PubMed Health⌕ Search

Biomedical subjects

Takayuki Ezaki

Publications and source records attributed to Takayuki Ezaki.

At least 19 recordsLinked to original sources
PubMed2007

The dnaJ gene as a novel phylogenetic marker for identification of Vibrio species.

The utility of the dnaJ gene for identifying Vibrio species was investigated by analyzing dnaJ sequences of 57 type strains and 22 clinical strains and comparing sequence homologies with those of the 16S rDNA gene and other housekeeping genes (recA, rpoA, hsp60). Among the 57 Vibrio species, the mean sequence similarity of the dnaJ gene (77.9%) was significantly less than that of the 16S rDNA gene (97.2%), indicating a high discriminatory power of the dnaJ gene. Most Vibrio species were, therefore, differentiated well by dnaJ sequence analysis. Compared to other housekeeping genes, the dnaJ gene showed better resolution than recA or rpoA for differentiating Vibrio coralliilyticus from Vibrio neptunius and Vibrio harveyi from Vibrio rotiferianus. Among the clinical strains, all 22 human pathogenic strains, including an atypical strain, were correctly identified by the dnaJ sequence. Our findings suggest that analysis of the dnaJ gene sequence can be used as a new tool for the identification of Vibrio species.

Bacterial Typing Techniques↗
PubMed2007

Legionella impletisoli sp. nov. and Legionella yabuuchiae sp. nov., isolated from soils contaminated with industrial wastes in Japan.

In this study, we tried to isolate legionellae from nine Legionella DNA-positive soil samples collected from four different sites contaminated with industrial wastes in Japan. Using culture methods with or without Acanthamoeba culbertsoni, a total of 22 isolates of legionellae were obtained from five of the nine samples. Identification of species and/or serogroups (SGs), performed by DNA-DNA hybridization and agglutination tests, revealed that the 22 isolates consisted of ten isolates of Legionella pneumophila including five SGs, five Legionella feeleii, and one each of Legionella dumoffii, Legionella longbeachae, and Legionella jamestownensis. The species of the remaining four isolates (strains OA1-1, -2, -3, and -4) could not be determined, suggesting that these isolates may belong to new species. The 16S rDNA sequences (1476-1488bp) of the isolates had similarities of less than 95.0% compared to other Legionella species. A phylogenetic tree created by analysis of the 16S rRNA (1270bp) genes demonstrated that the isolates formed distinct clusters within the genus Legionella. Quantitative DNA-DNA hybridization tests on the OA1 strains indicated that OA1-1 should be categorized as a new taxon, whereas OA1-2, -3, and -4 were also genetically independent in another taxon. Based on the evaluated phenotypic and phylogenetic characteristics, it is proposed that one of these isolates from the soils, OA1-1, be classified as a novel species, Legionella impletisoli sp. nov.; the type strain is strain OA1-1(T) (=JCM 13919(T)=DSMZ 18493(T)). The remaining three isolates belong to another novel Legionella species, Legionella yabuuchiae sp. nov.; the type strain is strain OA1-2(T) (=JCM 14148(T)=DSMZ 18492(T)). This is the first report on the isolation of legionellae from soils contaminated with industrial wastes.

Acanthamoeba↗
PubMed2007

dnaJ gene sequence-based assay for species identification and phylogenetic grouping in the genus Staphylococcus.

In the last few years, many attempts have been made to use conserved gene sequences for identification and for phylogenetic studies of Staphylococcus species. In an effort to identify a more reliable approach, a dnaJ gene sequence-based database was created. In this study, an approximately 883 bp portion of the dnaJ gene sequence from 45 staphylococcal type strains was compared with 16S rRNA and other conserved gene (hsp60, sodA and rpoB) sequences available in public databases. Nucleotide sequence comparisons revealed that the staphylococcal dnaJ gene showed higher discrimination (mean similarity 77.6 %) than the 16S rRNA (mean similarity 97.4 %), rpoB (mean similarity 86 %), hsp60 (mean similarity 82 %) and sodA (mean similarity 81.5 %) genes. Analysis of the dnaJ gene sequence from 20 Staphylococcus isolates representing two clinically important species showed <1 % sequence divergence. Phylogenetic data obtained from the dnaJ gene sequence were in general agreement with those of 16S rRNA gene sequence analysis and DNA-DNA reassociation studies. In conclusion, the dnaJ gene sequence-based assay is an effective alternative to currently used methods, including 16S rRNA gene sequencing, for identification and taxonomical analysis of Staphylococcus species.

