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

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  • L H Rasmussen
  • R Dargis
  • K Højholt
  • J J Christensen
  • O Skovgaard
  • U S Justesen
  • F S Rosenvinge
  • C Moser
  • O Lukjancenko
  • S Rasmussen
  • X C Nielsen
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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.

Original languageEnglish
JournalEuropean journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology
Volume35
Issue number10
Pages (from-to)1615-25
Number of pages11
ISSN0934-9723
DOIs
Publication statusPublished - Oct 2016

    Research areas

  • Cluster Analysis, Denmark, Endocarditis, Genetic Variation, Genome, Bacterial, Humans, Phylogeny, Retrospective Studies, Sequence Analysis, DNA, Streptococcal Infections, Streptococcus mitis, Journal Article

ID: 49908410