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 27, Number 7—July 2021
Research

Whole-Genome Analysis of Streptococcus pneumoniae Serotype 4 Causing Outbreak of Invasive Pneumococcal Disease, Alberta, Canada

James D. KellnerComments to Author , Leah J. Ricketson, Walter H.B. Demczuk, Irene Martin, Gregory J. Tyrrell, Otto G. Vanderkooi, and Michael R. Mulvey
Author affiliations: University of Calgary, Calgary, Alberta, Canada (J.D. Kellner, L.J. Ricketson, O.G. Vanderkooi); Alberta Health Services, Calgary Zone, Calgary (J.D. Kellner, O.G. Vanderkooi); National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada (W.H.B. Demczuk, I. Martin, M.R. Mulvey); University of Alberta, Edmonton, Alberta (G.J. Tyrrell); Alberta Precision Laboratories–Public Health, Edmonton (G.J. Tyrrell)

Main Article

Table 2

Results of multivariable logistic regressions of clinical and demographic factors associated with Streptococcus pneumoniae serotype 4 versus non–serotype 4 causing IPD, Calgary, Alberta, Canada, 2010–2018 (n = 967)*

Factors associated with serotype 4† Odds ratio (95% CI) p value
Male sex 2.1 (1.2–3.7) 0.007
Age ≥65 y 0.3 (0.1–0.7) 0.003
Homelessness 2.4 (1.4–4.1) 0.001
Illicit drug use 2.3 (1.4–3.8) 0.001
Alcohol abuse
0.9 (0.5–1.5)
0.698
Underlying condition an indication for pneumococcal vaccination (11)
No underlying condition increasing risk for IPD Referent Referent
Underlying condition, but immunocompetent 0.9 (0.6–1.5) 0.731
Underlying condition, immunocompromised
0.3 (0.1–0.7)
0.003
Primary diagnosis
Bacteremia or other invasive condition‡ Referent Referent
Pneumonia or empyema 3.6 (1.1–12.0) 0.034
Meningitis 2.8 (0.6–13.4) 0.202

*IPD, invasive pneumococcal disease. †Smoking status included in initial model but result was not significant and a large amount of data was missing, so it was removed from final model. ‡For example, pericarditis, peritonitis, abscess, endophthalmitis.

