Methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 398 (CC398) has recently been detected in pig farms of Japan as a major livestock-associated (LA) MRSA lineage. While the prevalence of MRSA in farm pigs and slaughterhouses in Japan has been investigated, the contamination in retail pork remains unclear. Therefore, we investigated the prevalence of LA-MRSA CC398 in retail pork and analyzed its antimicrobial susceptibility and phylogenetic characteristics. A total of 385 retail pork samples (268 domestic and 117 imported) were collected between 2021 and 2022. MRSA was detected in 3.1 % (12/385) of samples, with 4.1 % (11/268) in domestic pork and 0.8 % (1/117) in imported pork. All 12 isolates were identified as LA-MRSA CC398, resistant to methicillin and tetracycline, and some also to chloramphenicol, erythromycin, and levofloxacin. Phylogenetic analysis revealed that Japanese pig-derived ST398 isolates could be classified into 5 major clusters, with 12 isolates from retail pork distributed in clusters 2–4. Analysis of the Staphylococcal Cassette Chromosome mec (SCCmec) element structure revealed that many isolates in clusters 3 and 4 lacked an approximately 50.3 kb region containing the cassette chromosome recombinase (ccr) gene complex (type 5); they were classified as “ΨSCCmec.” In contrast, cluster 5 carried SCCmec type IVd. We also propose two novel ccr gene types: type 23 (A6B3), detected in clusters 2 and 5, and type 24 (A5B5), detected in cluster 4. These findings demonstrate that diverse LA-MRSA CC398 genotypes are distributed across farms, slaughterhouses, and retail pork in Japan, indicating that the livestock sector is a critical reservoir.
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