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Volume 22, Number 6—June 2016
Synopsis

Integration of Genomic and Other Epidemiologic Data to Investigate and Control a Cross-Institutional Outbreak of Streptococcus pyogenes

Victoria J. Chalker, Alyson Smith, Ali Al-Shahib, Stella Botchway, Emily Macdonald, Roger Daniel, Sarah Phillips, Steven Platt, Michel Doumith, Rediat Tewolde, Juliana Coelho, Keith A. Jolley, Anthony Underwood, and Noel McCarthyComments to Author 
Author affiliations: Public Health England, Colindale, UK (V.J. Chalker, A. Al-Shahib, R. Daniel, S. Phillips, S. Platt, M. Doumith, R. Tewolde, J. Coelho, A. Underwood); South East England Public Health England Centre, Chilton, UK (A. Smith, S. Botchway, E. Macdonald, N.D. McCarthy); University of Oxford Department of Zoology, Oxford, UK (K.A. Jolley, N.D. McCarthy); University of Warwick, Warwick Medical School, Coventry, UK (N.D. McCarthy)

Main Article

Figure 3

Pairwise allelic differences (across 1,514 genetic loci) among 6 isolates from a cross-institutional Streptococcus pyogenes outbreak in Oxfordshire, United Kingdom, and other isolates. Green indicates differences between each of the 6 Oxfordshire outbreak isolates and each of the other 33 isolates that occurred in other geographic areas in the United Kingdom around the time of the Oxfordshire outbreak or were reported by Turner et al. in 2013 (20). Red indicates differences between outbreak isol

Figure 3. Pairwise allelic differences (across 1,514 genetic loci) among 6 isolates from a cross-institutional Streptococcus pyogenes outbreak in Oxfordshire, United Kingdom, and other isolates. Green indicates differences between each of the 6 Oxfordshire outbreak isolates and each of the other 33 isolates that occurred in other geographic areas in the United Kingdom around the time of the Oxfordshire outbreak or were reported by Turner et al. in 2013 (20). Red indicates differences between outbreak isolates from the cluster described by Turner et al. (20). Blue indicates differences between each isolate in the Oxfordshire outbreak compared with each of the other 5 isolates in the outbreak.

