Genomics to understand the global landscape of linezolid resistance in Enterococcus faecium and Enterococcus faecalis

Abstract

Linezolid is an oxazolidinone antibiotic and is a last-line agent for treating infections caused by vancomycin-resistant Enterococcus (VRE). Limited work has been done to study the genomic epidemiology and population structure of linezolid-resistant Enterococcus (LRE) spp. in Victoria, Australia, and globally. We aimed to elucidate the genomic epidemiology and population structure of LRE in Victoria, Australia. We screened our local collection of Enterococcus faecalis and Enterococcus faecium for LRE from 2015 to 2023 and identified 15/349 (4.3 %) and 26/9,207 (0.28 %) E. faecalis and E. faecium, respectively, which had either or both phenotypic and genotypic resistance to linezolid. We next contextualized the Victorian LRE isolates with a global set of 684 E. faecalis and 324 E. faecium genomes from public databases. Integrated phylogenetic and epidemiologic data suggested that the LRE isolates in Victoria were likely introduced through multiple independent events from international travellers, with evidence of putative linear plasmids co-carrying vanA and linezolid resistance genes. We observed a predominance of the linezolid resistance-conferring optrA gene in E. faecalis irrespective of source origin in both the global and Victorian collections, whereas in E. faecium, cfr and cfr(B) occurred more frequently among clinical isolates, with no apparent geographical signatures. Our study provides a genomic snapshot of a large global collection of LRE isolates and establishes the epidemiological context for LRE circulating in Victoria, Australia.