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 strains 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, 22 S. mitis strains, 24 S. oralis strains, 6 S. infantis strains, and 1 S. peroris strain to test the capability of three single genes (rpoB, gyrB, and recA), 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 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 strains correctly using only one of the single genes. The MLSA schemes were unable to identify some of the S. pseudopneumoniae strains, which could be misidentified. KmerFinder identified all S. pseudopneumoniae strains but misidentified one S. mitis strain as S. pseudopneumoniae, and fastANI differentiated between S. pseudopneumoniae and S. pneumoniae using an ANI cutoff of 96%.

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假肺炎链球菌：使用全基因组序列验证物种鉴定方法

正确鉴定假肺炎链球菌是研究该细菌临床影响的先决条件。鉴定传统上依赖于表型方法。然而，这些表型特征已被证明是不可靠的，一些假肺炎链球菌菌株给出了相互矛盾的结果。因此，基于序列的鉴定方法越来越多地用于鉴定假肺炎链球菌。在这项研究中，我们使用了 64株假肺炎链球菌、59 株肺炎链球菌、22 株缓症链球菌、24株口腔链球菌、6株婴儿链球菌和 1 株猪链球菌。菌株测试三个单基因（rpoB、gyrB和recA）的能力、两个多位点序列分析 (MLSA) 方案、基于单核苷酸多态性 (SNP) 的系统发育工具 CSI phylogeny、基于 k-mer 的识别方法 ( KmerFinder)、使用 fastANI 的平均核苷酸同一性 (ANI) 和核心基因组分析来鉴定假肺炎链球菌。核心基因组分析和 CSI 系统发育能够将所有菌株聚集成与其各自物种相关的不同簇。仅使用一个单一基因是不可能正确识别所有假肺炎链球菌菌株的。MLSA计划无法识别某些假肺炎链球菌菌株，可能会被错误识别。KmerFinder 识别出所有假肺炎链球菌菌株，但将一种缓症链球菌菌株误识别为假肺炎链球菌， fastANI使用 96% 的 ANI 截止值区分假肺炎链球菌和肺炎链球菌。