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Linezolid (LZD) has become one of the most important antimicrobial agents for infections caused by gram-positive bacteria, including those caused by  Enterococcus  species. LZD-resistant (LR) genetic features include mutations in 23S rRNA/ribosomal proteins, a plasmid-borne 23S rRNA methyltransferase gene  cfr , and ribosomal protection genes ( optrA  and  poxtA ). Recently, a  cfr  gene variant,  cfr (B), was identified in a Tn 6218 -like transposon (Tn) in a  Clostridioides difficile  isolate. Here, we isolated an LR  Enterococcus faecalis  clinical isolate, KUB3006, from a urine specimen of a patient with urinary tract infection during hospitalization in 2017. Comparative and whole-genome analyses were performed to characterize the genetic features and overall antimicrobial resistance genes in  E. faecalis  isolate KUB3006. Complete genome sequencing of KUB3006 revealed that it carried  cfr (B) on a chromosomal Tn 6218 -like element. Surprisingly, this Tn 6218 -like element was almost (99%) identical to that of  C. difficile  Ox3196, which was isolated from a human in the UK in 2012, and to that of  Enterococcus faecium  5_Efcm_HA-NL, which was isolated from a human in the Netherlands in 2012. An additional oxazolidinone and phenicol resistance gene,  optrA , was also identified on a plasmid. KUB3006 is sequence type (ST) 729, suggesting that it is a minor ST that has not been reported previously and is unlikely to be a high-risk  E. faecalis  lineage. In summary, LR  E. faecalis  KUB3006 possesses a notable Tn 6218 -like-borne  cfr (B) and a plasmid-borne  optrA . This finding raises further concerns regarding the potential declining effectiveness of LZD treatment in the future.

frontiers in microbiology

Complete Genome Sequence and Characterization of Linezolid-Resistant Enterococcus faecalis Clinical Isolate KUB3006 Carrying a cfr(B)-Transposon on Its Chromosome and optrA-Plasmid