Abstract Background Clostridioides difficile infection (CDI) imposes a significant burden on pediatric populations. However, distinguishing CDI from asymptomatic carriers remains clinically challenging, adding complexity to diagnosis and treatment. So we aim to characterize genetic differences between strains from infected patients and asymptomatic carriers, and to explore associations between strain types and clinical status. Methods We conducted a 6-year retrospective cohort study of CDI and asymptomatic carriers in pediatric patients at Shanghai Children’s Hospital. Stool samples were collected and cultured for C.difficile, followed by whole-genome sequencing (WGS) to perform multilocus sequence typing (MLST), identify single-nucleotide polymorphisms (SNPs), and analyze Clusters of Orthologous Groups (COG). Mutations in toxin expression-related genes were examined to compare differences between groups. Additionally, we investigated variations in virulence genes, antimicrobial resistance genes, and quorum-sensing genes. Colonization factors (CFs) were also characterized to further explain potential mechanisms underlying colonization and infection. Results This study identified 23 sequence types (STs) among 39 asymptomatic carriers and 61 symptomatic patients, with the infection group exhibiting a broader ST diversity than the colonization group. COG analysis revealed a higher proportion of uncharacterized genes in the infection group. The distribution patterns of virulence genes, antimicrobial resistance genes, and quorum sensing genes were similar between the two groups, as were the mutations of toxin expression-related genes. Notably, six isolates of ST37 and ST54, which lacked tcdA but carried tcdB, exhibited high-frequency mutations. Finally, no significant differences were observed in the distribution of CFs between the two groups. Conclusion Our study represents an important milestone in mapping specific genomic features and their functional roles to identify factors involved in the development of C. difficile-associated disease severity. Conflict of interest: Tu, Lewen: No conflict of interest Wang, Runjie: No conflict of interest Liu, Gaojie: No conflict of interest Liu, Rulan: No conflict of interest Wang, Xufei: No conflict of interest Ye, Lin: No conflict of interest Mei, Yongchao: No conflict of interest Xiao, Fangfei: No conflict of interest Wang, Lu: No conflict of interest Wang, Yizhong: No conflict of interest Prof. Dr. Zhang, Ting: No conflict of interest Li, Xiaolu: No conflict of interest
Tu et al. (2026) studied this question.