Main Article

References
  1. Pilishvili  T, Lexau  C, Farley  MM, Hadler  J, Harrison  LH, Bennett  NM, et al.; Active Bacterial Core Surveillance/Emerging Infections Program Network. Sustained reductions in invasive pneumococcal disease in the era of conjugate vaccine. J Infect Dis. 2010;201:3241. DOIPubMedGoogle Scholar
  2. Kaplan  SL, Barson  WJ, Lin  PL, Romero  JR, Bradley  JS, Tan  TQ, et al. Early trends for invasive pneumococcal infections in children after the introduction of the 13-valent pneumococcal conjugate vaccine. Pediatr Infect Dis J. 2013;32:2037. DOIPubMedGoogle Scholar
  3. Leal  J, Vanderkooi  OG, Church  DL, Macdonald  J, Tyrrell  GJ, Kellner  JD. Eradication of invasive pneumococcal disease due to the seven-valent pneumococcal conjugate vaccine serotypes in Calgary, Alberta. Pediatr Infect Dis J. 2012;31:e16975. DOIPubMedGoogle Scholar
  4. Kellner  JD, Vanderkooi  OG, MacDonald  J, Church  DL, Tyrrell  GJ, Scheifele  DW. Changing epidemiology of invasive pneumococcal disease in Canada, 1998-2007: update from the Calgary-area Streptococcus pneumoniae research (CASPER) study. Clin Infect Dis. 2009;49:20512. DOIPubMedGoogle Scholar
  5. Demczuk  W, Griffith  A, Singh  R, Montes  K, Sawatzky  P, Martin  I, et al. National laboratory surveillance of invasive streptococcal disease in Canada—annual summary 2017. Winnipeg, Manitoba (Canada): Public Health Agency of Canada; 2017.
  6. Ricketson  LJ, Kellner  JD. Invasive pneumococcal disease (IPD) trends 1998 to mid-2019 in Calgary, Canada: an interrupted time series analysis: a CASPER study. International Symposium on Pneumococci and Pneumococcal Disease; 2022 Jun 19–23; Toronto, Ontario, Canada. Abstract 104 [cited 2020 Oct 19]. https://cslide.ctimeetingtech.com/isppd20/attendee/confcal/persons/120
  7. Martin  I, Lidder  R, Ricketson  LJ, Demczuk  WH, LeBlanc  JJ, Sadarangani  M, et al. Molecular identification and serotyping of pneumococcal nasopharyngeal carriage vs culture and quellung serotyping in healthy children: a Calgary S. pneumoniae Epidemiology Research (CASPER) study. International Symposium on Pneumococci and Pneumococcal Disease; 2022 Jun 19–23; Toronto, Ontario, Canada. Abstract 348 [cited 2020 Oct 19] https://cslide.ctimeetingtech.com/isppd20/attendee/person/663
  8. Vanderkooi  OG, Church  DL, MacDonald  J, Zucol  F, Kellner  JD. Community-based outbreaks in vulnerable populations of invasive infections caused by Streptococcus pneumoniae serotypes 5 and 8 in Calgary, Canada. PLoS One. 2011;6:e28547. DOIPubMedGoogle Scholar
  9. Lemay  J-A, Ricketson  LJ, Zwicker  L, Kellner  JD. Homelessness in adults with invasive pneumococcal disease (IPD) in Calgary, Canada. Open Forum Infect Dis. 2019;6:ofz362. DOIPubMedGoogle Scholar
  10. Austrian  R. The quellung reaction, a neglected microbiologic technique. Mt Sinai J Med. 1976;43:699709.PubMedGoogle Scholar
  11. Facklam  R, Washington  JA. Streptococcus and related catalase-negative Gram-positive cocci. In: Balows A, Hausler WJ, Hermann KL, Isenberg HD, Shadom HJ, editors. Manual of clinical microbiology. Washington: American Society for Microbiology; 1991. p. 238–57.
  12. Spellerberg  B, Brandt  C. Streptococcus. In: Jorgensen JH, Carroll KC, Funke G, et al., editors. Manual of clinical microbiology, 11th ed. Washington: American Society for Microbiology; 2015. p. 383–402.
  13. Pimenta  FC, Roundtree  A, Soysal  A, Bakir  M, du Plessis  M, Wolter  N, et al. Sequential triplex real-time PCR assay for detecting 21 pneumococcal capsular serotypes that account for a high global disease burden. J Clin Microbiol. 2013;51:64752. DOIPubMedGoogle Scholar
  14. Drancourt  M, Roux  V, Fournier  PE, Raoult  D. rpoB gene sequence-based identification of aerobic Gram-positive cocci of the genera Streptococcus, Enterococcus, Gemella, Abiotrophia, and Granulicatella. J Clin Microbiol. 2004;42:497504. DOIPubMedGoogle Scholar
  15. Clinical Laboratory and Standards Institute. Interpretive criteria for identification of bacteria and fungi by DNA target sequencing; approved guideline (MM18-A). Wayne (PA): The Institute; 2008.
  16. Clinical and Laboratory Standards Institute. Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically, 8th ed (M07–A8). Wayne (PA): The Institute; 2009.
  17. Clinical Laboratory and Standards Institute. Performance standards for antimicrobial susceptibility testing; 22nd informational supplement (M100–S22). Wayne (PA): The Institute; 2012.
