Genomics Insight into cfr -Mediated Linezolid-Resistant LA-MRSA in Italian Pig Holdings.

The genes encode for a 23S rRNA methyltransferase, conferring a multiresistance phenotype to phenicol, lincosamide, oxazolidinone, pleuromutilin, and streptogramin A antibiotics. These genes have been described in staphylococci, including methicillin-resistant (MRSA). In this study, we retrospectively performed an in-depth genomic characterisation of three -positive, multidrug-resistant (MDR) livestock-associated (LA) MRSA clonal complexes (CCs) 1 and 398 detected in different Italian pig holdings (2008-2011) during population studies on Italian livestock (2008-2014). We used a combined Illumina and Oxford Nanopore Technologies (ONT) whole genome sequencing (WGS) approach on two isolates (the 2008 CC1 and the 2010 CC398 isolates, but not the 2011 CC1 isolate). Interestingly, the three isolates presented different variants, with only one displaying a linezolid-resistant phenotype. In isolate 2008 CC1, the gene was identified within a Tn558 composite transposon-like structure flanked by IS elements located on a novel 44,826 bp plasmid. This represents the first report of CC1 LA-MRSA harbouring the gene in its functional variant. Differently, was chromosomally located in isolate 2010 CC398. Our findings have significant public health implications, confirm the need for the continuous genomic surveillance of -positive zoonotic LA-MRSA, and backdate presence in LA-MRSA from Italian pigs to at least 2008.