Population structure, epidemiology and antibiotic resistance patterns of Streptococcus pneumoniae serotype 5: prior to PCV-13 vaccine introduction in Eastern Gambia

Abstract

Background: Streptococcus pneumoniae serotype 5 is among the most common serotypes causing invasive pneumococcal disease (IPD) in The Gambia. We anticipate that introduction of the 13-valent pneumococcal conjugate vaccine (PCV-13) into routine vaccination in The Gambia will reduce serotype 5 IPD. However, the emergence of new clones that have altered their genetic repertoire through capsular switching or genetic recombination after vaccination with PCV-13 poses a threat to this public health effort. In order to monitor for potential genetic changes post-PCV-13 vaccination, we established the baseline population structure, epidemiology, and antibiotic resistance patterns of serotype 5 before the introduction of PCV-13.

Methods: Fifty-five invasive S. pneumoniae serotype 5 isolates were recovered from January 2009 to August 2011 in a population-based study in the Upper River Region of The Gambia. Serotyping was done by latex agglutination and confirmed by serotype-specific Polymerase Chain Reaction (PCR). Genotyping was undertaken using Multilocus Sequence Typing (MLST). Antimicrobial sensitivity was done using disc diffusion. Contingency table analyses were conducted using Pearson's Chi(2) and Fisher's exact test. Clustering was performed using Bionumerics version 6.5.

Results: MLST resolved S. pneumoniae serotype 5 isolates into 3 sequence types (ST), namely ST 289(6/55), ST 3339(19/55) and ST 3404(30/55). ST 289 was identified as the major clonal complex. ST 3339, the prevalent genotype in 2009 [84.6% (11/13)], was replaced by ST 3404 [70.4% (19/27)] in 2010 as the dominant ST. Interestingly, ST 3404 showed lower resistance to tetracycline and oxacillin (P < 0.001), an empirical surrogate to penicillin in The Gambia.

Conclusions: There has been an emergence of ST 3404 in The Gambia prior to the introduction of PCV-13. Our findings provide important background data for future assessment of the impact of PCV-13 into routine immunization in developing countries, such as The Gambia.

Fig. 1

Clustering of STs from diverse world regions by use of the minimum spanning algorithm. Each circle represents an ST. The area of each circle corresponds to the number of isolates of a given ST in the MLST database. A clonal complex is a group of STs sharing a minimum of 6 out of 7 alleles [31]. The inferred putative ancestor of all clonal complexes is ST 289. Green portions represent STs found in Gambia including those used for the study while the other colours represent STs found in the rest of the world

Fig. 2

Clustering of STs from The Gambia by use of the minimum spanning algorithm. Thick, short, solid lines connect single-locus variants; thick, longer, solid lines connect double-loci variants; Thick, very long, solid lines connect three-loci variants; dash and dotted lines connect four and five-loci variants respectively. Green portions represent STs identified during the study and red portions represent ST previously described from the rest of Gambia

Fig. 3

Plot showing temporal trends of serotype 5 and its observed ST’s from 2009–2011 in The Gambia. The x axis represents time in month-year with the zero point being Jan-09, whilst the y axis represents the number of serotype 5 IPDs recorded. ST 3339 was the prevalent genotype in 2009; ST 3404 peaked at the beginning of 2010 and has since been the dominant genotype for most observed IPD cases of serotype 5 origin