Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 26, Number 5—May 2020
Synopsis

Biphasic Outbreak of Invasive Group A Streptococcus Disease in Eldercare Facility, New Zealand

Kate A. Worthing, Anja Werno, Ramon Pink, Liam McIntyre, Glen P. Carter, Deborah A. Williamson1, and Mark R. Davies1Comments to Author 
Author affiliations: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia (K.A. Worthing, L. McIntyre, G.P. Carter, D.A. Williamson, M.R. Davies); Canterbury Health Laboratories, South Island, New Zealand (A. Werno); Canterbury District Health Board, South Island (R. Pink)

Main Article

Figure

Comparative genomic analyses of 55 (18 outbreak and 37 nonoutbreak) associated emm81 group A Streptococcus (GAS) isolates from New Zealand, 2014. A) Midpoint-rooted maximum-likelihood phylogenetic analysis of the emm81 GAS population based on alignment of 336 high-quality single-nucleotide polymorphisms. Green branches indicate nonoutbreak isolates and blue branches indicate the clonal outbreak isolates. Outbreak isolates obtained from eldercare residents (blue) and staff members (orange) were i

Figure. Comparative genomic analyses of 55 (18 outbreak and 37 nonoutbreak) associated emm81 group A Streptococcus (GAS) isolates from New Zealand, 2014. A) Midpoint-rooted maximum-likelihood phylogenetic analysis of the emm81 GAS population based on alignment of 336 high-quality single-nucleotide polymorphisms. Green branches indicate nonoutbreak isolates and blue branches indicate the clonal outbreak isolates. Outbreak isolates obtained from eldercare residents (blue) and staff members (orange) were indistinguishable at the whole-genome level. Numbers on major internal nodes indicate branch support as a percentage over 100 bootstrap replicates. The tree was created by using RAxML (13) and annotated by using iTOL (16). B) Comparative analyses of 55 emm81 draft genome assemblies from outbreak (blue) and nonoutbreak (green) isolates mapped against a new reference GAS genome from the outbreak, DMG1800716. A large DNA sequence coinciding with a 45.4-kb ICE, ICE-SpDMG1800716, is absent in the nonoutbreak isolates compared with all outbreak isolates. The image was created by using BLAST Ring Image Generator (12). C) Schematic representation and pairwise sequence comparison (BLASTn, https://blast.ncbi.nlm.nih.gov) of ICE-SpDMG1800716 relative to the closest known homologue, ICE-Sp1108 (17). The genomic integration site of ICE-SpDMG1800716 is shown relative to a nonoutbreak emm81 isolate, DMG1800744. Red bars refer to 100% BLASTn homology as determined by Easyfig (18). The macrolide resistance gene erm(TR) is shown in dark blue and the abortive infection genes (AbiE) in green. ICE, integrative conjugative element; SNPs, single-nucleotide polymorphisms.

