Supplementary material from "Sequencing of the variable region of <i>rpsB</i> to discriminate between <i>Streptococcus pneumoniae</i> and other streptococcal species"

Published on 2017-09-14T07:14:09Z (GMT) by
The vast majority of streptococci colonizing the human upper respiratory tract are commensals, only sporadically implicated in disease. Of these, the most pathogenic is Mitis group member, <i>Streptococcus pneumoniae</i>. Phenotypic and genetic similarities between streptococci can cause difficulties in species identification. Using ribosomal S2-gene sequences extracted from whole-genome sequences published from 501 streptococci, we developed a method to identify streptococcal species. We validated this method on non-pneumococcal isolates cultured from cases of severe streptococcal disease (<i>n</i> = 101) and from carriage (<i>n</i> = 103), and on non-typeable pneumococci from asymptomatic individuals (<i>n</i> = 17) and on whole-genome sequences of 1157 pneumococcal isolates from meningitis in the Netherlands. Following this, we tested 221 streptococcal isolates in molecular assays originally assumed specific for <i>S. pneumoniae</i>, targeting <i>cpsA</i>, <i>lytA</i>, <i>piaB</i>, <i>ply</i>, Spn9802, <i>zmpC</i> and capsule-type-specific genes. Cluster analysis of S2-sequences showed grouping according to species in line with published phylogenies of streptococcal core genomes. S2-typing convincingly distinguished pneumococci from non-pneumococcal species (99.2% sensitivity, 100% specificity). Molecular assays targeting regions of <i>lytA</i> and <i>piaB</i> were 100% specific for <i>S. pneumoniae</i>, whereas assays targeting <i>cpsA</i>, <i>ply</i>, Spn9802, <i>zmpC</i> and selected serotype-specific assays (but not capsular sequence typing) showed a lack of specificity. False positive results were over-represented in species associated with carriage, although no particular confounding signal was unique for carriage isolates.

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L. Wyllie, Anne; Pannekoek, Yvonne; Bovenkerk, Sandra; van Engelsdorp Gastelaars, Jody; Ferwerda, Bart; van de Beek, Diederik; A. M. Sanders, Elisabeth; Trzciński, Krzysztof; van der Ende, Arie (2017): Supplementary material from "Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species". The Royal Society. Collection.