Main Article

References
  1. Lamagni  TL, Darenberg  J, Luca-Harari  B, Siljander  T, Efstratiou  A, Henriques-Normark  B, Epidemiology of severe Streptococcus pyogenes disease in Europe. J Clin Microbiol. 2008;46:2359–67 . DOIPubMedGoogle Scholar
  2. Lepoutre  A, Doloy  A, Bidet  P, Leblond  A, Perrocheau  A, Bingen  E, Epidemiology of invasive Streptococcus pyogenes infections in France in 2007. J Clin Microbiol. 2011;49:4094–100. DOIPubMedGoogle Scholar
  3. O’Loughlin  RE, Roberson  A, Cieslak  PR, Lynfield  R, Gershman  K, Craig  A, The epidemiology of invasive group A streptococcal infection and potential vaccine implications: United States, 2000–2004. Clin Infect Dis. 2007;45:853–62. DOIPubMedGoogle Scholar
  4. Davies  HD, McGeer  A, Schwartz  B, Green  K, Cann  D, Simor  AE, Invasive group A streptococcal infections in Ontario, Canada. Ontario Group A Streptococcal Study Group. N Engl J Med. 1996;335:547–54 . DOIPubMedGoogle Scholar
  5. Lamagni  TL, Neal  S, Keshishian  C, Powell  D, Potz  N, Pebody  R, Predictors of death after severe Streptococcus pyogenes infection. Emerg Infect Dis. 2009;15:1304–7. DOIPubMedGoogle Scholar
  6. Muller  MP, Low  DE, Green  KA, Simor  AE, Loeb  M, Gregson  D, Clinical and epidemiologic features of group a streptococcal pneumonia in Ontario, Canada. Arch Intern Med. 2003;163:467–72. DOIPubMedGoogle Scholar
  7. Rainbow  J, Jewell  B, Danila  RN, Boxrud  D, Beall  B, Van Beneden  C, Invasive group a streptococcal disease in nursing homes, Minnesota, 1995–2006. Emerg Infect Dis. 2008;14:772–7 .PubMedGoogle Scholar
  8. Thigpen  MC, Richards  CL Jr, Lynfield  R, Barrett  NL, Harrison  LH, Arnold  KE, Invasive group A streptococcal infection in older adults in long-term care facilities and the community, United States, 1998–2003. Emerg Infect Dis. 2007;13:1852–9 .PubMedGoogle Scholar
  9. Zurawski  CA, Bardsley  M, Beall  B, Elliott  JA, Facklam  R, Schwartz  B, Invasive group A streptococcal disease in metropolitan Atlanta: a population-based assessment. Clin Infect Dis. 1998;27:150–7. DOIPubMedGoogle Scholar
  10. Daneman  N, Green  KA, Low  DE, Simor  AE, Willey  B, Schwartz  B, Surveillance for hospital outbreaks of invasive group A streptococcal infections in Ontario, Canada, 1992 to 2000. Ann Intern Med. 2007;147:234–41. DOIPubMedGoogle Scholar
  11. Steer  JA, Lamagni  T, Healy  B, Morgan  M, Dryden  M, Rao  B, Guidelines for prevention and control of group A streptococcal infection in acute healthcare and maternity settings in the UK. J Infect. 2012;64:1–18. DOIPubMedGoogle Scholar
  12. Jordan  HT, Richards  CL Jr, Burton  DC, Thigpen  MC, Van Beneden  CA. Group A streptococcal disease in long-term care facilities: descriptive epidemiology and potential control measures. Clin Infect Dis. 2007;45:742–52 and. DOIPubMedGoogle Scholar
  13. Cummins  A, Millership  S, Lamagni  T, Foster  K. Control measures for invasive group A streptococci (iGAS) outbreaks in care homes. J Infect. 2012;64:156–61. DOIPubMedGoogle Scholar
  14. Centers for Disease Control and Prevention. Invasive group A streptococcus in a skilled nursing facility—Pennsylvania, 2009–2010. MMWR Morb Mortal Wkly Rep. 2011;60:1445–9 .PubMedGoogle Scholar
  15. Greene  CM, Van Beneden  CA, Javadi  M, Skoff  TH, Beall  B, Facklam  R, Cluster of deaths from group A streptococcus in a long-term care facility—Georgia, 2001. Am J Infect Control. 2005;33:108–13. DOIPubMedGoogle Scholar
  16. Rahman  M. Outbreak of Streptococcus pyogenes infections in a geriatric hospital and control by mass treatment. J Hosp Infect. 1981;2:63–9. DOIPubMedGoogle Scholar
  17. Reid  RI, Briggs  RS, Seal  DV, Pearson  AD. Virulent Streptococcus pyogenes: outbreak and spread within a geriatric unit. J Infect. 1983;6:219–25. DOIPubMedGoogle Scholar
  18. McCarthy  N. An epidemiological view of microbial genomic data. Lancet Infect Dis. 2013;13:104–5. DOIPubMedGoogle Scholar
  19. Walker  TM, Lalor  MK, Broda  A, Saldana Ortega  L, Morgan  M, Parker  L, Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007–12, with whole pathogen genome sequences: an observational study. Lancet Respir Med. 2014;2:285–92.
  20. Turner  CE, Dryden  M, Holden  MT, Davies  FJ, Lawrenson  RA, Farzaneh  L, Molecular analysis of an outbreak of lethal postpartum sepsis caused by Streptococcus pyogenes. J Clin Microbiol. 2013;51:2089–95. DOIPubMedGoogle Scholar
