Department of Clinical Laboratory, Toho University Omori Medical Center, 6-11-1 Omori-nishi, Ota-ku, Tokyo, 143-8541, Japan; Department of Microbiology and Infectious Diseases, Toho University School of Medicine, 5-21-16, Omori-nishi, Ota-ku, Tokyo, 143-8540, Japan.
Department of Microbiology and Infectious Diseases, Toho University School of Medicine, 5-21-16, Omori-nishi, Ota-ku, Tokyo, 143-8540, Japan.
J Glob Antimicrob Resist. 2021 Mar;24:395-397. doi: 10.1016/j.jgar.2021.01.020. Epub 2021 Feb 9.
Pseudomonas is a Gram-negative bacterial genus with numerous member species. In this study, using whole-genome sequencing, we characterized a novel Pseudomonas sp. strain TUM18999, isolated as a pathogen from a human patient.
The TUM18999 strain was isolated from a patient's burn wound. Minimum inhibitory concentrations (MICs) were determined using the broth microdilution method. The whole-genome sequence was obtained using Miseq and MinION, and we conducted phylogenetic analysis based on single nucleotide polymorphisms of the core genome.
Antimicrobial susceptibility testing revealed a high ceftazidime MIC (32 mg/L). Moreover, carbapenemase production was confirmed using the modified carbapenem inactivation method. We found that the complete genome of TUM18999 was 6,826,062 bp long, with 6175 coding sequences (CDS) and a DNA G+C content (non-plasmid) of 66.4 mol%. Consistent with the high similarities with the 16S rRNA sequences of P. otitidis MCC10330 (98.6%) and P. alcaligenes NBRC 14159 (99.2%), similarities (<90%) were also observed with the gyrB genes of both strains. The average nucleotide identities for P. alcaligenes NBRC 14159 and P. otitidis MCC10330 were also <90%. The core-genome single nucleotide polymorphism phylogenetic tree indicated that the TUM18999 strain was most closely related to P. otitidis MCC10330. In addition, the TUM18999 strain carried the novel gene, species-specific subclass B3 metallo-β-lactamase (MBL), and its similarities with P. alcaligenes metallo-β-lactamase-1 (PAM-1) and P. otitidis metallo-β-lactamase-1 (POM-1) were 90.24% and 73.14%, respectively.
We characterized the complete whole genome sequence of the novel Pseudomonas sp. TUM18999 carrying the novel gene species-specific subclass B3 MBL.
假单胞菌是一个革兰氏阴性细菌属，拥有许多成员物种。在这项研究中，我们使用全基因组测序，对从人类患者中分离出的新型假单胞菌菌株 TUM18999 进行了表征。
TUM18999 菌株从患者的烧伤伤口中分离出来。使用肉汤微量稀释法测定最小抑菌浓度（MIC）。使用 Miseq 和 MinION 获得全基因组序列，并根据核心基因组的单核苷酸多态性进行系统发育分析。
抗菌药敏试验显示头孢他啶 MIC 值较高（32mg/L）。此外，使用改良碳青霉烯失活法证实了碳青霉烯酶的产生。我们发现 TUM18999 的完整基因组长 6826062bp，包含 6175 个编码序列（CDS）和非质粒 DNA G+C 含量为 66.4mol%。与 16S rRNA 序列与 P. otitidis MCC10330（98.6%）和 P. alcaligenes NBRC 14159（99.2%）高度相似一致，与这两个菌株的 gyrB 基因相似度也较低（<90%）。与 P. alcaligenes NBRC 14159 和 P. otitidis MCC10330 的平均核苷酸同一性也<90%。核心基因组单核苷酸多态性系统发育树表明，TUM18999 株与 P. otitidis MCC10330 最为密切相关。此外，TUM18999 株携带新型基因，物种特异性 B3 金属β-内酰胺酶（MBL），与 P. alcaligenes 金属β-内酰胺酶-1（PAM-1）和 P. otitidis 金属β-内酰胺酶-1（POM-1）的相似度分别为 90.24%和 73.14%。
我们对携带新型基因，物种特异性 B3 金属β-内酰胺酶的新型假单胞菌 TUM18999 进行了完整全基因组序列的特征描述。
