The aim of our study was to investigate phenotypic and genotypic features of streptococci misidentified (misID) as Streptococcus pneumoniae, obtained over 20 years from hospital patients in Poland. Sixty-three isolates demonstrating microbiological features typical for pneumococci (optochin susceptibility and/or bile solubility) were investigated by phenotypic tests, lytA and 16S rRNA gene polymorphism and whole-genome sequencing (WGS). All isolates had a 6-bp deletion in the lytA 3' terminus, characteristic for Mitis streptococc and all but two isolates lacked the pneumococcal signature cytosine at nucleotide position 203 in the 16S rRNA genes. The counterparts of psaA and ply were present in 100% and 81.0% of isolates, respectively; the spn9802 and spn9828 loci were characteristic for 49.2% and 38.1% of isolates, respectively. Phylogenetic trees and networks, based on the multilocus sequence analysis (MLSA) scheme, ribosomal multilocus sequence typing (rMLST) scheme and core-genome analysis, clearly separated investigated isolates from S. pneumoniae and demonstrated the polyclonal character of misID streptococci, associated with the Streptococcus pseudopneumoniae and Streptococcus mitis groups. While the S. pseudopneumoniae clade was relatively well defined in all three analyses, only the core-genome analysis revealed the presence of another cluster comprising a fraction of misID streptococci and a strain proposed elsewhere as a representative of a novel species in the Mitis group. Our findings point to complex phylogenetic and taxonomic relationships among S. mitis-like bacteria and support the notion that this group may in fact consist of several distinct species.

中文翻译：

---

来自微生物组的链球菌之间的关系，被误认为是肺炎链球菌。

我们研究的目的是调查20年来从波兰的医院患者获得的，被误识别为肺炎链球菌的链球菌（misID）的表型和基因型特征。通过表型测试，lytA和16S rRNA基因多态性以及全基因组测序（WGS），研究了63株分离株，这些分离株表现出典型的肺炎球菌微生物学特征（视光蛋白敏感性和/或胆汁溶解性）。所有分离株在lytA 3'末端具有6bp的缺失，这是链球菌的特征，除了两个分离株以外，所有分离株在16S rRNA基因的203位核苷酸上均缺乏肺炎球菌特征性胞嘧啶。psaA和ply的对应物分别存在于100％和81.0％的分离物中。spn9802和spn9828位点分别具有49.2％和38.1％的分离株特征性。系统发育树和网络基于多基因座序列分析（MLSA）方案，核糖体多基因座序列分型（rMLST）方案和核心基因组分析，清楚地从肺炎链球菌中分离了所研究的分离株，并证明了misID链球菌的多克隆特征，与假性肺炎链球菌和炎性链球菌组。尽管在所有三个分析中假肺炎链球菌的进化枝都定义相对良好，但只有核心基因组分析显示存在另一个簇，该簇包含一部分misID链球菌和其他地方提出的作为Mitis组新物种代表的菌株。我们的发现指出了类似类链球菌的细菌之间复杂的系统发育和分类学关系，并支持这一观点，即该群体实际上可能由几个不同的物种组成。