and quorum sensing (QS) pathways and exhibited strong biofilm formation ability. The DEGs of the ST37 genotype strains were mainly enriched in the phosphotransferase system (PTS), ribosome, and some sugar and amino acid metabolism pathways, suggesting that these isolates have increased proliferation and metabolic status. On the other hand, <i>C. difficile</i> R20291 had the highest level of toxin transcription, expression, and cytotoxicity among these four strains. These genotype strains had their own biological characteristics, which provided certain clues for analyzing the causes of these changes.IMPORTANCEThis study carried out a molecular epidemiological investigation of community-acquired <i>C. difficile</i> infection in Southwest China and revealed the characteristics of genotype pattern changes in the strains. <i>C. difficile</i> ST37 gradually replaced the ST3, ST35, and ST54 genotypes to become the dominant strains in this area. Moreover, some representative strains were used to study their biological features. The ST54 strain had strong biofilm formation ability, and ABC transporters, two-component systems, and quorum sensing pathways were enriched according to RNA-seq. The ST37 genotype strain was enriched in the PTS, ribosome, and several sugar and amino acid metabolism pathways. The antibiotic resistance rate of Clade 4 <i>C</i>. <i>difficile</i> was higher than that of clade 1 strains, especially for the resistance of <i>C. difficile</i> ST37 to quinolones. The biological characteristics of these representative strains might provide certain clues for investigating the reasons for these changes.