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.

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.

Figure 1. Prevalence of major clonal complexes (CCs) associated with invasive isolates collected in Kilifi.

The total number of isolates genotyped each year from 1994-2008 is stated in parentheses in the y-axis labels.

Figure 2. Fluctuation in the prevalence of major sequence types (STs) associated with invasive isolates from Kilifi.

Invasive isolates were collected from 1994-2008 and the major STs associated with serotypes 1 (Figure 2A) and 5 (Figure 2B) are depicted in each panel. The total number of isolates genotyped each year (see Methods) is stated in parentheses in the x-axis labels.

Figure 3. Fluctuation in the prevalence of major sequence types (STs) associated with invasive isolates from Kilifi.

Invasive isolates were collected from 1994-2008 and the major STs associated with serotypes 14 (Figure 3A) and 23F (Figure 3B) are depicted in each panel. The total number of isolates genotyped each year (see Methods) is stated in parentheses in the x-axis labels.

Figure 4. Five additional major sequence types (STs) associated with invasive isolates that circulated in Kilifi.

Major STs associated with serotypes 12F, 19A, 6B, 4 and 18C are depicted for each surveillance year from 1994-2008. The total number of isolates genotyped each year (see Methods) is stated in parentheses in the x-axis labels.