Bacterial Typing Techniques↗
PubMed2007

System for simultaneous detection of 16 pathogens related to urethritis to diagnose mixed infection.

OBJECTIVE: Urethritis is not always caused by a single pathogen, and isolation of more than two pathogens from one patient is not uncommon. We developed a method to simultaneously detect 16 pathogens related to urethritis. METHODS: We designed specific primers used for amplification of urethritis pathogens in our 16-well microplate assay. Sixteen microliters of each reaction mixture containing template DNA was added to each well to amplify 16 pathogens simultaneously. RESULTS: After we evaluated the specificity and sensitivity of this microplate polymerase chain reaction method, we used it to detect pathogens in clinical samples. Of 163 clinical samples, 49.7% (81/163) were positive for specific pathogens, and 6.7% (11/163) showed mixed infection. A specific pathogen was not identified in 43.6% (71/163) of cases. CONCLUSIONS: We developed a 16-well microplate assay with 16 specific primers to identify pathogens associated with urethritis.

Humans↗
PubMed2006

Emerging multiple mutations and high-level fluoroquinolone resistance in methicillin-resistant Staphylococcus aureus isolated from ocular infections.

We investigated the prevalence of mutations in the gyrA, gyrB, grlA, and grlB genes in 21 clinical isolates of methicillin-resistant Staphylococcus aureus recovered from ocular infections. These isolates were classified into 16 groups on the basis of pulsed-field gel electrophoresis (PFGE) patterns. Among these nonidentical strains, 9 different combinations of mutations were observed. We observed an unusually high frequency of mutations: 10 (62.5%) of the isolates had four or five mutations, 5 (31.3%) of the isolates had double mutations, and 1 isolate had a single mutation. Different mutations were detected in strains of the same PFGE type, and this is consistent with the independent acquisition of mutations. The minimun inhibitory concentrations values ranged from 0.5 to 512 microg/mL for levofloxacin and 0.125 to 128 microg/mL for gatifloxacin. Only 1 isolate was found to be susceptible to both agents. These results suggest that application of high concentration fluoroquinolone ophthalmic solutions selects for isolates presenting such mutations that may result in a high level of resistance to fluoroquinolones.

Drug Resistance, Bacterial↗
PubMed2006

dnaJ and gyrB gene sequence relationship among species and strains of genus Streptococcus.

The dnaJ and gyrB nucleotide sequences were determined for members of the genus Streptococcus. The average similarity between the species tested was 76.4% (69.7-100%) for dnaJ and 75.9 (70.1-98.7%) for gyrB. These data indicated that the dnaJ and gyrB genes are more divergent and more discriminatory than the 16S rDNA gene. Furthermore, the variation in the dnaJ nucleotide sequences among the mitis group was greater than that of the gyrB nucleotide sequences, especially between Streptococcus pneumoniae and Streptococcus mitis. Subsequently, the high discrimination power of dnaJ within the mitis group was confirmed. Thus, we conclude that the dnaJ and gyrB genes are efficient alternative targets for the classification of the genus Streptococcus, and that dnaJ is suitable for phylogenetic analysis of closely related Streptococcus strains.

Bacterial Proteins↗
PubMed2006

Involvement of Salmonella enterica serovar Typhi RpoS in resistance to NO-mediated host defense against serovar Typhi infection.

The involvement of nitric oxide (NO) in host defense and cytoprotective functions in murine salmonellosis has been reported. Salmonella mutants with the altered sigma factor RpoS (sigmaS) are less virulent and are susceptible to various stresses. This study investigated the role of the rpoS gene of Salmonella enterica serovar Typhi in NO-dependent host defense in vitro and in vivo. Wild-type mice and mice deficient in inducible NO synthase (iNOS) were infected intraperitoneally or orally with serovar Typhi strains. iNOS-deficient mice were more susceptible to infection by both wild-type and rpoS mutant strains of serovar Typhi and showed extensive apoptotic liver damage compared with wild-type mice. Intracellular killing of Salmonella was analyzed with RAW 264 macrophage-like cells and primary peritoneal macrophages from wild-type and iNOS-deficient mice after cells were infected with the serovar Typhi parent or rpoS mutant strain. The rpoS mutant was more susceptible to killing by macrophages than was the wild-type strain. Also, the wild-type strain produced more extensive apoptotic changes in macrophages than did rpoS mutant. These effects were nullified in RAW 264 cells treated with an NOS inhibitor and in iNOS-deficient primary macrophages. Peroxynitrite susceptibility assays of these strains were also performed. The rpoS mutant Typhi strain was more sensitive to in vitro peroxynitrite treatment than was the parent strain. Together these data show that NO has a significant host defense function during serovar Typhi infection, and that Salmonella RpoS, because it reacts to the presence of NO or its reactive derivatives, is thought to have a role in the pathogenicity of serovar Typhi.

