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Updated: Nov 29, 2025

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Streptococcus pseudopneumoniae: Use of Whole-Genome Sequences To Validate Species Identification Methods

Christian Salgård Jensen1, Katrine Højholt Iversen2, Rimtas Dargis3

  • 1The Regional Department of Clinical Microbiology, Slagelse, Region Zealand, Denmark csj@dadlnet.dk.

Journal of Clinical Microbiology
|November 19, 2020
PubMed

Insights

Accurate identification of Streptococcus pseudopneumoniae is crucial. Core genome analysis and CSI phylogeny reliably distinguished S. pseudopneumoniae, while single genes and MLSA methods showed limitations.

Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Accurate identification of Streptococcus pseudopneumoniae is essential for clinical impact studies.
  • Traditional phenotypic identification methods for S. pseudopneumoniae are unreliable.
  • Sequence-based methods are increasingly preferred for S. pseudopneumoniae identification.

Purpose of the Study:

  • To evaluate various sequence-based methods for accurate identification of S. pseudopneumoniae.
  • To compare the performance of single genes, multilocus sequence analysis (MLSA), SNP-based phylogeny, k-mer analysis, and average nucleotide identity (ANI).

Main Methods:

  • Tested 64 S. pseudopneumoniae strains alongside related species using single genes (rpoB, gyrB, recA), MLSA, CSI phylogeny, KmerFinder, fastANI, and core genome analysis.
  • Evaluated the ability of each method to correctly cluster and identify S. pseudopneumoniae strains.

Main Results:

  • Core genome analysis and CSI phylogeny successfully clustered all strains by species.
  • Single gene and MLSA methods failed to identify all S. pseudopneumoniae strains accurately.
  • KmerFinder identified all S. pseudopneumoniae but misidentified one S. mitis.
  • FastANI differentiated S. pseudopneumoniae from S. pneumoniae at 96% ANI cutoff.

Conclusions:

  • Core genome analysis and CSI phylogeny are robust methods for S. pseudopneumoniae identification.
  • MLSA and single-gene approaches are insufficient for reliable identification.
  • KmerFinder and fastANI show promise but require careful parameter selection.
Keywords:
Streptococcusgenotypic identificationidentificationmethodsmitis groupwhole-genome sequencing

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