Whole genome sequence of Enterococcus gallinarum EG81, a porcine strain harboring oxazolidinone-phenicol resistance gene optrA with chromosomal and plasmid location

Abstract Objectives The aim of this study was to characterise the whole genome sequence of linezolid-intermediate Enterococcus gallinarum strain EG81 of swine origin in China. Methods Whole genome of EG81 was sequenced using Illumina MiSeq platform combining with Nanopore PromethION platform, and assembled de novo using Canu v1.5. NCBI Prokaryotic Genome Annotation Pipeline (PGAP) was used to annotate the genome of EG81. Antimicrobial resistance genes were identified using CGE ResFinder 3.2. Results The genome of EG81 consists of one 3,433,237 bp chromosome and two plasmids, pEG81-1 (51,632 bp) and pEG81-2 (3,425 bp). A total of 3285 coding sequences and 80 RNA genes were predicted by PGAP. Oxazolidinone-phenicol resistance gene optrA is located on both chromosome and plasmid pEG81-1 associated with Tn554 and Tn558, respectively. In addition, EG81 harbors vanC1XY (vancomycin resistance), fexA (phenicol), dfrG (trimethoprim), aadD, ant(6)-Ia and ant(9)-Ia (aminoglycoside), erm(A) and erm(B) (macrolide), tet(L) and tet(M) (tetracycline). Conclusion Here we first report the oxazolidinone-phenicol gene optrA in E. gallinarum that is intrinsically resistant to vancomycin, which poses great threat to public health. The genome sequence of E. gallinarum EG81 provides valuable information for the dissemination of optrA among vancomycin-resistant enterococci.