Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci

Rasmussen, Louise; Dargis, Rimtas; Højholt, Katrine; Christensen, Jens Jørgen; Skovgaard, Ove; Justesen, Ulrik Stenz; Rosenvinge, Flemming Schønning; Moser, Claus; Lukjancenko, Oksana; Rasmussen, Simon; Nielsen, Xiaohui Chen

doi:10.1007/s10096-016-2700-2

Cited by 21 publications

(25 citation statements)

References 60 publications

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“…However, differences in the methods to divide the proteins into families are used; Zheng et al 41 used RAST for gene calling and FIGfams to assign the functional proteins 41,46,47 . The core-genome size found in this study is more consistent with a previous study of 80 Mitis group streptococci clinical isolates from six different species, where 591 core-genes were identified 48 .…”

Section: Discussionsupporting

confidence: 92%

“…Thirty-eight blood culture strains, S. sanguinis (n = 20) and S. gordonii (n = 18) from patients with verified IE were collected retrospectively (2006-2013) from the Capital Region of Denmark (RH strains), Region Zealand (AE, Y and B strains) and Region of Southern Denmark (OD strains). The bacterial DNA was extracted as described in Rasmussen et al 48 and paired-end sequenced using Illumina Hiseq. 2000 with 100X coverage (BGI-Tech Solutions, Hong Kong, China).…”

Section: Methodsmentioning

confidence: 99%

“…Statistics regarding the assembly performance were achieved using scripts from the Assemblathon 54 . Species identification was based on Multi Locus Sequence Analysis (MLSA), Single Nucleotide Polymorphisms (SNPs) and core-genome phylogeny as described in Rasmussen et al 48 . Additionally, we included 21 genomes isolated from healthy individuals from the oral cavity of S. sanguinis (n = 12) and S. gordonii (n = 9).…”

Section: Methodsmentioning

confidence: 99%

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Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii

Iversen

Rasmussen

Al-Nakeeb

et al. 2020

Sci Rep

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Streptococcus gordonii and Streptococcus sanguinis belong to the Mitis group streptococci, which mostly are commensals in the human oral cavity. Though they are oral commensals, they can escape their niche and cause infective endocarditis, a severe infection with high mortality. Several virulence factors important for the development of infective endocarditis have been described in these two species. However, the background for how the commensal bacteria, in some cases, become pathogenic is still not known. To gain a greater understanding of the mechanisms of the pathogenic potential, we performed a comparative analysis of 38 blood culture strains, S. sanguinis (n = 20) and S. gordonii (n = 18) from patients with verified infective endocarditis, along with 21 publicly available oral isolates from healthy individuals, S. sanguinis (n = 12) and S. gordonii (n = 9). Using whole genome sequencing data of the 59 streptococci genomes, functional profiles were constructed, using protein domain predictions based on the translated genes. These functional profiles were used for clustering, phylogenetics and machine learning. A clear separation could be made between the two species. No clear differences between oral isolates and clinical infective endocarditis isolates were found in any of the 675 translated core-genes. Additionally, random forest-based machine learning and clustering of the pan-genome data as well as amino acid variations in the core-genome could not separate the clinical and oral isolates. A total of 151 different virulence genes was identified in the 59 genomes. Among these homologs of genes important for adhesion and evasion of the immune system were found in all of the strains. Based on the functional profiles and virulence gene content of the genomes, we believe that all analysed strains had the ability to become pathogenic. The oral cavity is covered by a mixed-species biofilm. The composition of the biofilm, as well as the abundance of specific species has a great impact on the oral health 1. Among the pioneer colonizers of the oral cavity, we find Streptococcus sanguinis and Streptococcus gordonii 2,3. Both species are non-hemolytic streptococci and commensal members of the Mitis group. They are found to prevent dental caries by inhibiting the bacterial growth of the plaque forming Mutans streptococci 1,4. The oral cavity is an extreme environment; the bacteria have to cope with variations in temperature and pH, oxidative stress and strong hydrodynamic as well as mechanical forces caused by food consumption, chewing,

