Whole-genome sequencing of Enterococcus hirae CQP3-9, a strain carrying phenicol-oxazolidinone-tetracycline resistance gene poxtA of swine origin in china

Abstract Objectives The aim of this study was to characterize the whole genome sequence of the linezolid-intermediate E. hirae strain CQP3-9 isolated from a large-scale swine farm in Sichuan province of China in August 2018. Methods Illumina Miseq platform (400-bp pairs-end reads with 230-fold average coverage) and PacBio RS II sequencing instrument (100-fold average read depth) were used for genome sequencing. The chromosome and plasmids were assembled using software SMRT portal v.3.2.0. Acquired antimicrobial resistance genes were identified by ResFinder 3.1. Results The genome of E. hirae strain CQP3-9 consists of one 2695,881 bp chromosome, one 125,915 bp plasmid pCQP3-9_1 and one 33,132 bp plasmid pCQP3-9_2. The genome of CQP3-9 contains 2458 coding sequences and 89 RNA genes. poxtA is the only linezolid resistance gene in CQP3-9, which is located on plasmid pCQP3-9_2 that co-carries erm (B) (macrolide resistance), fexB (chloramphenicol and florfenicol), tet (M) and tet (L) (tetracycline). Conclusion Here we first report the phenicol-oxazolidinone-tetracycline resistance gene poxtA in E. hirae , which is located on a plasmid that co-carries erm (B), fexB , tet (L) and tet (M). The genome sequence of E. hirae CQP3-9 provides valuable information for the dissemination of poxtA among enterococci.