Main Article

References
  1. Walker  MJ, Barnett  TC, McArthur  JD, Cole  JN, Gillen  CM, Henningham  A, et al. Disease manifestations and pathogenic mechanisms of Group A Streptococcus. Clin Microbiol Rev. 2014;27:264–301. DOIPubMedGoogle Scholar
  2. Nelson  GE, Pondo  T, Toews  K-A, Farley  MM, Lindegren  ML, Lynfield  R, et al. Epidemiology of invasive group A streptococcal infections in the United States, 2005–2012. Clin Infect Dis. 2016;63:478–86. DOIPubMedGoogle Scholar
  3. Williamson  DA, Morgan  J, Hope  V, Fraser  JD, Moreland  NJ, Proft  T, et al. Increasing incidence of invasive group A streptococcus disease in New Zealand, 2002-2012: a national population-based study. J Infect. 2015;70:127–34. DOIPubMedGoogle Scholar
  4. Thigpen  MC, Richards  CL Jr, Lynfield  R, Barrett  NL, Harrison  LH, Arnold  KE, et al.; Active Bacterial Core surveillance / Emerging Infections Program Network. 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. DOIPubMedGoogle Scholar
  5. 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. DOIPubMedGoogle Scholar
  6. Davies  MR, Holden  MT, Coupland  P, Chen  JH, Venturini  C, Barnett  TC, et al. 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
  7. Beall  B, Facklam  R, Thompson  T. Sequencing emm-specific PCR products for routine and accurate typing of group A streptococci. J Clin Microbiol. 1996;34:953–8. DOIPubMedGoogle Scholar
  8. Chalker  VJ, Smith  A, Al-Shahib  A, Botchway  S, Macdonald  E, Daniel  R, et al. Integration of genomic and other epidemiologic data to investigate and control a cross-institutional outbreak of Streptococcus pyogenes. Emerg Infect Dis. 2016;22:973–80. DOIPubMedGoogle Scholar
  9. Nanduri  SA, Metcalf  BJ, Arwady  MA, Edens  C, Lavin  MA, Morgan  J, et al. Prolonged and large outbreak of invasive group A Streptococcus disease within a nursing home: repeated intrafacility transmission of a single strain. Clin Microbiol Infect. 2019;25:248.e1–7. DOIPubMedGoogle Scholar
  10. Seemann  T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9. DOIPubMedGoogle Scholar
  11. Bankevich  A, Nurk  S, Antipov  D, Gurevich  AA, Dvorkin  M, Kulikov  AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77. DOIPubMedGoogle Scholar
  12. Alikhan  N-F, Petty  NK, Ben Zakour  NL, Beatson  SA. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics. 2011;12:402. DOIPubMedGoogle Scholar
  13. Stamatakis  A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3. DOIPubMedGoogle Scholar
  14. Bouckaert  R, Heled  J, Kühnert  D, Vaughan  T, Wu  C-H, Xie  D, et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLOS Comput Biol. 2014;10:e1003537. DOIPubMedGoogle Scholar
  15. Rambaut  A, Lam  TT, Max Carvalho  L, Pybus  OG. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2016;2:vew007. DOIPubMedGoogle Scholar
  16. Letunic  I, Bork  P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44(W1):W242-5. DOIPubMedGoogle Scholar
  17. Brenciani  A, Tiberi  E, Bacciaglia  A, Petrelli  D, Varaldo  PE, Giovanetti  E. Two distinct genetic elements are responsible for erm(TR)-mediated erythromycin resistance in tetracycline-susceptible and tetracycline-resistant strains of Streptococcus pyogenes. Antimicrob Agents Chemother. 2011;55:2106–12. DOIPubMedGoogle Scholar
  18. Sullivan  MJ, Petty  NK, Beatson  SA. Easyfig: a genome comparison visualizer. Bioinformatics. 2011;27:1009–10. DOIPubMedGoogle Scholar
  19. Dale  JB, Penfound  TA, Chiang  EY, Walton  WJ. New 30-valent M protein-based vaccine evokes cross-opsonic antibodies against non-vaccine serotypes of group A streptococci. Vaccine. 2011;29:8175–8. DOIPubMedGoogle Scholar
  20. Cornick  JE, Kiran  AM, Vivancos  R, Van Aartsen  J, Clarke  J, Bevan  E, et al. Epidemiological and molecular characterization of an invasive group A Streptococcus emm32.2 outbreak. J Clin Microbiol. 2017;55:1837–46. DOIPubMedGoogle Scholar
  21. Galloway-Peña  J, Clement  ME, Sharma Kuinkel  BK, Ruffin  F, Flores  AR, Levinson  H, et al. Application of whole-genome sequencing to an unusual outbreak of invasive group A streptococcal disease. [-ofw.]. Open Forum Infect Dis. 2016;3:ofw042. DOIPubMedGoogle Scholar
  22. Williamson  DA, Roos  R, Verrall  A, Smith  A, Thomas  MG. Trends, demographics and disparities in outpatient antibiotic consumption in New Zealand: a national study. J Antimicrob Chemother. 2016;71:3593–8. DOIPubMedGoogle Scholar
  23. Dy  RL, Przybilski  R, Semeijn  K, Salmond  GPC, Fineran  PC. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Res. 2014;42:4590–605. DOIPubMedGoogle Scholar
  24. Mearkle  R, Saavedra-Campos  M, Lamagni  T, Usdin  M, Coelho  J, Chalker  V, et al. Household transmission of invasive group A Streptococcus infections in England: a population-based study, 2009, 2011 to 2013. Euro Surveill. 2017;22:30532. DOIPubMedGoogle Scholar
  25. Adebanjo  T, Apostol  M, Alden  N, Petit  S, Tunali  A, Torres  S, et al. Evaluating household transmission of invasive group A Streptococcus disease in the United States using population-based surveillance data, 2013–2016. Clin Infect Dis. 2019 Aug 13;(ciz716). Epub ahead of print.
  26. Ahmed  SS, Diebold  KE, Brandvold  JM, Ewaidah  SS, Black  S, Ogundimu  A, et al. The role of wound care in 2 group A streptococcal outbreaks in a Chicago skilled nursing facility, 2015‒2016. Open Forum Infect Dis. 2018;5:ofy145. DOIPubMedGoogle Scholar

Main Article

1These authors contributed equally to this article.

Page created: April 16, 2020
Page updated: April 16, 2020
Page reviewed: April 16, 2020
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external