Streptococcus pseudopneumoniae: Use of whole genome sequences to validate methods used for identification.

A correct identification of Streptococcus pseudopneumoniae is a prerequisite for investigating the clinical impact of the bacterium. The identification has traditionally relied on phenotypic methods. However, these phenotypic traits have been shown to be unreliable, with some S. pseudopneumoniae giving conflicting results. Therefore, sequence based identification methods have increasingly been used for identification of S. pseudopneumoniae In this study we used 64 S. pseudopneumoniae strains, 59 S. pneumoniae strains, 23 S. mitis strains, 25 S. oralis strains, seven S. infantis, and one S. peroris to test the capability of three single genes (rpoB, gyrB, recA), two MLSA schemes, the SNP based phylogeny tool CSI phylogeny, a k-mer based identification method (KmerFinder), Average Nucleotide Identity using fastANI and core genome analysis to identify S. pseudopneumoniae Core genome analysis and CSI phylogeny were able to cluster all strains into distinct clusters related to their respective species. It was not possible to identify all S. pseudopneumoniae correctly using only one of the single genes. The MLSA schemes were unable to identify some of the S. pseudopneumoniae strains, and some strains could be misidentified. KmerFinder identified all S. pseudopneumoniae strains but misidentified one S. mitis strain as S. pseudopneumoniae and fastANI could differentiate between S. pseudopneumoniae and S. pneumoniae using an ANI cut-off of 96%.