Animals↗
PubMed2006

Emergence of multidrug-resistant Corynebacterium striatum as a nosocomial pathogen in long-term hospitalized patients with underlying diseases.

During a 53-month period (March 1994 to August 1998), 48 Corynebacterium striatum isolates recovered from clinical specimens were characterized. The organisms were identified by both phenotypic characteristics and 16S rRNA gene sequence analysis. Thirty-six (75%) were isolated from sputum/bronchial aspirates, 10 (21%) from wound exudates/pus, 1 (2%) from vaginal discharge, and 1 (2%) from an otorrheic specimen. All 48 patients had been hospitalized for treatment of an underlying disease and had received antibiotics previously. The C. striatum isolates were considered pathogenic based on their abundance within polymorphonuclear neutrophils and their dominant growth in culture. Sensitivities of isolates to 11 antibiotics were determined by broth microdilution. MIC90 values of the isolates were 1 microg/mL for vancomycin, 16 microg/mL for penicillin and ampicillin, 32 microg/mL for minocycline, and > or = 32 microg/mL for cephalosporins, imipenem, ofloxacin, and macrolides. Restriction fragment-length polymorphism analysis with pulsed-field gel electrophoresis was used to determine the clonal identity. The pulse-field gel electrophoresis profiles revealed 14 distinct patterns with 20 subtypes. The isolates for the nosocomial outbreaks of C. striatum included 3 types (A, D, and E) with 4 subtypes (A1, A2, D2, and E). All 4 genotypes had broad-spectrum resistance to antimicrobial agents. Furthermore, type E strain isolated from 3 patients in the same ward was sensitive only to vancomycin. We conclude that C. striatum should be considered an emerging multidrug-resistant nosocomial pathogen in patients hospitalized for a prolonged period and/or in immunocompromised patients with such underlying conditions as cerebrovascular disease, pulmonary disease, diabetes, or malignancy.

Anti-Bacterial Agents↗
PubMed2006

Phylogenetic study and multiplex PCR-based detection of Burkholderia plantarii, Burkholderia glumae and Burkholderia gladioli using gyrB and rpoD sequences.

In order to develop a detection method for the rice pathogens Burkholderia plantarii, Burkholderia glumae and Burkholderia gladioli, the phylogeny of six plant-pathogenic Burkholderia species was analysed using the combined nucleotide sequences of gyrB and rpoD. B. plantarii, B. glumae and B. gladioli formed tight monophyletic branches supported by high bootstrap probabilities. The high sequence similarity revealed a close phylogenetic relationship between B. glumae and B. plantarii. B. plantarii strains were divided into three subclusters comprising rice strains, whereas the single Vanda strain occupied a unique position in the phylogenetic tree. The gyrB and rpoD sequences of all B. glumae strains examined were highly conserved. In contrast, B. gladioli strains demonstrated a far greater sequence diversity, but this diversity did not correlate with pathovar, host plant or geographical origin of the strains. A multiplex-PCR protocol using specific primers from the gyrB sequences was designed that allowed the specific detection and identification of B. plantarii, B. glumae and B. gladioli in rice seeds infected with these pathogenic species.

Bacterial Proteins↗
PubMed2006

A mixed bacterial infection of a bronchogenic lung cyst diagnosed by PCR.

An unusual paediatric case of a bronchogenic cyst infected with both Haemophilus influenzae type b and Streptococcus pneumoniae is described, which was detected not by culture of the purulent cyst fluid, but by real-time PCR amplification for several potential pathogens of DNA extracted from the fluid.

Base Sequence↗
PubMed2006

Virulence-defective strains of Salmonella enterica serovar Typhi as candidates for education at level 2 facilities.

