A5028006684- Antibiotic Resistance in Bacteria
- Streptococcal Infections and Treatments
- Plant Pathogenic Bacteria Studies
- Bacterial biofilms and quorum sensing
- Genomics and Phylogenetic Studies
- Infections and bacterial resistance
- Vibrio bacteria research studies
- Microbial infections and disease research
- Infective Endocarditis Diagnosis and Management
- Gut microbiota and health
- Microbial Community Ecology and Physiology
- Bacteriophages and microbial interactions
- Neonatal and Maternal Infections
- Tuberculosis Research and Epidemiology
- Plant-Microbe Interactions and Immunity
- Mycobacterium research and diagnosis
- Antimicrobial Resistance in Staphylococcus
- Gallbladder and Bile Duct Disorders
- Enterobacteriaceae and Cronobacter Research
- Pharmaceutical and Antibiotic Environmental Impacts
- Bacterial Identification and Susceptibility Testing
- Cassava research and cyanide
- Rabies epidemiology and control
- Antibiotics Pharmacokinetics and Efficacy
- Biosensors and Analytical Detection
Juntendo University
2018-2024
National Institute of Health Sciences
2024
Asahi Breweries (Japan)
2022
Osaka University
2022
The University of Tokyo
2014-2021
National Center for Global Health and Medicine
2018-2019
Abstract Large bowel preparation may cause a substantial change in the gut microbiota and metabolites. Here, we included prep group no-procedure control evaluated effects of on stability microbiome metabolome as well recovery. Gut compositions were analyzed by 16S rRNA sequencing capillary electrophoresis time-of-flight mass spectrometry, respectively. Analysis coefficients at genus species level weighted UniFrac distance showed that, compared with controls, composition was significantly...
In order to clarify the taxonomic position of serotypes 20, 22 and 26 Streptococcus suis , biochemical molecular genetic studies were performed on isolates (SUT-7, SUT-286 T SUT-319, SUT-328 SUT-380) reacted with specific antisera or from saliva healthy pigs as well reference strains 26. Comparative recN gene sequencing showed high relatedness among our isolates, but marked differences type strain S. NCTC 10234 i.e. 74.8–75.7 % sequence similarity. The genomic between other species genus...
The emergence of multidrug-resistant (MDR) Pseudomonas aeruginosa has become a serious worldwide medical problem. This study was designed to clarify the genetic and epidemiological properties MDR P. strains isolated from hospitals in Myanmar. Forty-five isolates obtained different patients seven Myanmar were screened using broth microdilution method. whole genomes sequenced MiSeq platform (Illumina). Phylogenetic trees constructed single nucleotide polymorphism concatemers. Multilocus...
It is generally difficult to specify the sources of infection by which domestic animals may acquire pathogens. Through 16S rRNA gene amplicon sequencing, we compared composition microbiota in saliva, vaginal mucus, and feces pigs, swabs feeder troughs water dispensers collected from pig farms Vietnam. The differed between samples each sample group. Streptococcus, Actinobacillus, Moraxella, Rothia were most abundant genera significantly discriminative saliva samples, regardless plasticity...
To clarify the taxonomic classification of Streptococcus suis serotype 33, we performed biochemical and molecular genetic analyses using isolates (GUT-183, GUT-184, GUT-185, GUT-186, GUT-187T, GUT-188, GUT-189, GUT-190, GUT-191, GUT-192 GUT-193) from bovine endocarditis. A comparative sequence analysis showed 99.2-100 % similarity among reference strain S. 33 our for 16S rRNA gene. These similarities were higher than those between isolate GUT-187T other streptococci. Comparison sodA genes...
A novel Gram-negative, aerobic, rod-shaped, non-spore-forming bacterial strain, RYU5T, was isolated from a stool sample of an inpatient at hospital in Okinawa, Japan. The optimal growth temperature RYU5T 30 °C. Phylogenetic analysis based on the sequences housekeeping genes, including 16S rRNA, rpoB, rpoD and gyrB showed that member Pseudomonas putida group located close to monteilii P. putida. Whole-genome comparisons, using average nucleotide identity digital DNA-DNA hybridization,...
Abstract Mycobacteroides ( Mycobacterium ) abscessus , which causes a variety of infectious diseases in humans, is becoming detected more frequently clinical specimens as cases are spreading worldwide. Taxonomically, M. composed three subspecies subsp. bolletii and massiliense, with different susceptibilities to macrolides. In order identify rapidly these subspecies, we determined useful biomarker proteins, including ribosomal protein L29, L30, hemophore-related protein, for distinguishing...
Three Gram-positive bacterial strains, BML-BC004, BML-BC017 and BML-BC059, isolated from blood samples 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 these strains more than 97.1 % similar to 18 type belonging the B. group. Whole-genome comparisons, average nucleotide identity (ANI) digital DNA-DNA hybridization (dDDH), confirmed that represented individual distinct...
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 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 fluorescens by bacterial identification system based on biochemical properties were...
A Gram-negative, aerobic, rod-shaped, non-spore-forming bacterium, designated as strain BML3T, was isolated from a sputum sample of hospital patient in Japan. Strain BML3T grew at temperatures 4 to 40 °C, 1.0-7.0 % (w/v) NaCl and pH 6.0-9.0. Results phylogenetic analysis based on the sequences housekeeping genes, including 16S rRNA gene rpoB, rpoD gyrB, showed that part Pseudomonas putida group located close asiatica, monteiliiand P. . Whole-genome comparisons, using average nucleotide...
