AUTHOR=Huang Zheren , Bai Yilin , Wang Qin , Yang Xue , Zhang Tiejun , Chen Xuan , Wang Hongning 

TITLE=Persistence of transferable oxazolidinone resistance genes in enterococcal isolates from a swine farm in China

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.1010513

DOI=10.3389/fmicb.2022.1010513

ISSN=1664-302X

ABSTRACT=<p>The appearance of transferable oxazolidinone resistance genes poses a major challenge to public health and environmental safety. These genes not only lead pathogenic bacteria to become resistant to linezolid but also reduce sensitivity to florfenicol, which is widely used in the veterinary field. To verify the dissemination of oxazolidinone resistance genes in enterococcal isolates from pigs at different production stages in a swine farm in China, we collected 355 enterococcal isolates that were resistant to florfenicol from 600 (150 per stage) fresh fecal swabs collected from a swine farm. Through initial PCR screening and whole-genome sequencing, 175 isolates harboring different oxazolidinone resistance genes were identified. All isolates carried the <italic>optrA</italic> gene. A total of 161 (92%, 161/175) isolates carried only the <italic>optrA</italic> gene. Three (1.71%, 3/175) isolates carried both the <italic>optrA</italic> and <italic>poxtA</italic> genes, and 11 (3.1%, 11/175) isolates contained the <italic>optrA</italic> gene and <italic>poxtA2</italic> and <italic>cfr(D)</italic> variants. A total of 175 isolates that harbored oxazolidinone resistance genes included 161 <italic>E. faecalis</italic>, 6 <italic>E. faecium</italic>, and 8 <italic>E. hirae</italic>. By sequencing the whole genomes, we found that the 161 isolates of <italic>E. faecalis</italic> belonged to 28 different STs, including 8 new STs, and the 6 isolates of <italic>E. faecium</italic> belonged to four different STs, including one new ST. The phylogenetic tree based on SNPs of the core genome showed that both clonal spread and horizontal transfer mediated the diffusion of oxazolidone resistance genes in enterococcal isolates at specific stages in pig farms. Moreover, enterococcal isolates carrying oxazolidone resistance genes could spread from breeding pigs to fattening pigs, while transferable oxazolidone resistance genes in enterococcal isolates could persist on a pig farm throughout all production stages. Representative enterococcal isolates with different oxazolidinone resistance genes were further studied through Nanopore sequencing. We identified a novel plasmid, pM4-80 L4 (15,008 bp), carrying the <italic>poxtA2</italic> and <italic>cfr(D)</italic> genes in enterococcal isolates at different stages. We also found three different plasmids harboring the <italic>poxtA</italic> gene with high genetic variation, and all <italic>poxtA</italic> genes were flanked by two copies of IS<italic>1216E</italic> elements. In addition, four genetically distinct plasmids carrying the <italic>optrA</italic> gene were identified, and Tn<italic>554</italic> was found to mediate chromosome-localized <italic>optrA</italic> gene transfer. Our study highlighted that transferable oxazolidinone resistance genes in enterococcal isolates could persist throughout all production stages on a pig farm, and the prevalence and dissemination of oxazolidinone resistance genes in enterococcal isolates from animal farms should be continually monitored.</p>