  18. Demczuk  WHB, Martin  I, Hoang  L, Van Caeseele  P, Lefebvre  B, Horsman  G, et al. Phylogenetic analysis of emergent Streptococcus pneumoniae serotype 22F causing invasive pneumococcal disease using whole genome sequencing. PLoS One. 2017;12:e0178040. DOIPubMedGoogle Scholar
  19. Andrews  S. FastQC: a quality control tool for high throughput sequence data, version 0.11.4 [cited 2020 June 29] https://www.bioinformatics.babraham.ac.uk/projects/fastqc
  20. Seemann  T. Shovill: faster SPAdes assembly of Illumina reads. 2017. [cited 2020 June 21] https://github.com/tseemann/shovill
  21. Petkau  A, Mabon  P, Sieffert  C, Knox  NC, Cabral  J, Iskander  M, et al. SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology. Microb Genom. 2017;3:e000116. DOIPubMedGoogle Scholar
  22. Rambaut  A. FigTree: molecular evolution, phylogenetics and epidemiology, version 1.4.3 [cited 2020 June 15] http://tree.bio.ed.ac.uk/software/figtree
  23. Ragonnet-Cronin  M, Hodcroft  E, Hué  S, Fearnhill  E, Delpech  V, Brown  AJ, et al.; UK HIV Drug Resistance Database. Automated analysis of phylogenetic clusters. BMC Bioinformatics. 2013;14:317. DOIPubMedGoogle Scholar
  24. Jolley  KA, Bray  JE, Maiden  MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 2018;3:124. DOIPubMedGoogle Scholar
  25. Tyrrell  GJ. The changing epidemiology of Streptococcus pneumoniae serotype 19A clonal complexes. J Infect Dis. 2011;203:13457. DOIPubMedGoogle Scholar
  26. Hausdorff  WP, Feikin  DR, Klugman  KP. Epidemiological differences among pneumococcal serotypes. Lancet Infect Dis. 2005;5:8393. DOIPubMedGoogle Scholar
  27. Miller  RR, Langille  MG, Montoya  V, Crisan  A, Stefanovic  A, Martin  I, et al. Genomic analysis of a serotype 5 Streptococcus pneumoniae outbreak in British Columbia, Canada, 2005–2009. Can J Infect Dis Med Microbiol. 2016;2016:5381871. DOIPubMedGoogle Scholar
  28. Kellner  JD, Scheifele  D, Vanderkooi  OG, Macdonald  J, Church  DL, Tyrrell  GJ. Effects of routine infant vaccination with the 7-valent pneumococcal conjugate vaccine on nasopharyngeal colonization with streptococcus pneumoniae in children in Calgary, Canada. Pediatr Infect Dis J. 2008;27:52632. DOIPubMedGoogle Scholar
  29. Linley  E, Bell  A, Gritzfeld  JF, Borrow  R. Should pneumococcal serotype 3 be included in serotype-specific immunoassays? Vaccines (Basel). 2019;7:4. DOIPubMedGoogle Scholar
  30. Tyrrell  GJ, Lovgren  M, Ibrahim  Q, Garg  S, Chui  L, Boone  TJ, et al. Epidemic of invasive pneumococcal disease, western Canada, 2005-2009. Emerg Infect Dis. 2012;18:73340. DOIPubMedGoogle Scholar
  31. McKee  G, Choi  A, Madill  C, Marriott  J, Kibsey  P, Hoyano  D II. Outbreak of invasive Streptococcus pneumoniae among an inner-city population in Victoria, British Columbia, 2016-2017. Can Commun Dis Rep. 2018;44:31722. DOIPubMedGoogle Scholar
  32. Hoge  CW, Reichler  MR, Dominguez  EA, Bremer  JC, Mastro  TD, Hendricks  KA, et al. An epidemic of pneumococcal disease in an overcrowded, inadequately ventilated jail. N Engl J Med. 1994;331:6438. DOIPubMedGoogle Scholar
  33. DeMaria  A Jr, Browne  K, Berk  SL, Sherwood  EJ, McCabe  WR. An outbreak of type 1 pneumococcal pneumonia in a men’s shelter. JAMA. 1980;244:14469. DOIPubMedGoogle Scholar
  34. Mercat  A, Nguyen  J, Dautzenberg  B. An outbreak of pneumococcal pneumonia in two men’s shelters. Chest. 1991;99:14751. DOIPubMedGoogle Scholar
  35. Gleich  S, Morad  Y, Echague  R, Miller  JR, Kornblum  J, Sampson  JS, et al. Streptococcus pneumoniae serotype 4 outbreak in a home for the aged: report and review of recent outbreaks. Infect Control Hosp Epidemiol. 2000;21:7117. DOIPubMedGoogle Scholar
  36. Plevneshi  A, Svoboda  T, Armstrong  I, Tyrrell  GJ, Miranda  A, Green  K, et al.; Toronto Invasive Bacterial Diseases Network. Population-based surveillance for invasive pneumococcal disease in homeless adults in Toronto. PLoS One. 2009;4:e7255. DOIPubMedGoogle Scholar
  37. Zivich  PN, Grabenstein  JD, Becker-Dreps  SI, Weber  DJ. Streptococcus pneumoniae outbreaks and implications for transmission and control: a systematic review. Pneumonia (Nathan). 2018;10:11. DOIPubMedGoogle Scholar

Main Article

Page created: April 23, 2021
Page updated: June 16, 2021
Page reviewed: June 16, 2021
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