Carried pneumococci in Massachusetts children: the contribution of clonal expansion and serotype switching

Abstract

Background: Vaccination against 7 serotypes of Streptococcus pneumoniae has led to the near extinction of vaccine serotypes in both disease and asymptomatic carriage. In carriage, vaccine serotypes have been replaced by nonvaccine serotypes.

Methods: We used multilocus sequence typing to analyze a sample of 294 isolates of S. pneumoniae carried by Massachusetts children (aged, 3 months-7 years) and examine the results for serotype switching and association with antimicrobial resistance.

Results: Eighty-six distinct sequence types (STs) were found, 10 of which exhibited a serotype other than that which would be expected from previous carriage samples. We interpret this as evidence of past or recent serotype switching. Switched variants include ST 320, which is a common and increasing source of multidrug resistance in this community. Switching events within serogroups were more common than expected by chance (P = 0.043 by a Monte Carlo approach). Using multilocus sequence typing data and eBURST analysis, we also describe clonal dynamics within the important replacement serotypes 19A, 15B/C, 35B, and the recently described 6C.

Conclusions: Some strains generated by serotype switching are increasingly important parts of the carriage population. In the case of 19A, it appears that the majority of increase is due to ST 320, a recently reported switched variant. This may have consequences for the STs causing invasive pneumococcal disease.

Figure 1

a) Comparative eBURST diagram showing the combined 2004 and 2007 samples. Each ST is represented by a point, the size of which is determined by the number of isolates with that ST in the combined dataset. STs differing at a single genetic locus are shown linked by a straight line. A clonal complex (CC) is a group of STs sharing 6 of 7 alleles with at least one other member of the group. Those STs which cannot be linked to any other in the sample are termed singletons and appear as unlinked points. For more information see http://spneumoniae.mlst.net/eburst/. The ST numbers are colored according to whether they were found only in 2004 (black), only in 2007 (green) or in both (pink). The 10 most common CCs in the combined sample are indicated. b) bar chart showing changes in the relative frequency of the 10 most common CCs in 2004 and 2007.

Figure 2

Histograms showing changes between 2004 and 2007 in the proportions of the sample for STs in the four most common serotypes: a) 19A, b) 15B/C, c) 35B and d) 6C. The levels of penicillin resistance are shown by the shading as indicated. To aid in comparing the results for the two years, isolates with the same ST are grouped between vertical dotted lines.

Figure 2

Histograms showing changes between 2004 and 2007 in the proportions of the sample for STs in the four most common serotypes: a) 19A, b) 15B/C, c) 35B and d) 6C. The levels of penicillin resistance are shown by the shading as indicated. To aid in comparing the results for the two years, isolates with the same ST are grouped between vertical dotted lines.

Figure 3

Comparative eBURST diagrams showing the combined 2004 and 2007 samples for the four most common serotypes: a) 19A, b) 15B/C, c) 35B and d) 6C. For details of interpreting eBURST diagrams please see the legend to Figure 1.