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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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Autores principales: Wyllie, Anne L., Pannekoek, Yvonne, Bovenkerk, Sandra, van Engelsdorp Gastelaars, Jody, Ferwerda, Bart, van de Beek, Diederik, Sanders, Elisabeth A. M., Trzciński, Krzysztof, van der Ende, Arie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Royal Society 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5627049/
https://www.ncbi.nlm.nih.gov/pubmed/28931649
http://dx.doi.org/10.1098/rsob.170074
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author Wyllie, Anne L.
Pannekoek, Yvonne
Bovenkerk, Sandra
van Engelsdorp Gastelaars, Jody
Ferwerda, Bart
van de Beek, Diederik
Sanders, Elisabeth A. M.
Trzciński, Krzysztof
van der Ende, Arie
author_facet Wyllie, Anne L.
Pannekoek, Yvonne
Bovenkerk, Sandra
van Engelsdorp Gastelaars, Jody
Ferwerda, Bart
van de Beek, Diederik
Sanders, Elisabeth A. M.
Trzciński, Krzysztof
van der Ende, Arie
author_sort Wyllie, Anne L.
collection PubMed
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 pubmed-56270492017-10-11 Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species Wyllie, Anne L. Pannekoek, Yvonne Bovenkerk, Sandra van Engelsdorp Gastelaars, Jody Ferwerda, Bart van de Beek, Diederik Sanders, Elisabeth A. M. Trzciński, Krzysztof van der Ende, Arie Open Biol Research 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. The Royal Society 2017-09-20 /pmc/articles/PMC5627049/ /pubmed/28931649 http://dx.doi.org/10.1098/rsob.170074 Text en © 2017 The Authors. http://creativecommons.org/licenses/by/4.0/ Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.
spellingShingle Research
Wyllie, Anne L.
Pannekoek, Yvonne
Bovenkerk, Sandra
van Engelsdorp Gastelaars, Jody
Ferwerda, Bart
van de Beek, Diederik
Sanders, Elisabeth A. M.
Trzciński, Krzysztof
van der Ende, Arie
Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species
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 Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5627049/
https://www.ncbi.nlm.nih.gov/pubmed/28931649
http://dx.doi.org/10.1098/rsob.170074
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