Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.
Front Cell Infect Microbiol. 2020 May 19;10:222. doi: 10.3389/fcimb.2020.00222. eCollection 2020.
Correct identifications of isolates and strains of the Mitis-Group of the genus are particularly difficult, due to high genetic similarity, resulting from horizontal gene transfer and homologous recombination, and unreliable phenotypic and genotypic biomarkers for differentiating the species. and are the most closely related species of the clade. In this study, publicly-available genome sequences for and were analyzed, using a pangenomic approach, to find candidates for species-unique gene markers; ten species-unique genes for and nine for were identified. These species-unique gene marker candidates were verified by PCR assays for identifying and strains isolated from clinical samples. All determined species-level unique gene markers for were detected in all clinical isolates, whereas fewer of the unique gene markers were present in more than 95% of the clinical isolates. In parallel, taxonomic identifications of the clinical isolates were confirmed, using conventional optochin sensitivity testing, targeted PCR-detection for the "Xisco" gene, as well as genomic ANIb similarity analyses for the genome sequences of selected strains. Using mass spectrometry-proteomics, species-specific peptide matches were observed for four of the gene markers and for three of the gene markers. Application of multiple species-level unique biomarkers of and , is proposed as a protocol for the routine clinical laboratory for improved, reliable differentiation, and identification of these pathogenic and commensal species.
正确鉴定 属的米氏群菌株特别困难，这是由于水平基因转移和同源重组导致的高度遗传相似性，以及用于区分物种的不可靠表型和基因型生物标志物。 和 是该进化枝中最密切相关的物种。在这项研究中，使用泛基因组方法分析了 和 公开可用的基因组序列，以寻找用于物种独特基因标记的候选物；鉴定出 10 个种独特基因和 9 个 种独特基因。通过 PCR 检测验证了这些种独特基因标记候选物，以鉴定从临床样本中分离的 和 菌株。所有确定的 种独特基因标记都在所有 临床分离株中检测到，而更多的 种独特基因标记在超过 95%的临床分离株中存在。同时，使用传统的光学敏感性测试、针对“Xisco”基因的靶向 PCR 检测以及选定菌株基因组序列的全基因组 ANIb 相似性分析，对临床分离株进行了分类鉴定。使用质谱蛋白质组学，观察到四个 基因标记和三个 基因标记的物种特异性肽匹配。提出了应用 和 多种种水平独特生物标志物的方案，作为常规临床实验室的协议，以改善、可靠地区分和鉴定这些致病性和共生性物种。
