Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci.
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.
Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark.|Department of Science and Environment, Roskilde University, Roskilde, Denmark.
L H
LH
Rasmussen
Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark.
R
R
Dargis
Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark.|DTU Systems Biology, Technical University of Denmark, Copenhagen, Denmark.
K
K
Højholt
Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark.|Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
J J
JJ
Christensen
Department of Science and Environment, Roskilde University, Roskilde, Denmark.
O
O
Skovgaard
Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark.|Department of Clinical Microbiology, University Hospital of Copenhagen, Copenhagen, Denmark.
U S
US
Justesen
Department of Clinical Microbiology, Vejle Hospital, Vejle, Denmark.
F S
FS
Rosenvinge
Department of Clinical Microbiology, University Hospital of Copenhagen, Copenhagen, Denmark.
C
C
Moser
National Food Institute, Technical University of Denmark, Copenhagen, Denmark.
O
O
Lukjancenko
DTU Systems Biology, Technical University of Denmark, Copenhagen, Denmark.
S
S
Rasmussen
Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark. xcn@regionsjaelland.dk.
X C
XC
Nielsen
D016000:Cluster Analysis; D003718:Denmark; D004696:Endocarditis / Q000382:microbiology; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D010802:Phylogeny; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA; D013290:Streptococcal Infections / Q000382:microbiology; D034361:Streptococcus mitis / Q000145:classification* / Q000235:genetics*