A longitudinal One Health genomic survey of Clostridium perfringens reveals extensive genomic diversity and novelty, frequent plasmid carriage, and source-structured resistome signatures

Objectives To define the population structure and clinically relevant genomic traits of Clostridium perfringens within a One Health framework across human, animal, and food sources. Methods We analyzed whole genome sequences from 100 isolates collected in Costa Rica from humans, animals, and food between 1997 and 2022, and assessed phylogenetic relationships, strain diversity, pangenome structure, toxin gene repertoires, antimicrobial resistance (AMR) genes, and signatures of plasmid mobility, including Tcp/Pcp genes. Results The collection revealed a wide range of diversity and novelty, with Costa Rican isolates broadly distributed across a globally diverse context, alongside several local monophyletic clusters and cross-source mixing withing the Costa Rican subset. No identical Sequence types (ST) were shared across sources, but we identified an animal-human single-locus variant (SLV) pair spanning ≥13 years. Pangenome analyses supported an open genome with a small core (16-17% of gene families). Virulence gene profiling showed universal plc , frequent pfo , and cpb2 enriched in humans. We detected 12 acquired antibiotic resistance genes (ARG). While the overall burden of AMR genes did not vary by source, there was a notable enrichment of tetracycline-associated genes in humans and aminoglycoside-associated genes in animals. Contigs of presumptive plasmid origin were observed in 46-71% of isolates, with widespread Tcp (55-71%) and Pcp (27-50%) markers and recurring ARG genomic neighborhoods, consistent with lateral gene transfer (LGT). Conclusions Costa Rican C. perfringens exhibit high genomic diversity, source-structured AMR composition, and frequent mobility potential, supporting One Health genomic surveillance to refine AMR risk assessment and food/veterinary/public health monitoring.