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

Louise Hesselbjerg Rasmussen, Rimtas Dargis, Katrine Højholt, Jens Jørgen Christensen, Ole Skovgaard, Ulrik S. Justesen, Flemming S. Rosenvinge, Claus Moser, Oksana Lukjancenko, Simon Rasmussen, Xiaohui Chen Nielsen

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

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.
OriginalsprogEngelsk
TidsskriftEuropean Journal of Clinical Microbiology & Infectious Diseases
Vol/bind35
Udgave nummer10
Sider (fra-til)1615-1625
ISSN0934-9723
DOI
StatusUdgivet - 20 jun. 2016

Citer dette

Rasmussen, Louise Hesselbjerg ; Dargis, Rimtas ; Højholt, Katrine ; Christensen, Jens Jørgen ; Skovgaard, Ole ; Justesen, Ulrik S. ; Rosenvinge, Flemming S. ; Moser, Claus ; Lukjancenko, Oksana ; Rasmussen, Simon ; Nielsen, Xiaohui Chen . / Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci. I: European Journal of Clinical Microbiology & Infectious Diseases. 2016 ; Bind 35, Nr. 10. s. 1615-1625.
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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, {Louise Hesselbjerg} and Rimtas Dargis and Katrine H{\o}jholt and Christensen, {Jens J{\o}rgen} and Ole Skovgaard and Justesen, {Ulrik S.} and Rosenvinge, {Flemming S.} and Claus Moser and Oksana Lukjancenko and Simon Rasmussen and Nielsen, {Xiaohui Chen}",
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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, bind 35, nr. 10, s. 1615-1625. https://doi.org/10.1007/s10096-016-2700-2

Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci. / Rasmussen, Louise Hesselbjerg; Dargis, Rimtas; Højholt, Katrine ; Christensen, Jens Jørgen; Skovgaard, Ole; Justesen, Ulrik S.; Rosenvinge, Flemming S.; Moser, Claus; Lukjancenko, Oksana; Rasmussen, Simon; Nielsen, Xiaohui Chen .

I: European Journal of Clinical Microbiology & Infectious Diseases, Bind 35, Nr. 10, 20.06.2016, s. 1615-1625.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

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

AU - Rasmussen, Louise Hesselbjerg

AU - Dargis, Rimtas

AU - Højholt, Katrine

AU - Christensen, Jens Jørgen

AU - Skovgaard, Ole

AU - Justesen, Ulrik S.

AU - Rosenvinge, Flemming S.

AU - Moser, Claus

AU - Lukjancenko, Oksana

AU - Rasmussen, Simon

AU - Nielsen, Xiaohui Chen

PY - 2016/6/20

Y1 - 2016/6/20

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

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 -