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Section: Discussionsupporting

confidence: 92%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii

Iversen

Rasmussen

Al-Nakeeb

et al. 2020

Sci Rep

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“…These differences can be explained, by that none of the essentiality datasets is from a S. oralis. Further, S. oralis has one of the smallest genomes in the MGS, having a genome size of 1.9 mio basepairs (Rasmussen et al, 2016). In contrast, both S. pneumoniae and S. sanguinis have larger genome sizes of around 2.1 and 2.4 mio basepairs, respectively, giving a relative larger amount of genes (Tettelin et al, 2001;Rasmussen et al, 2016).…”

Section: Verification Of Icj415 Using Experimental Essentiality Datamentioning

confidence: 99%

“…Sometimes these MGS are able to escape their oral niche and cause an infection of the heart valves, infective endocarditis (IE), a severe disease with a high mortality even with proper treatment. Of all the IE causing species in the MGS, Streptococcus oralis is the most common (Rasmussen et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen

et al. 2020

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The mitis group of streptococci (MGS) is a member of the healthy human microbiome in the oral cavity and upper respiratory tract. Troublingly, some MGS are able to escape this niche and cause infective endocarditis, a severe and devastating disease. Genome-scale models have been shown to be valuable in investigating metabolism of bacteria. Here we present the first genome-scale model, iCJ415, for Streptococcus oralis SK141. We validated the model using gene essentiality and amino acid auxotrophy data from closely related species. iCJ415 has 71-76% accuracy in predicting gene essentiality and 85% accuracy in predicting amino acid auxotrophy. Further, the phenotype of S. oralis was tested using the Biolog Phenotype microarrays, giving iCJ415 a 82% accuracy in predicting carbon sources. iCJ415 can be used to explore the metabolic differences within the MGS, and to explore the complicated metabolic interactions between different species in the human oral cavity.

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Relationships among streptococci from the mitis group, misidentified as Streptococcus pneumoniae

Sadowy

Bojarska

Kuch

et al. 2020

Eur J Clin Microbiol Infect Dis

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The aim of our study was to investigate phenotypic and genotypic features of streptococci misidentified (misID) as Streptococcus pneumoniae, obtained over 20 years from hospital patients in Poland. Sixty-three isolates demonstrating microbiological features typical for pneumococci (optochin susceptibility and/or bile solubility) were investigated by phenotypic tests, lytA and 16S rRNA gene polymorphism and whole-genome sequencing (WGS). All isolates had a 6-bp deletion in the lytA 3′ terminus, characteristic for Mitis streptococc and all but two isolates lacked the pneumococcal signature cytosine at nucleotide position 203 in the 16S rRNA genes. The counterparts of psaA and ply were present in 100% and 81.0% of isolates, respectively; the spn9802 and spn9828 loci were characteristic for 49.2% and 38.1% of isolates, respectively. Phylogenetic trees and networks, based on the multilocus sequence analysis (MLSA) scheme, ribosomal multilocus sequence typing (rMLST) scheme and core-genome analysis, clearly separated investigated isolates from S. pneumoniae and demonstrated the polyclonal character of misID streptococci, associated with the Streptococcus pseudopneumoniae and Streptococcus mitis groups. While the S. pseudopneumoniae clade was relatively well defined in all three analyses, only the core-genome analysis revealed the presence of another cluster comprising a fraction of misID streptococci and a strain proposed elsewhere as a representative of a novel species in the Mitis group. Our findings point to complex phylogenetic and taxonomic relationships among S. mitis-like bacteria and support the notion that this group may in fact consist of several distinct species.

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Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci

Cited by 21 publications

References 60 publications

Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii

Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii

Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen

Relationships among streptococci from the mitis group, misidentified as Streptococcus pneumoniae

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