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

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Author

Rasmussen, L H ; Dargis, R ; Højholt, K ; Christensen, J J ; Skovgaard, O ; Justesen, U S ; Rosenvinge, F S ; Moser, C ; Lukjancenko, O ; Rasmussen, S ; Nielsen, X C. / Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci. I: European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology. 2016 ; Bind 35, Nr. 10. s. 1615-25.

Bibtex

@article{3079bd229a764c9481d5708e89212dfc,
title = "Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci",
abstract = "Identification of Mitis group streptococci (MGS) to the species level is challenging for routine microbiology laboratories. Correct identification is crucial for the diagnosis of infective endocarditis, identification of treatment failure, and/or infection relapse. Eighty MGS from Danish patients with infective endocarditis were whole genome sequenced. We compared the phylogenetic analyses based on single genes (recA, sodA, gdh), multigene (MLSA), SNPs, and core-genome sequences. The six phylogenetic analyses generally showed a similar pattern of six monophyletic clusters, though a few differences were observed in single gene analyses. Species identification based on single gene analysis showed their limitations when more strains were included. In contrast, analyses incorporating more sequence data, like MLSA, SNPs and core-genome analyses, provided more distinct clustering. The core-genome tree showed the most distinct clustering.",
keywords = "Cluster Analysis, Denmark, Endocarditis, Genetic Variation, Genome, Bacterial, Humans, Phylogeny, Retrospective Studies, Sequence Analysis, DNA, Streptococcal Infections, Streptococcus mitis, Journal Article",
author = "Rasmussen, {L H} and R Dargis and K H{\o}jholt and Christensen, {J J} and O Skovgaard and Justesen, {U S} and Rosenvinge, {F S} and C Moser and O Lukjancenko and S Rasmussen and Nielsen, {X C}",
year = "2016",
month = "10",
doi = "10.1007/s10096-016-2700-2",
language = "English",
volume = "35",
pages = "1615--25",
journal = "European Journal of Clinical Microbiology and Infectious Diseases",
issn = "0934-9723",
publisher = "Springer",
number = "10",

}

RIS

TY - JOUR

T1 - Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci

AU - Rasmussen, L H

AU - Dargis, R

AU - Højholt, K

AU - Christensen, J J

AU - Skovgaard, O

AU - Justesen, U S

AU - Rosenvinge, F S

AU - Moser, C

AU - Lukjancenko, O

AU - Rasmussen, S

AU - Nielsen, X C

PY - 2016/10

Y1 - 2016/10

N2 - Identification of Mitis group streptococci (MGS) to the species level is challenging for routine microbiology laboratories. Correct identification is crucial for the diagnosis of infective endocarditis, identification of treatment failure, and/or infection relapse. Eighty MGS from Danish patients with infective endocarditis were whole genome sequenced. We compared the phylogenetic analyses based on single genes (recA, sodA, gdh), multigene (MLSA), SNPs, and core-genome sequences. The six phylogenetic analyses generally showed a similar pattern of six monophyletic clusters, though a few differences were observed in single gene analyses. Species identification based on single gene analysis showed their limitations when more strains were included. In contrast, analyses incorporating more sequence data, like MLSA, SNPs and core-genome analyses, provided more distinct clustering. The core-genome tree showed the most distinct clustering.

AB - Identification of Mitis group streptococci (MGS) to the species level is challenging for routine microbiology laboratories. Correct identification is crucial for the diagnosis of infective endocarditis, identification of treatment failure, and/or infection relapse. Eighty MGS from Danish patients with infective endocarditis were whole genome sequenced. We compared the phylogenetic analyses based on single genes (recA, sodA, gdh), multigene (MLSA), SNPs, and core-genome sequences. The six phylogenetic analyses generally showed a similar pattern of six monophyletic clusters, though a few differences were observed in single gene analyses. Species identification based on single gene analysis showed their limitations when more strains were included. In contrast, analyses incorporating more sequence data, like MLSA, SNPs and core-genome analyses, provided more distinct clustering. The core-genome tree showed the most distinct clustering.

KW - Cluster Analysis

KW - Denmark

KW - Endocarditis

KW - Genetic Variation

KW - Genome, Bacterial

KW - Humans

KW - Phylogeny

KW - Retrospective Studies

KW - Sequence Analysis, DNA

KW - Streptococcal Infections

KW - Streptococcus mitis

KW - Journal Article

U2 - 10.1007/s10096-016-2700-2

DO - 10.1007/s10096-016-2700-2

M3 - Journal article

VL - 35

SP - 1615

EP - 1625

JO - European Journal of Clinical Microbiology and Infectious Diseases

JF - European Journal of Clinical Microbiology and Infectious Diseases

SN - 0934-9723

IS - 10

ER -

ID: 49908410