A novel genetic variant of Streptococcus pneumoniae serotype 11A discovered in Fiji

Abstract

Objectives As part of annual cross-sectional Streptococcus pneumoniae carriage surveys in Fiji (2012–2015), we detected pneumococci in over 100 nasopharyngeal swabs that serotyped as ‘11F-like’ by microarray. We examined the genetic basis of this divergence in the 11F-like capsular polysaccharide ( cps ) locus compared to the reference 11F cps sequence. The impact of this diversity on capsule phenotype, and serotype results using genetic and serologic methods were determined. Methods Genomic DNA from representative 11F-like S. pneumoniae isolates obtained from the nasopharynx of Fijian children was extracted and subject to whole genome sequencing. Genetic and phylogenetic analyses were used to identify genetic changes in the cps locus. Capsular phenotypes were evaluated using the Quellung reaction and latex agglutination. Results Compared to published 11F sequences, the wcwC and wcrL genes of the 11F-like cps locus are phylogenetically divergent, and the gct gene contains a single nucleotide insertion within a homopolymeric region. These changes within the DNA sequence of the 11F-like cps locus have modified the antigenic properties of the capsule, such that 11F-like isolates serotype as 11A by Quellung reaction and latex agglutination. Conclusions This study demonstrates the ability of molecular serotyping by microarray to identify genetic variants of S. pneumoniae and highlights the potential for discrepant results between phenotypic and genotypic serotyping methods. We propose that 11F-like isolates are not a new serotype but rather are a novel genetic variant of serotype 11A. These findings have implications for invasive pneumococcal disease surveillance as well as studies investigating vaccine impact.

Pneumococcal carriage, density, and co-colonization dynamics: A longitudinal study in Indonesian infants

“…Serotypes 6B, NT2 (a non-encapsulated lineage), 19F, 23F, 34, and 15B/C were the most common (Figure 3). All serotype 11A pneumococci identified were typed as 11F-like variants by microarray (Manna et al, 2018). One hundred and twenty-two (38.4%) of the carriage episodes were due to serotypes included in PCV13.…”

Discovery of a Streptococcus pneumoniae serotype 33F capsular polysaccharide locus that lacks wcjE and contains a wcyO pseudogene

“…For example, we recently described a novel genetic variant of pneumococcal serotype 11A in Fiji. Genetically, the cps locus of these isolates is most closely related to the 11F cps locus, with only a few minor nucleotide changes resulting in the production of 11A capsule [ 4 ].…”

Two multi-fragment recombination events resulted in the β-lactam-resistant serotype 11A-ST6521 related to Spain9V-ST156 pneumococcal clone spreading in south-western Europe, 2008 to 2016

“…Moreover, a second lineage (11A-ST166) was detected in France and Portugal, as well as in several isolates deposited in the ENA, showing yet different recombination events. This lineage presented a variant of the serotype 11A capsular operon previously identified in Fiji [40]. The presence of a double insertion in the dihydropteroate synthase and the Tn6002 transposon carrying tet(M) and erm(B) was a hallmark of all four ST166 isolates suggesting that another horizontal DNA transfer event was pivotal in conferring antimicrobial resistance to lineage 2 (11A-ST166).…”