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An Outbreak of Streptococcus pyogenes in a Mental Health Facility: Advantage of Well-Timed Whole-Genome Sequencing Over emm Typing
- Sarah M. Bergin, Balamurugan Periaswamy, Timothy Barkham, Hong Choon Chua, Yee Ming Mok, Daniel Shuen Sheng Fung, Alex Hsin Chuan Su, Yen Ling Lee, Ming Lai Ivan Chua, Poh Yong Ng, Wei Jia Wendy Soon, Collins Wenhan Chu, Siyun Lucinda Tan, Mary Meehan, Brenda Sze Peng Ang, Yee Sin Leo, Matthew T. G. Holden, Partha De, Li Yang Hsu, Swaine L. Chen, Paola Florez de Sessions, Kalisvar Marimuthu
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- Journal:
- Infection Control & Hospital Epidemiology / Volume 39 / Issue 7 / July 2018
- Published online by Cambridge University Press:
- 09 May 2018, pp. 852-860
- Print publication:
- July 2018
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- Article
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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.
SETTINGA 2,000-bed tertiary-care psychiatric hospital.
METHODSActive 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.
RESULTSThe 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.
CONCLUSIONSWGS 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
Contributors
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- By Magdalena Anitescu, Charles E. Argoff, Arash Asher, Nyla Azam, Nomen Azeem, Sachin K. Bansal, Jose E. Barreto, Rodrigo A Benavides, Niteesh Bharara, Justin B. Boge, Robert B. Bolash, Thomas K. Bond, Christopher Centeno, Zachariah W. Chambers, Jonathan Chang, Grace Chen, Hamilton Chen, Jeffry Chen, Jianguo Cheng, Natalia Covarrubias, Claire J. Creutzfeldt, Gulshan Doulatram, Amirpasha Ehsan, Ike Eriator, Jeff Ericksen, Mark Etscheidt, Frank J. E. Falco, Jack Fu, Timothy Furnish, Annemarie E. Gallagher, Kingsuk Ganguly, Eugene Garvin, Cliff Gevirtz, Scott E. Glaser, Brandon J. Goff, Harry J. Gould, Christine Greco, Jay S. Grider, Maged Guirguis, Qiao Guo, Justin Hata, John Hau, Garett J. Helber, Eric R. Helm, Lori Hill Marshall, Dean Hommer, Jeffrey Hopcian, Eric S. Hsu, Jakun Ing, Tracy P. Jackson, Gaurav Jain, Chrystina Jeter, Alan David Kaye, James Kelly, Soorena Khojasteh, Ankur Khosla, Daniel Krashin, Monika A. Krzyzek, Prasad Lakshminarasimhiah, Steven Michael Lampert, Garrett LaSalle, Quan D. Le, Ankit Maheshwari, Edward R. Mariano, Joaquin Maury, John P. McCallin, John Michels, Natalia Murinova, Narendren Narayanasamy, Rebekah L. Nilson, Elliot Palmer, Vikram B. Patel, Devin Peck, Donald B. Penzien, Danielle Perret Karimi, Tilak Raj, Michael R. Rasmussen, Mohit Rastogi, Rahul Rastogi, Nashaat N. Rizk, Rinoo V. Shah, Paul A. Sloan, Julian Sosner, A. Raj Swain, Minyi Tan, Natacha Telusca, Santhosh A. Thomas, Andrea Trescot, Michael Truong, Jason Tucker, Richard D. Urman, Brandon A. Van Noord, Nihir Waghela, Irene Wu, Jiang Wu, Jijun Xu, Jinghui Xie, William Yancey
- Edited by Alan David Kaye, Louisiana State University, Rinoo V. Shah
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- Book:
- Case Studies in Pain Management
- Published online:
- 05 October 2014
- Print publication:
- 16 October 2014, pp xi-xv
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- Chapter
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