Phylogenetic Analysis of Invasive Serotype 1 Pneumococcus in South Africa, 1989 to 2013

Details

• Alternative Title:
  J Clin Microbiol
• Personal Author:
  du Plessis, Mignon ; Allam, Mushal ; Tempia, Stefano ; Wolter, Nicole ; de Gouveia, Linda ; von Mollendorf, Claire ; Jolley, Keith A. ; Mbelle, Nontombi ; Wadula, Jeannette ; Cornick, Jennifer E. ; Everett, Dean B. ; McGee, Lesley ; Breiman, Robert F. ; Gladstone, Rebecca A. ; Bentley, Stephen D. ; Klugman, Keith P. ; von Gottberg, Anne
• Description:
  Serotype 1 is an important cause of invasive pneumococcal disease in South Africa and has declined following the introduction of the 13-valent pneumococcal conjugate vaccine in 2011. We genetically characterized 912 invasive serotype 1 isolates from 1989 to 2013. Simpson's diversity index (D) and recombination ratios were calculated. Factors associated with sequence types (STs) were assessed. Clonal complex 217 represented 96% (872/912) of the sampled isolates. Following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13), ST diversity increased in children <5 years (D, 0.39 to 0.63, P = 0.002) and individuals >14 years (D, 0.35 to 0.54, P < 0.001): ST-217 declined proportionately in children <5 years (153/203 [75%] versus 21/37 [57%], P = 0.027) and individuals >14 years (242/305 [79%] versus 96/148 [65%], P = 0.001), whereas ST-9067 increased (4/684 [0.6%] versus 24/228 [11%], P < 0.001). Three subclades were identified within ST-217: ST-217C1 (353/382 [92%]), ST-217C2 (15/382 [4%]), and ST-217C3 (14/382 [4%]). ST-217C2, ST-217C3, and single-locus variant (SLV) ST-8314 (20/912 [2%]) were associated with nonsusceptibility to chloramphenicol, tetracycline, and co-trimoxazole. ST-8314 (20/912 [2%]) was also associated with increased nonsusceptibility to penicillin (P < 0.001). ST-217C3 and newly reported ST-9067 had higher recombination ratios than those of ST-217C1 (4.344 versus 0.091, P < 0.001; and 0.086 versus 0.013, P < 0.001, respectively). Increases in genetic diversity were noted post-PCV13, and lineages associated with antimicrobial nonsusceptibility were identified.
• Subjects:
  Bacteriology
• Source:
  J Clin Microbiol. 2016; 54(5):1326-1334.
• Pubmed ID:
  26962082
• Pubmed Central ID:
  PMC4844715
• Document Type:
  Journal Article
• Volume:
  54
• Issue:
  5
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:cfb3acc1e44b6f107cf27da551e598a364730fbbaa05d674c729b7342113d42c
• Download URL:
  https://stacks.cdc.gov/view/cdc/39341/cdc_39341_DS1.pdf
• File Type:
  [PDF - 683.44 KB ]