Detection of Oxazolidinone Resistance Genes and Characterization of Genetic Environments in Enterococci of Swine Origin, Italy

Abstract

One hundred forty-five florfenicol-resistant enterococci, isolated from swine fecal samples collected from 76 pig farms, were investigated for the presence of <i>optrA</i>, <i>cfr</i>, and <i>poxtA</i> genes by PCR. Thirty florfenicol-resistant <i>Enterococcus</i> isolates had at least one linezolid resistance gene. <i>optrA</i> was found to be the most widespread linezolid resistance gene (23/30), while <i>cfr</i> and <i>poxtA</i> were detected in 6/30 and 7/30 enterococcal isolates, respectively. WGS analysis also showed the presence of the <i>cfr</i>(D) gene in <i>Enterococcus faecalis</i> (<i>n</i> = 2 isolates) and in <i>Enterococcus avium</i> (<i>n</i> = 1 isolate). The linezolid resistance genes hybridized both on chromosome and plasmids ranging from ~25 to ~240 kb. Twelve isolates were able to transfer linezolid resistance genes to enterococci recipient. WGS analysis displayed a great variability of <i>optrA</i> genetic contexts identical or related to transposons (Tn<i>6628</i> and Tn<i>6674</i>), plasmids (pE035 and pWo27-9), and chromosomal regions. <i>cfr</i> environments showed identities with Tn<i>6644</i>-like transposon and a region from p12-2300 plasmid; <i>cfr</i>(D) genetic contexts were related to the corresponding region of the plasmid 4 of <i>Enterococcus faecium</i> E8014; <i>poxtA</i> was always found on Tn<i>6657</i>. Circular forms were obtained only for <i>optrA</i>- and <i>poxtA</i>-carrying genetic contexts. Clonality analysis revealed the presence of <i>E. faecalis</i> (ST16, ST27, ST476, and ST585) and <i>E. faecium</i> (ST21) clones previously isolated from humans. These results demonstrate a dissemination of linezolid resistance genes in enterococci of swine origin in Central Italy and confirm the spread of linezolid resistance in animal settings.