Real-time whole genome sequencing to control a Streptococcus pyogenes outbreak at a national orthopaedic hospital.
Bacteremia
/ epidemiology
Carrier State
/ epidemiology
Cross Infection
/ epidemiology
Disease Outbreaks
Disease Transmission, Infectious
/ prevention & control
Hospitals
Humans
Molecular Epidemiology
/ methods
Molecular Typing
/ methods
Retrospective Studies
Streptococcal Infections
/ epidemiology
Streptococcus pyogenes
/ classification
Whole Genome Sequencing
/ methods
Genomics
Group A streptococcus (GAS)
Outbreak
Streptococcus pyogenes
Whole-genome sequencing (WGS)
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:
Sep 2019
Sep 2019
Historique:
received:
10
05
2019
accepted:
01
07
2019
pubmed:
10
7
2019
medline:
31
12
2019
entrez:
9
7
2019
Statut:
ppublish
Résumé
Whole genome sequencing (WGS) of Streptococcus pyogenes linked to invasive disease has been used to identify and investigate outbreaks. The clinical application of WGS in real-time for outbreak control is seldom employed. A fatal case of bacteraemia at a national orthopaedic hospital prompted an outbreak investigation to identify carriers and halt transmission using real-time WGS. Retrospective surveillance was conducted to identify patients with Streptococcus pyogenes infections in the last year. Upon contact tracing, four patients and 179 staff were screened for Streptococcus pyogenes carriage. All isolates identified were emm-typed. WGS was performed in real-time on a subset of isolates. Twelve isolates of Streptococcus pyogenes from the index case, two patients and eight staff were identified. Six isolates were emm 1.0, including the index case and five staff isolates. The remaining isolates belonged to distinct emm types. WGS analysis was undertaken on the six emm 1.0 isolates. Five were indistinguishable by single nucleotide polymorphism (SNP) analysis, with 0 SNP distance, and one had one SNP difference, supporting the hypothesis of recent local transmission. All screen-positive healthcare workers were offered treatment with penicillin or clindamycin. No further cases were identified. The increased molecular discrimination of WGS confirmed the clustering of these cases and the outbreak was contained. This demonstrates the clinical utility of WGS in managing outbreaks of invasive Streptococcus pyogenes in real-time and we recommend its implementation as a routine clinical service.
Sections du résumé
BACKGROUND
BACKGROUND
Whole genome sequencing (WGS) of Streptococcus pyogenes linked to invasive disease has been used to identify and investigate outbreaks. The clinical application of WGS in real-time for outbreak control is seldom employed.
AIMS
OBJECTIVE
A fatal case of bacteraemia at a national orthopaedic hospital prompted an outbreak investigation to identify carriers and halt transmission using real-time WGS.
METHODS
METHODS
Retrospective surveillance was conducted to identify patients with Streptococcus pyogenes infections in the last year. Upon contact tracing, four patients and 179 staff were screened for Streptococcus pyogenes carriage. All isolates identified were emm-typed. WGS was performed in real-time on a subset of isolates.
FINDINGS
RESULTS
Twelve isolates of Streptococcus pyogenes from the index case, two patients and eight staff were identified. Six isolates were emm 1.0, including the index case and five staff isolates. The remaining isolates belonged to distinct emm types. WGS analysis was undertaken on the six emm 1.0 isolates. Five were indistinguishable by single nucleotide polymorphism (SNP) analysis, with 0 SNP distance, and one had one SNP difference, supporting the hypothesis of recent local transmission. All screen-positive healthcare workers were offered treatment with penicillin or clindamycin. No further cases were identified.
CONCLUSION
CONCLUSIONS
The increased molecular discrimination of WGS confirmed the clustering of these cases and the outbreak was contained. This demonstrates the clinical utility of WGS in managing outbreaks of invasive Streptococcus pyogenes in real-time and we recommend its implementation as a routine clinical service.
Identifiants
pubmed: 31283948
pii: S0195-6701(19)30281-6
doi: 10.1016/j.jhin.2019.07.003
pii:
doi:
Types de publication
Case Reports
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
21-26Informations de copyright
Copyright © 2019 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.