RT Journal Article
SR Electronic
T1 Emergence of <em>optrA</em>-mediated linezolid resistance in multiple lineages and plasmids of <em>Enterococcus faecalis</em> revealed by long read sequencing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.02.28.969568
DO 10.1101/2020.02.28.969568
A1 Martin P McHugh
A1 Benjamin J Parcell
A1 Kerry A Pettigrew
A1 Geoff Toner
A1 Elham Khatamzas
A1 Anne Marie Karcher
A1 Joanna Walker
A1 Robert Weir
A1 Danièle Meunier
A1 Katie L Hopkins
A1 Neil Woodford
A1 Kate E Templeton
A1 Stephen H Gillespie
A1 Matthew TG Holden
YR 2020
UL http://biorxiv.org/content/early/2020/02/29/2020.02.28.969568.abstract
AB Objectives To characterise the genetic environment of optrA in linezolid-resistant Enterococcus faecalis isolates from Scotland.Methods Linezolid-resistant E. faecalis were identified in three Scottish Health Boards and confirmed to carry the optrA gene at the national reference laboratory. WGS was performed with short read (Illumina MiSeq) and long read (Oxford Nanopore MinION) technologies to generate complete genome assemblies. Illumina reads for 94 E. faecalis bloodstream isolates were used to place the optrA-positive isolates in a larger UK phylogeny.Results Six optrA-positive linezolid-resistant E. faecalis were isolated from urogenital samples in three Scottish Health Boards (2014-2017). No epidemiological links were identified between the patients, four were community-based, and only one had recent linezolid exposure. Reference-based mapping confirmed the isolates were genetically distinct (&gt;13,900 core SNPs). optrA was located on a plasmid in each isolate and these plasmids showed limited nucleotide similarity. There was variable presence of transposable elements surrounding optrA, (including IS1216, IS3, and Tn3) and not always as a recognisable gene cassette. OptrA amino acid sequences were also divergent, resulting in four protein variants differing in 1-20 residues. One isolate belonged to ST16 and clustered with three other isolates in the UK collection (76-182 SNPs), otherwise the optrA-positive isolates were genetically distinct from the bloodstream isolates (&gt;6,000 SNPs).Conclusions We report multiple variants of the linezolid resistance gene optrA in diverse E. faecalis strain and plasmid backgrounds, suggesting multiple introductions of the gene into the E. faecalis population and selection driving recent emergence.