An Outbreak of Streptococcus pyogenes in a Mental Health Facility: Advantage of Well-Timed Whole-Genome Sequencing Over emm Typing
| Autor: | Hong Choon Chua, Alex Hsin Chuan Su, Daniel Fung, Balamurugan Periaswamy, Yee Sin Leo, Kalisvar Marimuthu, Paola Florez de Sessions, Matthew T. G. Holden, Sarah M. Bergin, Poh Yong Ng, Timothy Barkham, Swaine L. Chen, Yee Ming Mok, Li Yang Hsu, Yen Ling Lee, Siyun Lucinda Tan, Partha Pratim De, Mary Meehan, Brenda Ang, Collins Wenhan Chu, Ming Lai Ivan Chua, Wei Jia Wendy Soon |
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| Přispěvatelé: | University of St Andrews. School of Medicine, University of St Andrews. Infection and Global Health Division, University of St Andrews. Biomedical Sciences Research Complex, University of St Andrews. Infection Group |
| Rok vydání: | 2018 |
| Předmět: |
Hospitals
Psychiatric 0301 basic medicine Microbiology (medical) RZ Other systems of medicine Genotype Streptococcus pyogenes Epidemiology 030106 microbiology Biology medicine.disease_cause Polymorphism Single Nucleotide Genome Disease Outbreaks 03 medical and health sciences SDG 3 - Good Health and Well-being RA0421 RZ Emm type Streptococcal Infections RA0421 Public health. Hygiene. Preventive Medicine medicine Humans SNP Skin Whole genome sequencing Genetics Cross Infection Likelihood Functions Molecular Epidemiology Singapore Whole Genome Sequencing Phylogenetic tree Outbreak DAS Infectious Diseases Multilocus sequence typing Databases Nucleic Acid Sentinel Surveillance Multilocus Sequence Typing |
| Zdroj: | Infection Control & Hospital Epidemiology. 39:852-860 |
| ISSN: | 1559-6834 0899-823X |
| DOI: | 10.1017/ice.2018.101 |
| Popis: | OBJECTIVEWe 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 |
| Databáze: | OpenAIRE |
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