Novel SCCmec type XV (7A) and two pseudo-SCCmec variants in foodborne MRSA in China

Background: Staphylococcal cassette chromosome mec (SCCmec) elements are highly diverse and have been classified into 14 types. Novel SCCmec variants have been frequently detected from humans and animals but rarely from food. Objectives: To characterize a novel SCCmec type and two SCCmec variants identified from food-associated MRSA in China. Methods: Three MRSA (NV_1, NT_611 and NT_8) collected from retail foods in China were subjected to WGS and the SCCmec elements were determined. Results: The novel SCCmecXV identified in NV_1 carried the mec gene complex class A (mecI-mecR1-mecA-IS431) and the ccr gene complex 7 (ccrA1B6), and a Tn558-mediated phenicol exporter gene fexA was detected in this SCCmecXV cassette. The pseudo-SCCmec elements ψSCCmecNT_611 and ψSCCmecNT_8 showed a truncated SCCmec pattern, carrying the class C2 mec gene complex but missing the ccr genes. The ψSCCmecNT_611 element shared more similarities with those of Staphylococcus haemolyticus (AB478934.1) and carried a heavy metal resistance gene cluster cadD-cadX-arsC-arsB-arsR-copA. The ψSCCmecNT_8 MRSA exhibited a highly resistant phenotype, showing the absence of a 19.3 kb segment compared with the reference SCCmecXII element (CP019945.1). Notably, a 46 kb region containing multiple transposons encoding antimicrobial or metal resistance genes flanked by IS431 or IS256 was identified ∼30 kb downstream from the mec gene complex in ψSCCmecNT_8, which might explain such high resistance in MRSA NT_8. Conclusions: Our finding of novel and pseudo-SCCmec elements reflected the ongoing intra/interspecies genetic rearrangements in staphylococci. Further study will be needed to investigate the biological significance and prevalence of those SCCmec variants along the food chain.