Genome MLST scheme for tracing genetic diversity and multidrug resistance of food animal-derived Clostridium perfringens

<i>Clostridium perfringens</i> is an important food-borne anaerobic bacterium that can cause chronic disease in humans and animals. The complex toxins that it produces can cause diarrhea, necrotizing enteritis, and even death. This study aimed to evaluate the presence of antibiotic resistance genes and determinants of toxin production in various strains of <i>C. perfringens</i>, derived from different geographical locations and animal sources, through whole-genome sequencing (WGS) and bioinformatics analysis. Antimicrobial resistance testing revealed a notable prevalence of resistance among isolates, with 39.5 % being resistant to clindamycin and 32.6 % resistant to tetracycline. Additionally, 29.1 % of the isolates were found to be resistant to at least two classes of commonly used antibiotics. T<i>etA</i>(<i>P</i>) and <i>tetB</i>(<i>P</i>), associated with tetracycline resistance, were the most frequently identified resistance genes, present in 93.0 % and 79.0 % of the isolates, respectively. Virulence genes encoding extracellular collagenases (<i>colA</i> and <i>colSI</i>), alpha-toxin (<i>plc</i>), and sialidase (<i>nanH</i>) were detected in 85 isolates, representing 99 % of all sequenced strains. Notably, the gene encoding <i>C. perfringens</i> enterotoxin (<i>cpe</i>) was identified in only one isolate, which originated from chicken. Multi-locus sequence typing revealed that the 86 representative isolates belonged to 49 sequence types (STs), including 33 unique, previously uncharacterized STs. Furthermore, 30.23 % of these STs were grouped into six clonal complexes (CCs). CgSNP analysis of globally circulating isolates demonstrated that the prevalence of the virulence gene <i>cpe</i> was higher in these isolates than in clinical strains. The identification of multi-drug resistance and toxin-encoding genes among the isolates underscores the concerning spread of antimicrobial resistance among <i>C. perfringens</i> affecting both animals and humans. The diversity of CRISPR/Cas system provided addition insight into complex genetic correlations and evolutionary dynamics of pathogenic <i>C. perfringens</i>. Notably, the phage SD72 exhibited a broad inhibitory effect against <i>C. perfringens</i> isolates, irrespective of STs types and antimicrobial resistance (74/86, 80.1 %). These findings highlight the urgent need for enhanced epidemic surveillance of <i>C. perfringens</i> in livestock settings to mitigate the risks of human transmission via environmental or food sources. Additionally, bacteriophages present a promising avenue as bio-antimicrobial agents for controlling the transmission of <i>C. perfringens</i> from animal sources to humans.