First comprehensive genome analysis and antimicrobial resistance profile of Clostridium innocuum from a domestic cat

This study aimed to investigate the molecular and phenotypic properties of a C. innocuum isolate from a healthy cat, which was previously misidentified as C. difficile by molecular testing (tpi-PCR). To resolve the misidentification and obtain more information on the isolate at the genetic level, whole genome sequencing (WGS) on the long-read sequencing platform Oxford Nanopore PromethION was performed. WGS data were analysed to identify virulence factors, antibiotic resistance, and hypothetical prophage genes. The isolate was identified as C. innocuum as a result of WGS. While several virulence genes, including pilM, yabQ, HrcA, and CptIN family toxins, were detected, toxin-coding genes in other Clostridium species were not detected. Four prophage regions were detected; three appeared as intact phage sites, while one was incomplete. The isolate was susceptible to ampicillin, clindamycin, vancomycin, and metronidazole but was resistant to meropenem using the E-test method. The genome also contained resistance genes such as tet(M), aph(2″)-Ia, and VanT, VanW, VanY, VanG, and VanZ. Genetic similarities between our isolate and those obtained from global human-derived metagenome-associated genomes (MAGs) and non-MAG genomes from healthy humans and animals were illustrated through WGS-SNP-based phylogenetic analyses. This study provides insights into the phenotypic and genotypic characteristics of C. innocuum, an emerging pathogen. Taken together, the isolation of this agent-possessing intrinsic resistance mechanisms and emerging after the treatment of C. difficile infections from a domestic cat highlights its potential threat to public health. Nevertheless, many clinical questions remain unanswered, underscoring the need for further research to deepen our understanding of this pathogen and to develop effective control and treatment strategies.