title: Integration of Genomic and Other Epidemiologic Data to Investigate and Control a Cross-Institutional Outbreak of Streptococcus pyogenes.
abstract: Single-strain outbreaks of Streptococcus pyogenes infections are common and often go undetected. In 2013, two clusters of invasive group A Streptococcus (iGAS) infection were identified in independent but closely located care homes in Oxfordshire, United Kingdom. Investigation included visits to each home, chart review, staff survey, microbiologic sampling, and genome sequencing. S. pyogenes emm type 1.0, the most common circulating type nationally, was identified from all cases yielding GAS isolates. A tailored whole-genome reference population comprising epidemiologically relevant contemporaneous isolates and published isolates was assembled. Data were analyzed independently using whole-genome multilocus sequencing and single-nucleotide polymorphism analyses. Six isolates from staff and residents of the homes formed a single cluster that was separated from the reference population by both analytical approaches. No further cases occurred after mass chemoprophylaxis and enhanced infection control. Our findings demonstrate the ability of 2 independent analytical approaches to enable robust conclusions from nonstandardized whole-genome analysis to support public health practice.
authors.forename: Victoria J
authors.initials: VJ
authors.lastname: Chalker
authors.forename: Alyson
authors.initials: A
authors.lastname: Smith
authors.forename: Ali
authors.initials: A
authors.lastname: Al-Shahib
authors.forename: Stella
authors.initials: S
authors.lastname: Botchway
authors.forename: Emily
authors.initials: E
authors.lastname: Macdonald
authors.forename: Roger
authors.initials: R
authors.lastname: Daniel
authors.forename: Sarah
authors.initials: S
authors.lastname: Phillips
authors.forename: Steven
authors.initials: S
authors.lastname: Platt
authors.forename: Michel
authors.initials: M
authors.lastname: Doumith
authors.forename: Rediat
authors.initials: R
authors.lastname: Tewolde
authors.forename: Juliana
authors.initials: J
authors.lastname: Coelho
authors.forename: Keith A
authors.initials: KA
authors.lastname: Jolley
authors.forename: Anthony
authors.initials: A
authors.lastname: Underwood
authors.forename: Noel D
authors.initials: ND
authors.lastname: McCarthy
mesh_terms: D000483:Alleles; D019295:Computational Biology / Q000379:methods; D003428:Cross Infection / Q000453:epidemiology*; D004196:Disease Outbreaks; D024881:Drug Resistance, Bacterial; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D006268:Health Facilities; D006801:Humans; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D013290:Streptococcal Infections / Q000453:epidemiology* / Q000382:microbiology* / Q000517:prevention & control / Q000635:transmission; D013297:Streptococcus pyogenes / Q000187:drug effects / Q000235:genetics* / Q000472:pathogenicity; D006113:United Kingdom / Q000453:epidemiology; D014774:Virulence / Q000235:genetics; D000073336:Whole Genome Sequencing
keywords: Group A Streptococcus; Streptococcus pyogenes; bacteria; epidemiologic data; genome; genomic data; iGAS; infection control; invasive group A streptococcal infection; investigation; outbreak; streptococci; whole-genome sequencing