infection control & hospital epidemiology july 2018, vol. 39, no. 7 original article
An Outbreak of Streptococcus pyogenes in a Mental Health Facility: Advantage of Well-Timed Whole-Genome Sequencing Over emm Typing
Sarah M. Bergin, FRCPath;1,a Balamurugan Periaswamy, PhD;2,a Timothy Barkham, FRCPath;1,3 Hong Choon Chua, MMed (Psych);4 Yee Ming Mok, MMed(Psych);4 Daniel Shuen Sheng Fung, MMed(Psych);4 Alex Hsin Chuan Su, MMed(Psych);4 Yen Ling Lee, BSc;2 Ming Lai Ivan Chua, BSc;2 Poh Yong Ng, MSc;2 Wei Jia Wendy Soon, PhD;2 Collins Wenhan Chu, MSc;2 Siyun Lucinda Tan, MRCP;5 Mary Meehan, PhD;6 Brenda Sze Peng Ang, MPH;7,8 Yee Sin Leo, MPH, FAMS, FRCP;7,8,9,10 Matthew T. G. Holden, PhD;11 Partha De, MSc, FRCPath;1,8 Li Yang Hsu, MPH;7,9 Swaine L. Chen, MD, PhD;2,10,b Paola Florez de Sessions, PhD;2,b Kalisvar Marimuthu, FAMS, MRCP7,10,b
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. Wecompared the ability ofWGSand 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. WGShad 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;39:852–860
Streptococcus pyogenes is a human pathogen causing a range of illnesses from pharyngitis and impetigo to necrotizing fasciitis and streptococcal toxic shock syndrome. The epithelial sur- faces of the throat and skin are the principal sites of asymp- tomatic S. pyogenes colonization and the sites of most new S. pyogenes acquisition and transmission.1,2
Healthcare-associated outbreaks of invasive S. pyogenes infections in both acute-care3–5 and long-term care facilities6–12 have been well described. Between 5% and 12% of cases of severe S. pyogenes infection are healthcare associated.1,4,5 The control of outbreaks in both acute- care and long-term care facilities is challenging, partly
Affiliations: 1. Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore; 2. Genome Institute of Singapore, Singapore; 3. Yong Loo Lin
School of Medicine, National University of Singapore, Singapore; 4. Institute of Mental Health, Singapore; 5. National Skin Center, Singapore; 6. Irish Menin- gitis and Sepsis Reference Laboratory, Temple Street Children’s University Hospital, Dublin, Ireland; 7. Department of Infectious Diseases, Institute of Infectious Diseases and Epidemiology, Tan Tock Seng Hospital, Singapore; 8. Lee Kong Chien School of Medicine, Nanyang Technological University, Singapore; 9. Saw Swee Hock School of Public Health, National University of Singapore, Singapore; 10. Yong Loo Lin School of Medicine, National University
of Singapore, Singapore; 11. University of St Andrews, St Andrews, Scotland. a First authors of equal contribution. b Authors of equal contribution.
© 2018 by The Society for Healthcare Epidemiology of America. All rights reserved. 0899-823X/2018/3907-0013. DOI: 10.1017/ice.2018.101 Received January 19, 2018; accepted April 8, 2018; electronically published May 9, 2018
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