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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci. / Rasmussen, L H; Dargis, R; Højholt, K; Christensen, J J; Skovgaard, O; Justesen, U S; Rosenvinge, F S; Moser, C; Lukjancenko, O; Rasmussen, Simon; Nielsen, X C.

In: European Journal of Clinical Microbiology & Infectious Diseases, Vol. 35, No. 10, 10.2016, p. 1615-1625.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Rasmussen, LH, Dargis, R, Højholt, K, Christensen, JJ, Skovgaard, O, Justesen, US, Rosenvinge, FS, Moser, C, Lukjancenko, O, Rasmussen, S & Nielsen, XC 2016, 'Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci', European Journal of Clinical Microbiology & Infectious Diseases, vol. 35, no. 10, pp. 1615-1625. https://doi.org/10.1007/s10096-016-2700-2

APA

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. (2016). Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci. European Journal of Clinical Microbiology & Infectious Diseases, 35(10), 1615-1625. https://doi.org/10.1007/s10096-016-2700-2

Vancouver

Rasmussen LH, Dargis R, Højholt K, Christensen JJ, Skovgaard O, Justesen US et al. Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci. European Journal of Clinical Microbiology & Infectious Diseases. 2016 Oct;35(10):1615-1625. https://doi.org/10.1007/s10096-016-2700-2

Author

Rasmussen, L H ; Dargis, R ; Højholt, K ; Christensen, J J ; Skovgaard, O ; Justesen, U S ; Rosenvinge, F S ; Moser, C ; Lukjancenko, O ; Rasmussen, Simon ; Nielsen, X C. / Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci. In: European Journal of Clinical Microbiology & Infectious Diseases. 2016 ; Vol. 35, No. 10. pp. 1615-1625.

Bibtex

@article{fec76840309a4aeda49bf6d87a177f8d,
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.",
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 Simon Rasmussen and Nielsen, {X C}",
year = "2016",
month = oct,
doi = "10.1007/s10096-016-2700-2",
language = "English",
volume = "35",
pages = "1615--1625",
journal = "European Journal of Clinical Microbiology & 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, Simon

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.

U2 - 10.1007/s10096-016-2700-2

DO - 10.1007/s10096-016-2700-2

M3 - Journal article

C2 - 27325438

VL - 35

SP - 1615

EP - 1625

JO - European Journal of Clinical Microbiology & Infectious Diseases

JF - European Journal of Clinical Microbiology & Infectious Diseases

SN - 0934-9723

IS - 10

ER -

ID: 177559782