Genomic Characterization of the Emerging Pathogen <named-content content-type="genus-species">Streptococcus pseudopneumoniae</named-content>

ABSTRACT Streptococcus pseudopneumoniae is a close relative of the major human pathogen S. pneumoniae. It is increasingly associated with lower-respiratory-tract infections (LRTI) and a high prevalence of antimicrobial resistance (AMR). S. pseudopneumoniae is difficult to identify using traditional...

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Autores principales:	Geneviève Garriss, Priyanka Nannapaneni, Alexandra S. Simões, Sarah Browall, Karthik Subramanian, Raquel Sá-Leão, Herman Goossens, Herminia de Lencastre, Birgitta Henriques-Normark
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	infectious disease Streptococcus pseudopneumoniae Streptococcus pneumoniae bacterial diagnostics comparative genomics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/0bc1f1ef40f84d038a186ac45502dafb
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spelling	oai:doaj.org-article:0bc1f1ef40f84d038a186ac45502dafb2021-11-15T15:55:25ZGenomic Characterization of the Emerging Pathogen <named-content content-type="genus-species">Streptococcus pseudopneumoniae</named-content>10.1128/mBio.01286-192150-7511https://doaj.org/article/0bc1f1ef40f84d038a186ac45502dafb2019-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01286-19https://doaj.org/toc/2150-7511ABSTRACT Streptococcus pseudopneumoniae is a close relative of the major human pathogen S. pneumoniae. It is increasingly associated with lower-respiratory-tract infections (LRTI) and a high prevalence of antimicrobial resistance (AMR). S. pseudopneumoniae is difficult to identify using traditional typing methods due to similarities with S. pneumoniae and other members of the mitis group (SMG). Using whole-genome sequencing of LRTI isolates and a comparative genomic approach, we found that a large number of pneumococcal virulence and colonization genes are present in the core S. pseudopneumoniae genome. We also reveal an impressive number of novel surface-exposed proteins encoded by the genome of this species. In addition, we propose a new and entirely specific molecular marker useful for the identification of S. pseudopneumoniae. Phylogenetic analyses of S. pseudopneumoniae show that specific clades are associated with allelic variants of core proteins. Resistance to tetracycline and macrolides, the two most common types of resistance, were found to be encoded by Tn916-like integrating conjugative elements and Mega-2. Overall, we found a tight association of genotypic determinants of AMR and phenotypic AMR with a specific lineage of S. pseudopneumoniae. Taken together, our results shed light on the distribution in S. pseudopneumoniae of genes known to be important during invasive disease and colonization and provide insight into features that could contribute to virulence, colonization, and adaptation. IMPORTANCE S. pseudopneumoniae is an overlooked pathogen emerging as the causative agent of lower-respiratory-tract infections and associated with chronic obstructive pulmonary disease (COPD) and exacerbation of COPD. However, much remains unknown on its clinical importance and epidemiology, mainly due to the lack of specific markers to distinguish it from S. pneumoniae. Here, we provide a new molecular marker entirely specific for S. pseudopneumoniae and offer a comprehensive view of the virulence and colonization genes found in this species. Finally, our results pave the way for further studies aiming at understanding the pathogenesis and epidemiology of S. pseudopneumoniae.Geneviève GarrissPriyanka NannapaneniAlexandra S. SimõesSarah BrowallKarthik SubramanianRaquel Sá-LeãoHerman GoossensHerminia de LencastreBirgitta Henriques-NormarkAmerican Society for Microbiologyarticleinfectious diseaseStreptococcus pseudopneumoniaeStreptococcus pneumoniaebacterial diagnosticscomparative genomicsMicrobiologyQR1-502ENmBio, Vol 10, Iss 3 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	infectious disease Streptococcus pseudopneumoniae Streptococcus pneumoniae bacterial diagnostics comparative genomics Microbiology QR1-502
