AUTHOR=Kuroda Makoto , Sekizuka Tsuyoshi , Matsui Hidehito , Suzuki Katsunori , Seki Hiroyuki , Saito Mitsumasa , Hanaki Hideaki 

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

JOURNAL=Frontiers in Microbiology

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2018.02576

DOI=10.3389/fmicb.2018.02576

ISSN=1664-302X

ABSTRACT=<p>Linezolid (LZD) has become one of the most important antimicrobial agents for infections caused by gram-positive bacteria, including those caused by <italic>Enterococcus</italic> species. LZD-resistant (LR) genetic features include mutations in 23S rRNA/ribosomal proteins, a plasmid-borne 23S rRNA methyltransferase gene <italic>cfr</italic>, and ribosomal protection genes (<italic>optrA</italic> and <italic>poxtA</italic>). Recently, a <italic>cfr</italic> gene variant, <italic>cfr</italic>(B), was identified in a Tn<italic>6218</italic>-like transposon (Tn) in a <italic>Clostridioides difficile</italic> isolate. Here, we isolated an LR <italic>Enterococcus faecalis</italic> 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 <italic>E. faecalis</italic> isolate KUB3006. Complete genome sequencing of KUB3006 revealed that it carried <italic>cfr</italic>(B) on a chromosomal Tn<italic>6218</italic>-like element. Surprisingly, this Tn<italic>6218</italic>-like element was almost (99%) identical to that of <italic>C. difficile</italic> Ox3196, which was isolated from a human in the UK in 2012, and to that of <italic>Enterococcus faecium</italic> 5_Efcm_HA-NL, which was isolated from a human in the Netherlands in 2012. An additional oxazolidinone and phenicol resistance gene, <italic>optrA</italic>, 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 <italic>E. faecalis</italic> lineage. In summary, LR <italic>E. faecalis</italic> KUB3006 possesses a notable Tn<italic>6218</italic>-like-borne <italic>cfr</italic>(B) and a plasmid-borne <italic>optrA</italic>. This finding raises further concerns regarding the potential declining effectiveness of LZD treatment in the future.</p>