The use of biosafety level 3 pathogens is an essential element of education and training at medical schools. We previously reported on invasion-defective strains of Salmonella enterica serovar Typhi, GTC 3P408 (DeltainvA, DeltasipB) and GTC 3P409 (DeltainvA, DeltasipB, and DeltaviaB), as candidates for use in educational programs. Vi negative strains of S. enterica serovar Typhi became extremely sensitive to complement attack but showed increased invasiveness. Therefore, this study was conducted to construct two virulencedefective strains, GTC 3P460 (DeltainvA, DeltasipB, and DeltarpoS) and GTC 3P461 (DeltainvA, DeltasipB, DeltaviaB, and DeltarpoS), of S. enterica serovar Typhi by deleting rpoS from the GTC 3P409 and GTC 3P408 strains. Stress tests demonstrated that GTC 3P460 and GTC 3P461 are sensitive to conditions of starvation, acid stress and oxidative stress. These results suggest that these virulence-defective strains have difficulty surviving in the gastric environment and in macrophages, characteristics that make them ideal candidates for education at level 2 facilities. Colony morphology and conventional biochemical features of these strains are identical to the parent strain S. enterica serovar Typhi GIFU 10007.

Antigens, Bacterial↗
PubMed2006

Mycobacterium kumamotonense Sp. Nov. recovered from clinical specimen and the first isolation report of Mycobacterium arupense in Japan: Novel slowly growing, nonchromogenic clinical isolates related to Mycobacterium terrae complex.

Three mycobacterium strains isolated from clinical specimens in Japan were provisionally assigned to the genus Mycobacterium based on their phenotypical characteristics. These isolates were further investigated to determine their specific taxonomic statuses. Mycolic acid analysis and 16S rRNA gene, rpoB, and hsp65 sequence data for the isolates showed that they are most similar to M. terrae complex. DNA-DNA hybridization studies indicated that the three strains were of two species and were distinguishable from M. terrae, M. nonchromogenicum, and M. hiberniae. Therefore, these strains represent two novel species within the genus Mycobacterium. However, one potential new species should have been considered as M. arupense with the 16S rRNA gene and hsp65 sequences similarities of 99.8% and 100% respectively; it was isolated from human specimens in the United States and was proposed in June 2006 as a new species. This report describes the first isolation of M. arupense in Japan, suggesting that the organism is clinically relevant. In addition, we propose the novel species designation Mycobacterium kumamotonense sp. nov. The type strain is CST 7247(T) (=GTC 2729(T), =JCM 13453(T), =CCUG 51961(T)).

Bacterial Proteins↗
PubMed2006

[RNA amplification from low numbers of bacteria in human blood to solve low sensitivity problem of conventional PCR amplification].

Blood culture from a febrile patient is often unsuccessful when a number of bacteria is lower than 10 CFU/ml in circulation. Theoretically, PCR amplification of bacteria in this low bacterial level in human blood is beyond the sensitivity of PCR method. RNA based Amplification (NASBA) method is more sensitive than PCR base assay because living bacteria carries several hundred to thousand RNA molecules in a cell. Increasing evidences also revealed another problem that human blood stream is often contaminated with bacterial genome. This often cause false positive results and bring difficulty of the interpretation to determine causative agent. Direct DNA amplification should be limited to severe causative agent such as Haemophilus influenzae, Streptococcus pneumoniae, Neisseria meningitides, and etc. and also applied only for slow growing and fastidious pathogens such as mycoplasmae, chlamydiae, bartonellae, mycobacteria, and etc. Most cases blood culture should be carried out first and genetic amplification should be selected as a next step to detect pathogens from a blood culture bottle, because in these cases, patients are not in life threatening stages. These attempts also decrease the chance to detect circulating bacterial DNA fragment in blood stream.

Bacterial Infections↗
PubMed2005

Lytic enzyme, labiase for a broad range of Gram-positive bacteria and its application to analyze functional DNA/RNA.

The lytic activity of labiase and achromopeptidase for bacterial DNA/RNA extraction were compared. Rapid lysis of many bacterial strains was observed with labiase followed by SDS treatment. Both labiase and achromopeptidase showed high lytic activity against bacterial strains with the A1alpha chemotype (e.g., Aerococcus viridans) and the A3alpha chemotype (e.g., Staphylococcus epidermidis) for cell wall peptidoglycan structures. The lytic activity of labiase was higher than that of achromopeptidase against strains with the A1gamma chemotype (e.g., Bacillus subtilis). The activity of labiase was not detrimentally affected with increasing NaCl concentration. Labiase lysates were successfully used for rapid extraction of DNA and RNA, whereas achromopeptidase lysates degraded RNA. The DNA and RNA obtained were successfully used for 16S rRNA amplification and real-time RT-PCR detection. It is concluded that labiase is useful for rapid lysis of a wide variety of Gram-positive bacteria and can be used for DNA/RNA isolation protocols.

