Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species

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, Streptococcus pneumoniae. Phenotypic and genetic similarities between streptococci can cause difficulties in sp...

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Main Authors: Anne L. Wyllie, Yvonne Pannekoek, Sandra Bovenkerk, Jody van Engelsdorp Gastelaars, Bart Ferwerda, Diederik van de Beek, Elisabeth A. M. Sanders, Krzysztof Trzciński, Arie van der Ende
Format: Article
Language:English
Published: The Royal Society 2017-01-01
Series:Open Biology
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Online Access:https://royalsocietypublishing.org/doi/pdf/10.1098/rsob.170074
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author Anne L. Wyllie
Yvonne Pannekoek
Sandra Bovenkerk
Jody van Engelsdorp Gastelaars
Bart Ferwerda
Diederik van de Beek
Elisabeth A. M. Sanders
Krzysztof Trzciński
Arie van der Ende
author_facet Anne L. Wyllie
Yvonne Pannekoek
Sandra Bovenkerk
Jody van Engelsdorp Gastelaars
Bart Ferwerda
Diederik van de Beek
Elisabeth A. M. Sanders
Krzysztof Trzciński
Arie van der Ende
author_sort Anne L. Wyllie
collection DOAJ
description 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, Streptococcus pneumoniae. 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 (n = 101) and from carriage (n = 103), and on non-typeable pneumococci from asymptomatic individuals (n = 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 S. pneumoniae, targeting cpsA, lytA, piaB, ply, Spn9802, zmpC 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 lytA and piaB were 100% specific for S. pneumoniae, whereas assays targeting cpsA, ply, Spn9802, zmpC 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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spelling doaj.art-88366f97d27941058845e122bdfd2c1c2022-12-21T23:57:59ZengThe Royal SocietyOpen Biology2046-24412017-01-017910.1098/rsob.170074170074Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal speciesAnne L. WyllieYvonne PannekoekSandra BovenkerkJody van Engelsdorp GastelaarsBart FerwerdaDiederik van de BeekElisabeth A. M. SandersKrzysztof TrzcińskiArie van der EndeThe 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, Streptococcus pneumoniae. 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 (n = 101) and from carriage (n = 103), and on non-typeable pneumococci from asymptomatic individuals (n = 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 S. pneumoniae, targeting cpsA, lytA, piaB, ply, Spn9802, zmpC 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 lytA and piaB were 100% specific for S. pneumoniae, whereas assays targeting cpsA, ply, Spn9802, zmpC 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.https://royalsocietypublishing.org/doi/pdf/10.1098/rsob.170074mitis group streptococcistreptococcus pneumoniaecarriageinvasive diseaseribosomal s2-typing
spellingShingle Anne L. Wyllie
Yvonne Pannekoek
Sandra Bovenkerk
Jody van Engelsdorp Gastelaars
Bart Ferwerda
Diederik van de Beek
Elisabeth A. M. Sanders
Krzysztof Trzciński
Arie van der Ende
Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species
Open Biology
mitis group streptococci
streptococcus pneumoniae
carriage
invasive disease
ribosomal s2-typing
title Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species
title_full Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species
title_fullStr Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species
title_full_unstemmed Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species
title_short Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species
title_sort sequencing of the variable region of rpsb to discriminate between streptococcus pneumoniae and other streptococcal species
topic mitis group streptococci
streptococcus pneumoniae
carriage
invasive disease
ribosomal s2-typing
url https://royalsocietypublishing.org/doi/pdf/10.1098/rsob.170074
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