spellingShingle	infectious disease Streptococcus pseudopneumoniae Streptococcus pneumoniae bacterial diagnostics comparative genomics Microbiology QR1-502 Geneviève Garriss Priyanka Nannapaneni Alexandra S. Simões Sarah Browall Karthik Subramanian Raquel Sá-Leão Herman Goossens Herminia de Lencastre Birgitta Henriques-Normark Genomic Characterization of the Emerging Pathogen <named-content content-type="genus-species">Streptococcus pseudopneumoniae</named-content>
description	ABSTRACT Streptococcus pseudopneumoniae is a close relative of the major human pathogen S. pneumoniae. It is increasingly associated with lower-respiratory-tract infections (LRTI) and a high prevalence of antimicrobial resistance (AMR). S. pseudopneumoniae is difficult to identify using traditional typing methods due to similarities with S. pneumoniae and other members of the mitis group (SMG). Using whole-genome sequencing of LRTI isolates and a comparative genomic approach, we found that a large number of pneumococcal virulence and colonization genes are present in the core S. pseudopneumoniae genome. We also reveal an impressive number of novel surface-exposed proteins encoded by the genome of this species. In addition, we propose a new and entirely specific molecular marker useful for the identification of S. pseudopneumoniae. Phylogenetic analyses of S. pseudopneumoniae show that specific clades are associated with allelic variants of core proteins. Resistance to tetracycline and macrolides, the two most common types of resistance, were found to be encoded by Tn916-like integrating conjugative elements and Mega-2. Overall, we found a tight association of genotypic determinants of AMR and phenotypic AMR with a specific lineage of S. pseudopneumoniae. Taken together, our results shed light on the distribution in S. pseudopneumoniae of genes known to be important during invasive disease and colonization and provide insight into features that could contribute to virulence, colonization, and adaptation. IMPORTANCE S. pseudopneumoniae is an overlooked pathogen emerging as the causative agent of lower-respiratory-tract infections and associated with chronic obstructive pulmonary disease (COPD) and exacerbation of COPD. However, much remains unknown on its clinical importance and epidemiology, mainly due to the lack of specific markers to distinguish it from S. pneumoniae. Here, we provide a new molecular marker entirely specific for S. pseudopneumoniae and offer a comprehensive view of the virulence and colonization genes found in this species. Finally, our results pave the way for further studies aiming at understanding the pathogenesis and epidemiology of S. pseudopneumoniae.
format	article
author	Geneviève Garriss Priyanka Nannapaneni Alexandra S. Simões Sarah Browall Karthik Subramanian Raquel Sá-Leão Herman Goossens Herminia de Lencastre Birgitta Henriques-Normark
author_facet	Geneviève Garriss Priyanka Nannapaneni Alexandra S. Simões Sarah Browall Karthik Subramanian Raquel Sá-Leão Herman Goossens Herminia de Lencastre Birgitta Henriques-Normark
author_sort	Geneviève Garriss
title	Genomic Characterization of the Emerging Pathogen <named-content content-type="genus-species">Streptococcus pseudopneumoniae</named-content>
title_short	Genomic Characterization of the Emerging Pathogen <named-content content-type="genus-species">Streptococcus pseudopneumoniae</named-content>
title_full	Genomic Characterization of the Emerging Pathogen <named-content content-type="genus-species">Streptococcus pseudopneumoniae</named-content>
title_fullStr	Genomic Characterization of the Emerging Pathogen <named-content content-type="genus-species">Streptococcus pseudopneumoniae</named-content>
title_full_unstemmed	Genomic Characterization of the Emerging Pathogen <named-content content-type="genus-species">Streptococcus pseudopneumoniae</named-content>
title_sort	genomic characterization of the emerging pathogen <named-content content-type="genus-species">streptococcus pseudopneumoniae</named-content>
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/0bc1f1ef40f84d038a186ac45502dafb
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Genomic Characterization of the Emerging Pathogen <named-content content-type="genus-species">Streptococcus pseudopneumoniae</named-content>

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