Complete whole-genome sequence of the novel Pseudomonas species strain TUM18999, isolated from a patient with a burn wound in Japan. (March 2021)

• Record Type: Journal Article
• Authors: Yamada, Kageto; Aoki, Kotaro; Nagasawa, Tatsuya; Sasaki, Masakazu; Murakami, Hinako; Ishii, Toshiaki; Ujiie, Shinji; Morita, Toshisuke; Ishii, Yoshikazu; Tateda, Kazuhiro
• Is Part Of: Journal of global antimicrobial resistance. Volume 24(2021)
• Page Start: 395
• Page End: 397
• Publication Date: 2021-03
• Subjects: Pseudomonas species -- Metallo-β-lactamase -- Average nucleotide identity -- Whole-genome sequencing; Drug resistance -- Periodicals; Drug resistance -- Periodicals; Drug resistance; Periodicals; 616.9041
• DOI: 10.1016/j.jgar.2021.01.020
• Languages: English
• ISSNs: 2213-7165

Abstract

Abstract: Objectives: 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. Methods: 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. Results: 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. Conclusion: We characterized the complete whole genome sequence of the novel Pseudomonas sp. TUM18999 carrying the novel gene species-specific subclass B3 MBL.