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

• Published in: Journal of clinical microbiology 2021-01, Vol.59 (2)
• Main Authors: Jensen, Christian Salgård, Iversen, Katrine Højholt, Dargis, Rimtas, Shewmaker, Patricia, Rasmussen, Simon, Christensen, Jens Jørgen, Nielsen, Xiaohui Chen
• Format: Article
• Language: English
• Subjects: Bacteriology; Genome, Bacterial - genetics; Phylogeny; Sequence Analysis, DNA; Streptococcus - genetics; Streptococcus pneumoniae - genetics
• ISSN: 0095-1137; 1098-660X
• DOI: 10.1128/JCM.02503-20

A correct identification of 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 strains giving conflicting results. Therefore, sequence-based identification methods have increasingly been used for identification of In this study, we used 64 strains, 59 strains, 22 strains, 24 strains, 6 strains, and 1 strain to test the capability of three single genes ( , , and ), two multilocus sequence analysis (MLSA) schemes, the single nucleotide polymorphism (SNP)-based phylogeny tool CSI phylogeny, a k-mer-based identification method (KmerFinder), average nucleotide identity (ANI) using fastANI, and core genome analysis to identify 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 strains correctly using only one of the single genes. The MLSA schemes were unable to identify some of the strains, which could be misidentified. KmerFinder identified all strains but misidentified one strain as , and fastANI differentiated between and using an ANI cutoff of 96%.