Genomic Characterization, Phylogenetic Origin, and Antimicrobial Resistance Profile of a Clostridioides difficile ST01 Isolate: An Integrative Study

This study presents a comprehensive genomic, phylogenetic, and phenotypic analysis of a clinical Clostridioides difficile strain A-1, identified as sequence type ST1 (ribotype RT027), isolated from a patient in Nanjing, China. Whole-genome sequencing placed the isolate within the epidemic Clade 2 lineage, harboring characteristic virulence markers: the binary toxin genes (cdtA and cdtB) and an 18-nucleotide in-frame deletion in the toxin regulatory gene tcdC. Phenotypic toxin detection confirmed a toxigenic profile. Genomic annotation further identified a complete flagellar system and key adhesin genes, supporting enhanced colonization and pathogenic potential.Antimicrobial susceptibility testing revealed resistance to metronidazole, levofloxacin, and clindamycin, with corresponding resistance genotypes (nimB, gyrA mutation, and CDD-2). Despite being phenotypically susceptible to vancomycin, the isolate carried an rpoC mutation linked to vancomycin resistance, indicating potential for resistance development under selection pressure. Broader genomic screening detected additional resistance determinants, including AAC(6')-Ie-APH(2'')-Ia, the efflux pump gene cdeA, and an EF-Tu mutation, suggesting a substantial and mobilizable resistome.Phylogenetically, strain A-1 clustered with global ST1/RT027 lineages and carried S-layer cassette variant 4 (secA2-4/slpA-117), a feature associated with epidemic success. This integrated analysis demonstrates the convergence of high virulence, multidrug resistance, and successful clonal lineage traits in a single clinical isolate. The findings underscore the value of genomic surveillance for early detection, outbreak tracing, and guiding infection control and therapy against emerging hypervirulent C. difficile clones.