  21. Ben Zakour  NL, Venturini  C, Beatson  SA, Walker  MJ. Analysis of a Streptococcus pyogenes puerperal sepsis cluster by use of whole-genome sequencing. J Clin Microbiol. 2012;50:2224–8. DOIPubMedGoogle Scholar
  22. Health Protection Agency. Group A Streptococcus Working Group. Interim UK guidelines for management of close community contacts of invasive group A streptococcal disease. Commun Dis Public Health. 2004;7:354–61 .PubMedGoogle Scholar
  23. Johnson  DR, Kaplan  EL, Sramek  J, Bicova  R, Havlicek  JHH, Havlickova  H, Laboratory diagnosis of group A streptococcal infections. Geneva: World Health Organization; 1996 [cited 2014 Dec 20]. http://apps.who.int/iris/bitstream/10665/41879/1/9241544953_eng.pdf
  24. Bidet  P, Lesteven  E, Doit  C, Liguori  S, Mariani-Kurkdjian  P, Bonacorsi  S, Subtyping of emm1 group A streptococci causing invasive infections in France. J Clin Microbiol. 2009;47:4146–9. DOIPubMedGoogle Scholar
  25. Li  H, Durbin  R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics. 2010;26:589–95. DOIPubMedGoogle Scholar
  26. McKenna  A, Hanna  M, Banks  E, Sivachenko  A, Cibulskis  K, Kernytsky  A, The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–303. DOIPubMedGoogle Scholar
  27. Zerbino  DR, Birney  E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–9 . DOIPubMedGoogle Scholar
  28. Maiden  MC, van Rensburg  MJ, Bray  JE, Earle  SG, Ford  SA, Jolley  KA, MLST revisited: the gene-by-gene approach to bacterial genomics. Nat Rev Microbiol. 2013;11:728–36. DOIPubMedGoogle Scholar
  29. Stamatakis  A. RAxML-VI-HPC: maximum likelihood–based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22:2688–90. DOIPubMedGoogle Scholar
  30. Jolley  KA, Maiden  MCJ. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics. 2010;11:595. DOIPubMedGoogle Scholar
  31. Tamura  K, Peterson  D, Peterson  N, Stecher  G, Nei  M, Kumar  S. MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28:2731–9. DOIPubMedGoogle Scholar
  32. Banks  DJ, Beres  SB, Musser  JM. The fundamental contribution of phages to GAS evolution, genome diversification and strain emergence. Trends Microbiol. 2002;10:515–21. DOIPubMedGoogle Scholar
  33. Schwartz  B, Ussery  XT. Group A streptococcal outbreaks in nursing homes. Infect Control Hosp Epidemiol. 1992;13:742–7. DOIPubMedGoogle Scholar
  34. Thigpen  MC, Thomas  DM, Gloss  D, Park  SY, Khan  AJ, Fogelman  VL, Nursing home outbreak of invasive group A streptococcal infections caused by 2 distinct strains. Infect Control Hosp Epidemiol. 2007;28:68–74 .PubMedGoogle Scholar
  35. Stanley  J, Desai  M, Xerry  J, Tanna  A, Efstratiou  A, George  R. High-resolution genotyping elucidates the epidemiology of group A streptococcus outbreaks. J Infect Dis. 1996;174:500–6. DOIPubMedGoogle Scholar
  36. Athey  TB, Teatero  S, Li  A, Marchand-Austin  A, Beall  BW, Fittipaldi  N. Deriving group A Streptococcus typing information from short-read whole-genome sequencing data. J Clin Microbiol. 2014;52:1871–6. DOIPubMedGoogle Scholar
  37. Davies  MR, Holden  MT, Coupland  P, Chen  JH, Venturini  C, Barnett  TC, Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance. Nat Genet. 2015;47:84–7. DOIPubMedGoogle Scholar
  38. Smith  A, Li  A, Tolomeo  O, Tyrrell  GJ, Jamieson  F, Fisman  D. Mass antibiotic treatment for group A streptococcus outbreaks in two long-term care facilities. Emerg Infect Dis. 2003;9:1260–5. DOIPubMedGoogle Scholar
  39. Arnold  KE, Schweitzer  JL, Wallace  B, Salter  M, Neeman  R, Hlady  WG, Tightly clustered outbreak of group A streptococcal disease at a long-term care facility. Infect Control Hosp Epidemiol. 2006;27:1377–84. DOIPubMedGoogle Scholar
  40. Milne  LM, Lamagni  T, Efstratiou  A, Foley  C, Gilman  J, Lilley  M, Streptococcus pyogenes cluster in a care home in England April to June 2010. Euro Surveill. 2011;16:20021 .PubMedGoogle Scholar

Main Article

CrossRef reports the first author should be "High" not "Jordan" in reference 12 "Jordan, Richards, Burton, Thigpen, Van Beneden, 2007".

Reference has only first page number. Please provide the last page number if article is longer than one page. (in reference 30 "Jolley, Maiden, 2010").

CrossRef reports the year should be "2014" not "2015" in reference 37 "Davies, Holden, Coupland, Chen, Venturini, Barnett, et al., 2015".

Reference has only first page number. Please provide the last page number if article is longer than one page. (in reference 40 "Milne, Lamagni, Efstratiou, Foley, Gilman, Lilley, et al., 2011").

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