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5 results on '"Masahito Shimojima"'

1. Whole-Genome Sequencing-Based Re-Identification of Pseudomonas putida/fluorescens Clinical Isolates Identified by Biochemical Bacterial Identification Systems

Author

Mari Tohya, Kanae Teramoto, Shin Watanabe, Tomomi Hishinuma, Masahito Shimojima, Miho Ogawa, Tatsuya Tada, Yoko Tabe, and Teruo Kirikae

Subjects
Pseudomonas, human pathogen, re-identification, whole-genome sequencing, MALDI-TOF MS, Microbiology, QR1-502
Abstract

ABSTRACT The genus Pseudomonas, a complex Gram-negative genus, includes species isolated from various environments, plants, animals, and humans. We compared whole-genome sequencing (WGS) with clinical bacteriological methods and evaluated matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) to identify Pseudomonas species. Clinical isolates (N = 42) identified as P. putida or P. fluorescens by a bacterial identification system based on biochemical properties were reexamined by another identification system based on biochemical properties, two systems based on MALDI-TOF MS, and WGS. WGS revealed that 30 of the 42 isolates belonged to one of 14 known Pseudomonas species, respectively. The remaining 12 belonged to one of 9 proposed novel Pseudomonas species, respectively. MALDI-TOF MS analysis showed that the 9 novel species had unique major peaks. These results suggest that WGS is the optimal method to identify Pseudomonas species and that MALDI-TOF MS may complement WGS in identification. Based on their morphologic, physiologic, and biochemical properties, we propose nine novel Pseudomonas species. IMPORTANCE Most of the clinical isolates, identified as P. putida or P. fluorescens, were misidentified in clinical laboratories. Whole-genome sequencing (WGS) revealed that these isolates belonged to different Pseudomonas species, including novel species. WGS is a gold-standard method to identify Pseudomonas species, and MALDI-TOF MS analysis has the potential to complement WGS to reliably identify them.

Published
2022
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3. Whole-Genome Sequencing-Based Re-Identification of Pseudomonas putida / fluorescens Clinical Isolates Identified by Biochemical Bacterial Identification Systems

Author

Mari Tohya, Kanae Teramoto, Shin Watanabe, Tomomi Hishinuma, Masahito Shimojima, Miho Ogawa, Tatsuya Tada, Yoko Tabe, and Teruo Kirikae

Subjects
Microbiology (medical), Infectious Diseases, General Immunology and Microbiology, Ecology, Physiology, Genetics, Cell Biology
Abstract

Most of the clinical isolates, identified as P. putida or P. fluorescens , were misidentified in clinical laboratories. Whole-genome sequencing (WGS) revealed that these isolates belonged to different Pseudomonas species, including novel species. WGS is a gold-standard method to identify Pseudomonas species, and MALDI-TOF MS analysis has the potential to complement WGS to reliably identify them.

Published
2022

4. Three novel species of the

Author

Mari, Tohya, Tomomi, Hishinuma, Shin, Watanabe, Masahito, Shimojima, Miho, Ogawa, Tatsuya, Tada, and Teruo, Kirikae

Subjects
DNA, Bacterial, Base Composition, Blood, Bacillus cereus, Japan, RNA, Ribosomal, 16S, Fatty Acids, Humans, Nucleic Acid Hybridization, Sequence Analysis, DNA, Phylogeny, Bacterial Typing Techniques
Abstract

Three Gram-positive bacterial strains, BML-BC004, BML-BC017 and BML-BC059, isolated from blood samples from three inpatients in Japan, were identified as members of

Published
2021

5. Three novel species of the Bacillus cereus group isolated from clinical samples in Japan

Author

Teruo Kirikae, Miho Ogawa, Tomomi Hishinuma, Shin Watanabe, Masahito Shimojima, Tatsuya Tada, and Mari Tohya

Subjects
Bacillus (shape), Strain (chemistry), Phylogenetic tree, Bacillus cereus, General Medicine, Biology, 16S ribosomal RNA, biology.organism_classification, Microbiology, Cereus, Group (periodic table), Gene, Ecology, Evolution, Behavior and Systematics
Abstract

Three Gram-positive bacterial strains, BML-BC004, BML-BC017 and BML-BC059, isolated from blood samples from three inpatients in Japan, were identified as members of Bacillus cereus using matrix-assisted laser desorption ionization time-of-flight MS. The 16S rRNA gene sequences of these three strains were more than 97.1 % similar to 18 type strains belonging to the B. cereus group. Whole-genome comparisons, using average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH), confirmed that the three strains represented three individual distinct species belonging to the B. cereus group. A phylogenetic tree showed that BML-BC004, BML-BC017 and BML-BC059 were located close to B. luti , B. mobilis and B. paramycoides , respectively. Based on these phylogenetic and phenotypic data, including values below the threshold for ANI and dDDH, the three strains should be classified as representing three different novel species of the B. cereus group: Bacillus sanguinis sp. nov., with type strain BML-BC004T (=DSM 111102T=JCM 34122T), Bacillus paramobilis sp. nov., with type strain BML-BC017T (=DSM 111100T=JCM 34124T) and Bacillus hominis sp. nov., with type strain BML-BC059T (=DSM 111101T=JCM 34125T).

Published
2021

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