Population Genetic Structure of Streptococcus pneumoniae in Kilifi, Kenya, Prior to the Introduction of Pneumococcal Conjugate Vaccine
Author(s)
Type
Journal Article
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.
Methods and Findings:
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.
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.
Methods and Findings:
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.
Date Issued
2013-11-25
Date Acceptance
2013-10-23
Citation
PLOS ONE, 2013, 8 (11)
ISSN
1932-6203
Publisher
PUBLIC LIBRARY OF SCIENCE
Journal / Book Title
PLOS ONE
Volume
8
Issue
11
Copyright Statement
© 2013 Brueggemann et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which
permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Identifier
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000327543500108&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
Subjects
Science & Technology
Multidisciplinary Sciences
Science & Technology - Other Topics
UNITED-STATES
SEROTYPE 19A
INVASIVE-DISEASE
CAPSULAR SEROTYPES
CHILDREN
CARRIAGE
EPIDEMIOLOGY
MENINGITIS
CLONES
IMPACT
Genes, Bacterial
Genetics, Population
Humans
Kenya
Pneumococcal Vaccines
Streptococcus pneumoniae
MD Multidisciplinary
General Science & Technology
Publication Status
Published
Article Number
ARTN e81539