Population structure of hyperinvasive serotype 12F, clonal complex 218 Streptococcus pneumoniae revealed by multilocus boxB sequence typing

Abstract

At least four outbreaks of invasive disease caused by serotype 12F, clonal complex 218 Streptococcus pneumoniae have occurred in the United States over the past two decades. We studied the population structure of this clonal complex using a sample of 203 outbreak and surveillance isolates that were collected over 22 years from 34 US states and eight other countries. Conventional multilocus sequence typing identified five types and distinguished a single outbreak from the others. To improve typing resolution, multilocus boxB sequence typing (MLBT) was developed from 10 variable boxB minisatellite loci. MLBT identified 86 types and distinguished between each of the four outbreaks. Diversity across boxB loci tended to be positively correlated with repeat array size and, overall, best fit the infinite alleles mutation model. Multilocus linkage disequilibrium was strong, but pairwise disequilibrium decreased with the physical distance between loci and was strongest in one large region of the chromosome, indicating recent recombinations. Two major clusters were identified in the sample, and they were differentiated geographically, as western and more easterly US clusters, and temporally, as clusters that predominated before and after the licensure of pneumococcal conjugate vaccines. The diversity and linkage disequilibrium within these two clusters also differed, suggesting different population dynamics. MLBT revealed hidden aspects of the population structure of these hyperinvasive pneumococci, and it may provide a useful adjunct tool for outbreak investigations, surveillance, and population genetics studies of other pneumococcal clonal complexes.

Molecular Characterization of Streptococcus pneumoniae Serotype 12F Isolates Associated with Rural Community Outbreaks in Alaska

“…The multiple BTs found from this outbreak are consistent with ongoing transmission (i.e., growth and mutation) of the bacteria in a community over a period of time and contrasts with the indistinguishable BTs from the institutional outbreaks of 12F disease identified previously in Texas (1989) (22), Maryland (1992 with a single exception) (23), and California (2004) (19,24). Most pneumococcal outbreaks reported in the recent literature were short lived (1 to 2 months) and occurred among closed or institutional populations such as day care or military groups (7).…”

“…The first appearance in Alaska of this BT was in cases in region F and Anchorage in 2001. This BT was also found among invasive isolates from California in 1995 and 1996 (19), indicating its broader geographic distribution. We note that the two outbreak clones, PFGE type A/ST1527/ BT88 and PFGE type B/ST218/BT5, differ considerably from each other at the genetic level.…”

“…A total of 92 IPD and carriage isolates were further characterized by a new sequence-typing method specifically developed with 12F pneumococci (19). Briefly, BOX elements are short repetitive sequences that occur in intergenic regions throughout the pneumococcal chromosome and often consist of single boxA and boxC modules that flank one or more copies of the 45-bp boxB module.…”

Whole-Genome Sequencing Reveals the Origin and Rapid Evolution of an Emerging Outbreak Strain ofStreptococcus pneumoniae12F

“…Finally, the 12F capsular polysaccharide is expressed by at least 4 different multilocus sequence typing (MLST)-defined clonal complexes (CC218, CC969, CC1527, CC3524). The 2003-2006 outbreak in Alaska was caused by CC1527 [8], but all of the other listed outbreaks were caused by CC218 [13]. Within CC218, there are 2 major genetic clusters identified by their predominant sequence type as ST218 and ST220 (singleallele variant of ST218); both cause outbreaks and both are globally dispersed.…”

Information theoretic alignment free variant calling

“…Further investigations of the variants found for the bacterial dataset using a known reference ✻✼ sequence revealed variants associated with boxB repeat regions, a repeat previously used for ✻✽ population structure mapping (Rakov, Ubukata, and Robinson, 2011), suggesting the model can ✻✾ generate features for more complex genetic elements. These results suggest the variants are ✼✵ capturing genotypic variation well and can model heritable traits in different organisms.…”