title: Population genetic structure of Streptococcus pneumoniae in Kilifi, Kenya, prior to the introduction of pneumococcal conjugate vaccine.
abstract: BACKGROUND
  The 10-valent pneumococcal conjugate vaccine (PCV10) was introduced in Kenya in 2011. Introduction of any PCV will perturb the existing pneumococcal population structure, thus the aim was to genotype pneumococci collected in Kilifi before PCV10.
  
  
  RESULTS
  Using multilocus sequence typing (MLST), we genotyped >1100 invasive and carriage pneumococci from children, the largest collection genotyped from a single resource-poor country and reported to date. Serotype 1 was the most common serotype causing invasive disease and was rarely detected in carriage; all serotype 1 isolates were members of clonal complex (CC) 217. There were temporal fluctuations in the major circulating sequence types (STs); and although 1-3 major serotype 1, 14 or 23F STs co-circulated annually, the two major serotype 5 STs mainly circulated independently. Major STs/CCs also included isolates of serotypes 3, 12F, 18C and 19A and each shared ≤ 2 MLST alleles with STs that circulate widely elsewhere. Major CCs associated with non-PCV10 serotypes were predominantly represented by carriage isolates, although serotype 19A and 12F CCs were largely invasive and a serotype 10A CC was equally represented by invasive and carriage isolates.
  
  
  CONCLUSIONS
  Understanding the pre-PCV10 population genetic structure in Kilifi will allow for the detection of changes in prevalence of the circulating genotypes and evidence for capsular switching post-vaccine implementation.
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom ; Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
authors.forename: Angela B
authors.initials: AB
authors.lastname: Brueggemann
authors.forename: Beth Mbesu
authors.initials: BM
authors.lastname: Muroki
authors.forename: Benard W
authors.initials: BW
authors.lastname: Kulohoma
authors.forename: Angela
authors.initials: A
authors.lastname: Karani
authors.forename: Eva
authors.initials: E
authors.lastname: Wanjiru
authors.forename: Susan
authors.initials: S
authors.lastname: Morpeth
authors.forename: Tatu
authors.initials: T
authors.lastname: Kamau
authors.forename: Shahnaaz
authors.initials: S
authors.lastname: Sharif
authors.forename: J Anthony G
authors.initials: JA
authors.lastname: Scott
mesh_terms: D005798:Genes, Bacterial; D005828:Genetics, Population; D006801:Humans; D007630:Kenya; D022242:Pneumococcal Vaccines / Q000008:administration & dosage*; D013296:Streptococcus pneumoniae / Q000235:genetics*
chemical_list: D022242:Pneumococcal Vaccines