Hospital outbreak of linezolid-resistant and vancomycin-resistant ST80 Enterococcus faecium harbouring an optrA-encoding conjugative plasmid investigated by whole-genome sequencing.
Anti-Bacterial Agents
/ pharmacology
Disease Outbreaks
Drug Resistance, Multiple, Bacterial
/ genetics
Enterococcus faecium
/ drug effects
Genes, Bacterial
Genotype
Gram-Positive Bacterial Infections
/ epidemiology
Hospitals
Humans
Ireland
/ epidemiology
Linezolid
/ pharmacology
Microbial Sensitivity Tests
Phenotype
Plasmids
/ genetics
RNA, Ribosomal, 23S
/ genetics
Vancomycin
/ pharmacology
Whole Genome Sequencing
Conjugative plasmid
Linezolid resistance
Nosocomial outbreak
Vancomycin-resistant Enterococcus faecium
optrA
Journal
The Journal of hospital infection
ISSN: 1532-2939
Titre abrégé: J Hosp Infect
Pays: England
ID NLM: 8007166
Informations de publication
Date de publication:
Aug 2020
Aug 2020
Historique:
received:
30
03
2020
accepted:
11
05
2020
pubmed:
23
5
2020
medline:
8
6
2021
entrez:
23
5
2020
Statut:
ppublish
Résumé
Linezolid is an antibiotic used to treat infections caused by multi-drug-resistant Gram-positive bacteria. Linezolid resistance in enterococci has been reported with increasing frequency, with a recent rise in resistance encoded by optrA, poxtA or cfr. To investigate a hospital outbreak of linezolid- and vancomycin-resistant Enterococcus faecium (LVREfm) using whole-genome sequencing (WGS). Thirty-nine VREfm from patient screening (19 isolates, 17 patients) and environmental sites (20 isolates) recovered in October 2019 were investigated. Isolates were screened using polymerase chain reaction for optrA, poxtA and cfr, and underwent Illumina MiSeq WGS. Isolate relatedness was assessed using E. faecium core genome multi-locus sequence typing (cgMLST). One LVREfm underwent MinION long-read WGS (Oxford Nanopore Technologies) and hybrid assembly with MiSeq short-read sequences to resolve an optrA-encoding plasmid. Twenty isolates (51.3%) were LVREfm and optrA-positive, including the LVREfm from the index patient. A closely related cluster of 28 sequence type (ST) 80 isolates was identified by cgMLST, including all 20 LVREfm and eight linezolid-susceptible VREfm, with an average allelic difference of two (range 0-10), indicating an outbreak. Nineteen (95%) LVREfm harboured a 56,684-bp conjugative plasmid (pEfmO_03). The remaining LVREfm exhibited 44.1% sequence coverage to pEfmO_03. The presence of pEfmO_03 in LVREfm and the close relatedness of the outbreak cluster isolates indicated the spread of a single strain. The outbreak was terminated by enhanced infection prevention and control (IPC) and environmental cleaning measures, ceasing ward admissions and ward-dedicated staff. WGS was central in investigating an outbreak of ST80 LVREfm. The rapid implementation of enhanced IPC measures terminated the outbreak.
Sections du résumé
BACKGROUND
BACKGROUND
Linezolid is an antibiotic used to treat infections caused by multi-drug-resistant Gram-positive bacteria. Linezolid resistance in enterococci has been reported with increasing frequency, with a recent rise in resistance encoded by optrA, poxtA or cfr.
AIM
OBJECTIVE
To investigate a hospital outbreak of linezolid- and vancomycin-resistant Enterococcus faecium (LVREfm) using whole-genome sequencing (WGS).
METHODS
METHODS
Thirty-nine VREfm from patient screening (19 isolates, 17 patients) and environmental sites (20 isolates) recovered in October 2019 were investigated. Isolates were screened using polymerase chain reaction for optrA, poxtA and cfr, and underwent Illumina MiSeq WGS. Isolate relatedness was assessed using E. faecium core genome multi-locus sequence typing (cgMLST). One LVREfm underwent MinION long-read WGS (Oxford Nanopore Technologies) and hybrid assembly with MiSeq short-read sequences to resolve an optrA-encoding plasmid.
FINDINGS
RESULTS
Twenty isolates (51.3%) were LVREfm and optrA-positive, including the LVREfm from the index patient. A closely related cluster of 28 sequence type (ST) 80 isolates was identified by cgMLST, including all 20 LVREfm and eight linezolid-susceptible VREfm, with an average allelic difference of two (range 0-10), indicating an outbreak. Nineteen (95%) LVREfm harboured a 56,684-bp conjugative plasmid (pEfmO_03). The remaining LVREfm exhibited 44.1% sequence coverage to pEfmO_03. The presence of pEfmO_03 in LVREfm and the close relatedness of the outbreak cluster isolates indicated the spread of a single strain. The outbreak was terminated by enhanced infection prevention and control (IPC) and environmental cleaning measures, ceasing ward admissions and ward-dedicated staff.
CONCLUSION
CONCLUSIONS
WGS was central in investigating an outbreak of ST80 LVREfm. The rapid implementation of enhanced IPC measures terminated the outbreak.
Identifiants
pubmed: 32439548
pii: S0195-6701(20)30244-9
doi: 10.1016/j.jhin.2020.05.013
pii:
doi:
Substances chimiques
Anti-Bacterial Agents
0
RNA, Ribosomal, 23S
0
Vancomycin
6Q205EH1VU
Linezolid
ISQ9I6J12J
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
726-735Informations de copyright
Copyright © 2020 The Author(s). Published by Elsevier Ltd.. All rights reserved.