Bacterial Outer Membrane Proteins↗
PubMed2005

Prevalence of Staphylococcus epidermidis strains with biofilm-forming ability in isolates from conjunctiva and facial skin.

PURPOSE: To compare the prevalence of biofilm-forming strains of Staphylococcus epidermidis in the conjunctival and facial skin microflora. DESIGN: Experimental study. METHODS: The prevalence of biofilm-forming ability of 10 S epidermidis strains obtained from the conjunctival sac of healthy volunteers was compared with 40 strains obtained from the facial skin of healthy volunteers. The ability to form biofilm was determined by the presence of the icaA gene, and the production of biofilm was examined by qualitative (Congo red agar [CRA]) and quantitative (microtiter plate) assays. Additionally, the prevalence of 36 S epidermidis strains obtained from the conjunctival sac of precataract patients to form biofilm was investigated. RESULTS: The icaA gene was detected in 60% of the isolates from the conjunctival sac of volunteers and 15% of those from the facial skin. Fifty percent of the isolates from the conjunctiva of volunteers and 5% from the facial skin were CRA positive. Biofilm production was significantly greater in isolates from the conjunctiva of volunteers. Of the nine pairs of isolates found in the same volunteers, six conjunctival sac isolates were positive for the icaA gene with biofilm-forming ability except one strain, whereas only one of the facial skin isolates was positive for the icaA gene and none exhibited biofilm-forming phenotype. Sixty-nine percent and 44% of the isolates from the conjunctival sac of precataract patients were positive for icaA gene and CRA test, respectively. CONCLUSIONS: The prevalence of biofilm-forming S epidermidis isolates is higher in the conjunctival sac than the facial skin.

Aged↗
PubMed2005

Differential effects of diethylcarbamazine, tetracycline and the combination on Brugia pahangi adult females in vitro.

Anti-filarial effects of diethylcarbamazine (DEC), tetracycline (TC) and the combination on Brugia pahangi adult females were studied in 7-day cell-free culture, in terms of microfilaria release, parasite motility, MTT assay for parasite viability and embryogram. TC 50 microg/ml (TC50) effectively reduced microfilaria release from day 1 of culture. Combined with DEC 100 microg/ml (DEC100) or DEC 500 microg/ml (DEC500), microfilaria release reduced further and synergistically. TC50 also reduced motility, but DEC100 and DEC500 did not. The combination of TC50 and DEC500 reduced motility synergistically. The MTT assay supported the results of motility study in general. The embryogram showed that only DEC500 reduced the total number of intrauterine embryos, especially ova, indicating that DEC500 inhibited early embryogenesis. TC50 did not affect the total number of embryos, but resulted in apparent accumulation of microfilariae in the uterus, suggesting that the drug inhibited release of microfilariae in this in vitro system. These results clarified different anti-female mechanisms between DEC and TC. A PCR-based study showed that endosymbiont bacteria, Wolbachia, in B. pahangi females decreased significantly after TC treatment. However, this study could not determine whether the effects of TC were direct or Wolbachia-mediated.

Animals↗
PubMed2005

High genetic similarity of Streptococcus agalactiae and Streptococcus difficilis: S. difficilis Eldar et al. 1995 is a later synonym of S. agalactiae Lehmann and Neumann 1896 (Approved Lists 1980).

The genetic relationship between Streptococcus agalactiae and Streptococcus difficilis was studied. S. difficilis was originally described as serologically non-typable but was later reported to be a group B, type Ib streptococcus. Upon comparative analysis of five gene sequences, it was found that S. agalactiae and S. difficilis are closely related. Sequence similarity values between these two species were 100.0 % for 16S rRNA, 99.6 % for gyrB, 98.6 % for sodA, 99.5 % for gyrA and 99.8 % for parC genes. These data strongly suggest that S. agalactiae and S. difficilis are synonyms. The biochemical characteristics of S. difficilis, which differ slightly from those of typical S. agalactiae, are similar to those of other group B, type Ib streptococci isolated from fish and frogs. Whole genome DNA-DNA hybridization values between the type strains of both species were greater than 78.6 %. On the basis of these data, it is proposed that S. difficilis is a later synonym of S. agalactiae.

Animals↗