How long fecal samples can withstand a period of refrigeration or room temperature, and the appropriate preservative, are largely unknown. Cary-Blair transport medium has been used for many years because it is inexpensive prevents bacterial overgrowth. However, its effectiveness metagenomic analyses never tested. We found that microbial compositions using 16S rRNA sequence left at 4°C 3 7 days 25°C 1, 3, differed significantly from stored -80°C in no-preservative method. Whereas remained...
The aim of this study was to clarify the genetic and epidemiological properties multidrug-resistant Acinetobacter baumannii in medical settings Myanmar.A total 45 A. clinical isolates were obtained Myanmar. whole genomes sequenced by a next generation sequencer, phylogenetic tree constructed from single nucleotide polymorphism concatemers. Multilocus sequence types deduced drug resistance genes identified.Thirty-eight MDR seven hospitals majority belonged ST2. Of 38 isolates, 5 harbored...
This study was conducted to clarify the taxonomic status of species Pseudomonas fuscovaginae and shirazica. Whole genome sequences for type strains P. shirazica were compared against closely related putida group fluorescens species. Average nucleotide identity digital DNA-DNA hybridization values between LMG 2158T asplenii ATCC 23835T 98.4 85.5 %, VM14T asiatica RYU5T 99.3 95.3 %. These greater than recognized thresholds bacterial delineation, indicating that they belong same genomospecies,...
The emergence of carbapenem-resistant Pseudomonas aeruginosa has become a serious worldwide medical problem. aim this study was to determine the genetic and epidemiological properties P. strains isolated from hospitals in Nepal.A total 43 isolates obtained patients two Nepal between 2018 2020 were analysed. Their whole genomes sequenced by next-generation sequencing. A phylogenetic tree constructed single nucleotide polymorphism (SNP) concatemers. Multilocus sequence typing (MLST) performed...
Pseudomonas asiatica is a recently proposed species of the genus This study describes eight isolates carbapenem-resistant P. harboring blaNDM-1 and blaVIM-2, genes encoding metallo-β-lactamase (MBL). These were obtained from urine samples patients hospitalized in Myanmar. resistant to carbapenems but susceptible colistin. All positive for carbapenemase inactivation method, CIMTrisII, seven on an immunochromatographic assay NDM-type MBL. One isolate was highly aminoglycosides. Whole-genome...
The aim of this study was to determine the genetic and epidemiological properties Pseudomonas aeruginosa strains producing VIM-type metallo-β-lactamases isolated from patients in Japan.A total 1860 clinical isolates carbapenem-resistant P. were obtained hospitalised Japan 2012-2018. Carbapenem-resistant screened for blaVIM genes by PCR. Antimicrobial susceptibility determined broth microdilution method. whole genomes these sequenced using a next-generation sequencer, phylogenetic analysis...
Abstract During the exploration of microbial natural resources, two strains Pseudomonas , PS14 T and PS24 were isolated from samples taken Izu Oshima, a volcanic island located 120 km southwest central Tokyo. Phylogenetic analysis based on 16S rRNA gene sequences showed that was most similar to baetica a390 (99.6%) helmanticensis OHA11 (99.5%), qingdaonensis JJ3 (98.8%) lutea OK2 (98.7%). The major fatty acids these C 16:0 17:0 cyclo, summed feature 3 (C 16:1 ω6c and/or ω7c), 8 18:1 ω7c...
The taxonomic classification of Pseudomonas species has been revised and updated several times. This study utilized average nucleotide identity (ANI) digital DNA–DNA hybridization (dDDH) cutoff values 95 70 %, respectively, to re-identify the strains deposited in GenBank as P. aeruginosa , fluorescens putida . Of 264 strains, 259 were correctly identified but remaining five not. All 28 had incorrectly Four these re-identified, including two kilonensis one each brassicacearum 24 could not be...
Four Providencia rettgeri isolates and one stuartii isolate were obtained from urine samples of five patients in 2018 Japan. All the resistant to imipenem meropenem, three highly both carbapenems, with MICs 512 μg/ml. The carbapenem-resistant harbored blaIMP-70, encoding a variant IMP-1 metallo-β-lactamase two amino acid substitutions (Val67Phe Phe87Val), other blaIMP-1 blaIMP-11, respectively. Whole-genome sequencing revealed that an copies on chromosome four copy blaIMP-11 or blaIMP-70...
OBJECTIVE To evaluate colonization of Streptococcus suis and parasuis on pig farms in Japan to identify sources infections. SAMPLE Saliva, feces, vaginal swab samples from 84 healthy pigs several growth stages 4 feed troughs water dispensers at those farms. PROCEDURES Samples were collected August 2015 June 2016. Two quantitative PCR (qPCR) assays (one for S the other parasuis) designed use study. The novel qPCR used combination with previously described serotype 2 or 1/2 total bacteria....
A total of 38 isolates carbapenem-resistant Klebsiella pneumoniae harboring blaNDM were obtained during surveillance 10 hospitals in Myanmar. Of these isolates, 19 (50%) harbored genes encoding 16S rRNA methylases, such as armA or rmtB. The K. strains tested belonged to 17 sequence types (STs), including the high-risk clonal lineages ST101 and ST147. ST147 carried IncFII plasmids blaNDM-5 IncFIB(pQil) blaNDM-1, respectively. These results indicate that blaNDM-1 have been spreading...
Surveillance of 10 hospitals and a regional public health laboratory in Myanmar identified 31 isolates carbapenem-resistant Enterobacter cloacae complex harboring blaNDM-type Of these isolates, 19 were highly resistant to aminoglycosides harbored one or more genes encoding 16S rRNA methylases, including armA, rmtB, rmtC, and/or rmtE the 16 xiangfangensis ST200, with armA on chromosome plasmid blaNDM-1 indicating that clonally disseminated nationwide Myanmar.IMPORTANCE The emergence...