Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea.
Department of Urology, Chung-Ang University College of Medicine, Seoul, Republic of Korea.
PLoS One. 2020 May 13;15(5):e0232850. doi: 10.1371/journal.pone.0232850. eCollection 2020.
Whole genome sequencing (WGS) has become an accessible tool in clinical microbiology, and it allowed us to identify a novel Cupriavidus species. We isolated Gram-negative bacillus from the blood of an immunocompromised patient, and phenotypical and molecular identifications were performed. Phenotypic identification discrepancies were noted between the Vitek 2 (bioMérieux, Marcy-l'Étoile, France) and Vitek MS systems (bioMérieux). Using 16S rRNA gene sequencing, it was impossible to identify the pathogen to the species levels. WGS was performed using the Illumina MiSeq platform (Illumina, San Diego, CA), and genomic sequence database searching with a TrueBacTM ID-Genome system (ChunLab, Inc., Seoul, Republic of Korea) showed no strains with average nucleotide identity values higher than 95.0%, which is the cut-off for species-level identification. Phylogenetic analysis indicated that the bacteria was a new Cupriavidus species that formed a subcluster with Cupriavidus gilardii. WGS holds great promise for accurate molecular identification beyond 16S rRNA gene sequencing in clinical microbiology.
全基因组测序（WGS）已成为临床微生物学中一种易于使用的工具，它使我们能够鉴定出一种新型的贪铜菌。我们从一位免疫功能低下患者的血液中分离出革兰氏阴性杆菌，并进行了表型和分子鉴定。Vitek 2（生物梅里埃，马西-勒埃托勒，法国）和 Vitek MS 系统（生物梅里埃）之间的表型鉴定存在差异。使用 16S rRNA 基因测序，无法将病原体鉴定到种水平。使用 Illumina MiSeq 平台（Illumina，圣地亚哥，加利福尼亚州）进行 WGS，使用 TrueBacTM ID-Genome 系统（ChunLab，Inc.，韩国首尔）对基因组序列数据库进行搜索，没有平均核苷酸同一性值高于 95.0%的菌株，这是种水平鉴定的截止值。系统发育分析表明，该细菌是一种新的贪铜菌，与铜绿假单胞菌形成了一个亚群。WGS 在临床微生物学中，除了 16S rRNA 基因测序之外，对于准确的分子鉴定具有很大的潜力。
