Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes

Abstract

Linezolid-resistant <i>Enterococcus faecalis</i> (LREfs) carrying <i>optrA</i> are increasingly reported globally from multiple sources, but we lack a comprehensive analysis of human and animal <i>optrA</i>-LREfs strains. To assess if <i>optrA</i> is dispersed in isolates with varied genetic backgrounds or with common genetic features, we investigated the phylogenetic structure, genetic content [antimicrobial resistance (AMR), virulence, prophages, plasmidome] and <i>optrA</i>-containing platforms of 27 publicly available <i>optrA</i>-positive <i>E. faecalis</i> genomes from different hosts in seven countries. At the genome-level analysis, an in-house database with 64 virulence genes was tested for the first time. Our analysis showed a diversity of clones and adaptive gene sequences related to a wide range of genera from <i>Firmicutes</i>. Phylogenies of core and accessory genomes were not congruent, and at least PAI-associated and prophage genes contribute to such differences. Epidemiologically unrelated clones (ST21, ST476-like and ST489) obtained from human clinical and animal hosts in different continents over eight years (2010-2017) could be phylogenetically related (3-126 SNPs difference). <i>optrA</i> was located on the chromosome within a Tn<i>6674</i>-like element (<i>n</i>=10) or on medium-size plasmids (30-60 kb; <i>n</i>=14) belonging to main plasmid families (RepA_N/Inc18/Rep_3). In most cases, the immediate gene vicinity of <i>optrA</i> was generally identical in chromosomal (Tn<i>6674</i>) or plasmid (<i>impB-fexA-optrA</i>) backbones. Tn<i>6674</i> was always inserted into the same ∆<i>radC</i> integration site and embedded in a 32 kb chromosomal platform common to strains from different origins (patients, healthy humans, and animals) in Europe, Africa, and Asia during 2012-2017. This platform is conserved among hundreds of <i>E. faecalis</i> genomes and proposed as a chromosomal hotspot for <i>optrA</i> integration. The finding of <i>optrA</i> in strains sharing common adaptive features and genetic backgrounds across different hosts and countries suggests the occurrence of common and independent genetic events occurring in distant regions and might explain the easy <i>de novo</i> generation of <i>optrA</i>-positive strains. It also anticipates a dramatic increase of <i>optrA</i> carriage and spread with a serious impact on the efficacy of linezolid for the treatment of Gram-positive infections.