Complete genome sequence and characterization of Clostridium perfringens type D carrying optrA-plasmid and Tn6218-like transposon

Molecular characterization of emerging multi-drug resistant Clostridium perfringens isolated from pork production chains in Korea

Clostridium perfringens is a common cause of foodborne illnesses and is involved in human and animal gastrointestinal diseases. Surveillance of C. perfringens in the pork production chain is crucial to manage the risk of pathogen transmission. This study aimed to investigate the prevalence, antimicrobial resistance profile, and genomic characteristics of C. perfringens in pork production chains in Korea. The overall prevalence of C. perfringens was 23.6% (330/1397), with 48.8 (178/365), 16.6 (138/832), and 7.0% (14/200) in pig farms, slaughterhouses, and retail markets, respectively. Toxinotyping revealed 98.9% type A and 1.1% type C isolates. Among them, 29.1% carried the beta-2 toxin gene. Antimicrobial susceptibility tests identified 20 multi-drug resistant isolates, with the highest resistance against tetracycline (65.1%). Whole-genome sequencing further revealed 17 antimicrobial resistance and 12 virulence genes. Subsequent phylogenetic analysis identified three clonal clusters, two of which revealed a clonal relationship with human clinical isolates reported in China. The ST408 isolate from the retail pork meat, IJCP45, harboured the optrA gene in a plasmid and was identical to known optrA-carrying plasmids in C. perfringens from livestock in China, suggesting the introduction and dissemination of optrA by the transmission of a specific plasmid in east Asian countries. To our knowledge, this is the first comprehensive study of C. perfringens in the pork meat production system as an "One Health" approach. The study findings provide baseline data for the distribution and genetic characteristics of pig-associated C. perfringens in Korea and indicate the zoonotic transmission potential of C. perfringens from pigs to humans.

IS6 family insertion sequences promote optrA dissemination between plasmids varying in transfer abilities

Plasmids are the primary vectors for intercellular transfer of the oxazolidinone and phenicol cross-resistance gene optrA, while insertion sequences (ISs) are mobile genetic elements that can mobilize plasmid-borne optrA intracellularly. However, little is known about how the IS-mediated intracellular mobility facilitates the dissemination of the optrA gene between plasmid categories that vary in transfer abilities, including non-mobilizable, mobilizable, and conjugative plasmids. Here, we performed a holistic genomic study of 52 optrA-carrying plasmids obtained from searches guided by the Comprehensive Antibiotic Resistance Database. Among the 132 ISs identified within 10 kbp from the optrA gene in the plasmids, IS6 family genes were the most prevalent (86/132). Homologous gene arrays containing IS6 family genes were shared between different plasmids, especially between mobilizable and conjugative plasmids. All these indicated the central role of IS6 family genes in disseminating plasmid-borne optrA. Thirty-three of the 52 plasmids were harbored by Enterococcus faecalis found mainly in humans and animals. By Nanopore sequencing and inverse PCR, the potential of the enterococcal optrA to be transmitted from a mobilizable plasmid to a conjugative plasmid mediated by IS6 family genes was further confirmed in Enterococcus faecalis strains recovered from the effluents of anaerobic digestion systems for treating chicken manure. Our findings highlight the increased intercellular transfer abilities and dissemination risk of plasmid-borne optrA gene caused by IS-mediated intracellular mobility, and underscore the importance of routinely monitoring the dynamic genetic contexts of clinically important antibiotic resistance genes to effectively control this critical public health threat. KEY POINTS: • IS6 was prevalent in optrA-plasmids varying in intercellular transfer abilities. • Enterococcal optrA-plasmids were widespread among human, animal, and the environment. • IS6 elevated the dissemination risk of enterococcal optrA-plasmids.

Genome characteristics of the optrA-positive Clostridium perfringens strain QHY-2 carrying a novel plasmid type

Clostridium perfringens is a bacterial species of importance to both public and animal health. The gene optrA is the first gene that confers resistance to the tedizolid, a last-resort antimicrobial agent in human medicine. Herein, we whole-genome sequenced and analyzed one optrA-positive C. perfringens strain QHY-2 from Tibetan sheep in Qinghai province and identified one optrA plasmid pQHY-2. The plasmid shared similar structure with the optrA-positive plasmids p2C45 and p21-D-5b previously identified in C. perfringens, demonstrating the potential horizontal transmission of the optrA plasmids among C. perfringens strains. Annotation of the optrA-positive plasmids showed optrA and erm(A) located on a segment flanked by IS element IS1216E, and fexA, optrA, and erm(A) located on a segment flanked by IS element ISVlu1, which revealed the possible dissemination mechanism. Additionally, a Tn6218-like transposon carrying aac(6')-aph(2″) and erm(B) was also detected on pQHY-2, demonstrating the transposition of Tn6218 and spread of antibiotic resistance among Clostridium bacteria. Molecular analysis indicated the optrA-positive plasmids belonged to a plasmid type distinct from the pCW3-like plasmids, pCP13-like plasmids, or pIP404-like plasmids. Further structure analysis showed they might be formed by inserting segments into plasmid pCPCPI53k-r1_1, which coexist with two pCW3-like plasmids and one pCP13-like plasmid in C. perfringens strain CPI 53k-r1 isolated from a healthy human in Finland. IMPORTANCE Antimicrobial resistance is now a global concern posing threats to food safety and public health. The pCW3-like plasmids can encode several main toxin genes and three antibiotic resistance genes (ARGs), including tetA(P), tetB(P), and erm(B), which used to be considered as the main carrier of ARGs in Clostridium perfringens. In this study, we found the optrA plasmids, which belonged to a novel plasmid type, could also harbor many other ARGs, indicating this type of plasmid might be the potential repository of ARGs in C. perfringens. Additionally, this type of plasmid could coexist with the pCW3-like plasmids and pCP13-like plasmids that encoded toxin genes associated with gastrointestinal diseases, which showed the potential threat to public health.