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An Outbreak of Streptococcus pyogenes in a Mental Health Facility: Advantage of Well-Timed Whole-Genome Sequencing Over emm Typing

Published online by Cambridge University Press:  09 May 2018

Sarah M. Bergin
Affiliation:
Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore
Balamurugan Periaswamy
Affiliation:
Genome Institute of Singapore, Singapore
Timothy Barkham
Affiliation:
Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore Yong Loo Lin School of Medicine, National University of Singapore, Singapore
Hong Choon Chua
Affiliation:
Institute of Mental Health, Singapore
Yee Ming Mok
Affiliation:
Institute of Mental Health, Singapore
Daniel Shuen Sheng Fung
Affiliation:
Institute of Mental Health, Singapore
Alex Hsin Chuan Su
Affiliation:
Institute of Mental Health, Singapore
Yen Ling Lee
Affiliation:
Genome Institute of Singapore, Singapore
Ming Lai Ivan Chua
Affiliation:
Genome Institute of Singapore, Singapore
Poh Yong Ng
Affiliation:
Genome Institute of Singapore, Singapore
Wei Jia Wendy Soon
Affiliation:
Genome Institute of Singapore, Singapore
Collins Wenhan Chu
Affiliation:
Genome Institute of Singapore, Singapore
Siyun Lucinda Tan
Affiliation:
National Skin Center, Singapore
Mary Meehan
Affiliation:
Irish Meningitis and Sepsis Reference Laboratory, Temple Street Children’s University Hospital, Dublin, Ireland
Brenda Sze Peng Ang
Affiliation:
Department of Infectious Diseases, Institute of Infectious Diseases and Epidemiology, Tan Tock Seng Hospital, Singapore Lee Kong Chien School of Medicine, Nanyang Technological University, Singapore
Yee Sin Leo
Affiliation:
Department of Infectious Diseases, Institute of Infectious Diseases and Epidemiology, Tan Tock Seng Hospital, Singapore Lee Kong Chien School of Medicine, Nanyang Technological University, Singapore Saw Swee Hock School of Public Health, National University of Singapore, Singapore Yong Loo Lin School of Medicine, National University of Singapore, Singapore
Matthew T. G. Holden
Affiliation:
University of St Andrews, St Andrews, Scotland
Partha De
Affiliation:
Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore Lee Kong Chien School of Medicine, Nanyang Technological University, Singapore
Li Yang Hsu
Affiliation:
Department of Infectious Diseases, Institute of Infectious Diseases and Epidemiology, Tan Tock Seng Hospital, Singapore Saw Swee Hock School of Public Health, National University of Singapore, Singapore
Swaine L. Chen
Affiliation:
Genome Institute of Singapore, Singapore Yong Loo Lin School of Medicine, National University of Singapore, Singapore
Paola Florez de Sessions
Affiliation:
Genome Institute of Singapore, Singapore
Kalisvar Marimuthu
Affiliation:
Department of Infectious Diseases, Institute of Infectious Diseases and Epidemiology, Tan Tock Seng Hospital, Singapore Yong Loo Lin School of Medicine, National University of Singapore, Singapore
Corresponding

Abstract

OBJECTIVE

We report the utility of whole-genome sequencing (WGS) conducted in a clinically relevant time frame (ie, sufficient for guiding management decision), in managing a Streptococcus pyogenes outbreak, and present a comparison of its performance with emm typing.

SETTING

A 2,000-bed tertiary-care psychiatric hospital.

METHODS

Active surveillance was conducted to identify new cases of S. pyogenes. WGS guided targeted epidemiological investigations, and infection control measures were implemented. Single-nucleotide polymorphism (SNP)–based genome phylogeny, emm typing, and multilocus sequence typing (MLST) were performed. We compared the ability of WGS and emm typing to correctly identify person-to-person transmission and to guide the management of the outbreak.

RESULTS

The study included 204 patients and 152 staff. We identified 35 patients and 2 staff members with S. pyogenes. WGS revealed polyclonal S. pyogenes infections with 3 genetically distinct phylogenetic clusters (C1–C3). Cluster C1 isolates were all emm type 4, sequence type 915 and had pairwise SNP differences of 0–5, which suggested recent person-to-person transmissions. Epidemiological investigation revealed that cluster C1 was mediated by dermal colonization and transmission of S. pyogenes in a male residential ward. Clusters C2 and C3 were genomically diverse, with pairwise SNP differences of 21–45 and 26–58, and emm 11 and mostly emm120, respectively. Clusters C2 and C3, which may have been considered person-to-person transmissions by emm typing, were shown by WGS to be unlikely by integrating pairwise SNP differences with epidemiology.

CONCLUSIONS

WGS had higher resolution than emm typing in identifying clusters with recent and ongoing person-to-person transmissions, which allowed implementation of targeted intervention to control the outbreak.

Infect Control Hosp Epidemiol 2018;852–860

Type
Original Article
Copyright
© 2018 by The Society for Healthcare Epidemiology of America. All rights reserved. 

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Footnotes

a

First authors of equal contribution.

b

Authors of equal contribution.

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