AUTHOR=Yang Xue , Zhang Tiejun , Lei Chang-Wei , Wang Qin , Huang Zheren , Chen Xuan , Wang Hong-Ning 

TITLE=Florfenicol and oxazolidone resistance status in livestock farms revealed by short- and long-read metagenomic sequencing

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.1018901

DOI=10.3389/fmicb.2022.1018901

ISSN=1664-302X

ABSTRACT=<p>Antibiotic resistance genes (ARGs) as a novel type of environmental pollutant pose a health risk to humans. Oxazolidinones are one of the most important antibiotics for the treatment of Gram-positive bacterial infections in humans. Although oxazolidinones are not utilized in the livestock industry, florfenicol is commonly used on farms to treat bacterial infections, which may contribute to the spread of the <italic>cfr</italic>, <italic>optrA</italic>, and <italic>poxtA</italic> genes on farms. Using metagenomics sequencing, we looked into the antibiotic resistome context of florfenicol and oxazolidinone in 10 large-scale commercial farms in China. We identified 490 different resistance genes and 1,515 bacterial genera in the fecal samples obtained from 10 farms. Florfenicol-resistant <italic>Kurthia</italic>, <italic>Escherichia</italic>, and <italic>Proteus</italic> were widely present in these samples. The situation of florfenicol and oxazolidone resistance in pig farms is even more severe. The total number of genes and the abundance of drug resistance genes were higher in pigs than in chickens, including <italic>optrA</italic> and <italic>poxtA</italic>. All the samples we collected had a high abundance of <italic>fexA</italic> and <italic>floR</italic>. Through nanopore metagenomic analysis of the genetic environment, we found that plasmids, integrative and conjugative element (ICE), and transposons (Tn<italic>7</italic>-like and Tn<italic>558</italic>) may play an important role in the spread of <italic>floR</italic>, <italic>cfr</italic>, and <italic>optrA</italic>. Our findings suggest that florfenicol and oxazolidinone resistance genes have diverse genetic environments and are at risk of co-transmission with, for example, tetracycline and aminoglycoside resistance genes. The spread of florfenicol- and oxazolidinone–resistant bacteria on animal farms should be continuously monitored.</p>