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•16S rRNA sequence of AV208 was 100% with Aerococcus urinaeequiand 99.9% with A. viridans•There was 96.24% ANI between AV208 and A. urinaeequi, and it was higher than that with Aerococcus viridans(94.9%)•AV208 was resistant to many drugs including vancomycin with a MIC >256 μg mL−1•A Tn1546transposon-like structure was located in the genome of strain AV208•Whole-genome sequencing combined with ANI could give an accurate identification

•27 linezolid-non-susceptible-Enterococcuswere identified at a tertiary care hospital of China.•OptrAwas the main gene mediating LNSE in 23 isolates, with ST16 E. faecalisclonal dissemination.•PCR-based sequencing and WGS revealed 7 optrAvariants in 16 isolates.•OptrAwas found downstream of fexAby searching pE349 sequence on WGS data.•This is the first report on the prevalence of LNSE and the optrAgene in Nanjing, China.

•S. capitiswas the main linezolid-resistant strain in CoNS•Linezolid resistance was mediated mainly by 23S rRNA V mutations and acquisition of cfr•Linezolid-resistant S. capitishas stronger biofilm-forming ability•The detection rate of the bapgene in LRSC strains was higher than that in LSSC•Mass spectrometric biomarkers can identify linezolid-resistant S. capitis