Biomedical subjects

Yoshiaki Kawamura

Publications and source records attributed to Yoshiaki Kawamura.

At least 19 recordsLinked to original sources

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↗

PubMed2006

Helicobacter cinaedi cellulitis and bacteremia in immunocompetent hosts after orthopedic surgery.

At various times after orthopedic operations (more than a few weeks, with an average of 29.9 days), 11 patients had a sudden onset of high temperature (average 38.9 degrees C) and local cellulitis at different sites on the operated sides. The wounds had completely healed, without complicated infections, when the cellulitis occurred. The clinical picture of cellulitis in all patients was atypical: diffuse salmon-pink skin color, local heat, swelling, spontaneous pain, and tenderness but no eruptions. No patient had any underlying immunocompromising conditions or had been given immunosuppressive agents. Gram-negative spiral bacteria were isolated from blood cultures and were identified as Helicobacter cinaedi on the basis of 16S rRNA gene sequencing and DNA-DNA hybridization using standard strains. By means of phylogenetic analysis, we divided these clinical isolates into two clones. The H. cinaedi strain isolated via fecal cultures from two patients without intestinal symptoms was the same clone as the blood isolate. All isolates were quite susceptible to various antibiotics, and clinical and inflammatory symptoms of bacteremia and cellulitis improved after treatment with penicillins and cephalosporins. A relatively high incidence of recurrence of the same disease was observed, however. Almost all patients responded immunologically to the infection, as evidenced by the production of serum antibody against H. cinaedi. We thus suggest that H. cinaedi should not be regarded as simply an opportunistic pathogen but that it may be a pathogen in immunocompetent hosts and may cause infections together with bacteremia and cellulitis.

Adult↗

PubMed2006

Physiological and serological variation in Streptococcus mitis biovar 1 from the human oral cavity during the first year of life.

OBJECTIVE: The purpose of the study was to explore the physiological and antigenic diversity of a large number of Streptococcus mitis biovar 1 isolates in order to begin to determine whether these properties contribute to species persistence. DESIGN: S. mitis biovar 1 was collected from four infants from birth to the first year of age. At each of eight to nine visits, 60 isolates each were obtained from the cheeks, tongue and incisors (once erupted) yielding 4440 in total. These were tested for production of neuraminidase, beta1-N-acetylglucosaminidase, beta1-N-acetylgalactosaminidase, IgA1 protease and amylase-binding. Antigenic diversity was examined by ELISA and Western immunoblotting using antisera raised against S. mitis biovar 1 NCTC 12261(T) and SK145. RESULTS: Three thousand three hundred and thirty (75%) of the isolates were identified as S. mitis biovar 1 and 3144 (94.4%) could be divided into four large phenotypic groups based on glycosidase production. Fifty-four percent of the isolates produced IgA1 protease, but production was disproportionate among the phenotypes. Between one-third and one-half of the strains of each phenotype bound salivary alpha-amylase. Antisera against strains NCTC 12261(T) and SK145 displayed different patterns of reactivity with randomly selected representatives of the four phenotypes. CONCLUSIONS: S. mitis biovar 1 is physiologically and antigenically diverse, properties which could aid strains in avoiding host immunity and promote re-colonization of a habitat or transfer to a new habitat.

Antigens, Bacterial↗

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

Use of DNA arrays to identify a mutation in the negative regulator, csrR, responsible for the high virulence of a naturally occurring type M3 group A streptococcus clinical isolate.

We previously reported that type M3 group A streptococcus (GAS) showed a wide range of 50% lethal dose values in mice. Analysis using DNA arrays indicated that the most virulent strain, M3-f, expressed significantly higher levels of the products of several virulence genes than did the other M3 isolates. Sequencing of the csrS, csrR, luxS, and rgg genes in the isolates showed that the M-3f csrR gene contained a specific point mutation. Disruption of wild-type (wt) csrR in an M3 strain increased its virulence and the expression of hyaluronic acid, whereas complementation with wt but not type M3-f csrR attenuated these changes. Expression experiments showed that type M3-f CsrR counteracted the effects of wt CsrR. Although wt CsrR bound to the hasA promoter region, type M3-f CsrR did not. Thus, the high virulence of the type M3-f strain is associated with the decreased binding of type M3-f CsrR to its target sequences.

Amino Acid Sequence↗

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

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

Capsule of Streptococcus pyogenes is essential for delayed death of mice in a model of streptococcal toxic shock syndrome.

We have previously reported a mouse model of severe group A streptococcal infection (Microbiol. Immunol. 45: 777-786, 2001). When we injected Streptococcus pyogenes strains intramuscularly, the mice suffered from acute phase of infection for a few days but recovered from the illness and gained body weight. These mice, however, began to die after 3 weeks of infection, which we called 'delayed death.' Bacterial strains isolated from organs of the dead mice showed thick capsules. We, therefore, constructed a hyaluronic acid capsule gene, hasA, knockout mutant by homologous recombination and the effect of capsule on the death was observed. hasA knockout strain did not cause delayed death, though it caused acute death at high doses of infection. According to this result, the capsule is a critical pathogenic factor for causing the delayed death in our mouse model.

Animals↗

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↗

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

Postoperative low-grade endophthalmitis caused by biofilm-producing coccus bacteria attached to posterior surface of intraocular lens.

We report a case of low-grade inflammation that developed in the anterior segment after cataract extraction with intraocular lens (IOL) implantation. The 57-year-old patient complained of blurred vision 2 weeks after phacoemulsification and IOL implantation in the right eye. Slitlamp biomicroscopy showed many nonpigmented keratoprecipitates. After antibiotic therapy failed, the IOL was removed and aqueous collected. Scanning electron microscopy of the IOL demonstrated many biofilm-producing cocci with slime on the IOL, and aqueous smears showed gram-positive cocci. Two weeks after removal of the IOL, the inflammation disappeared.

Aqueous Humor↗

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↗

PubMed2005

Paenibacillus motobuensis sp. nov., isolated from a composting machine utilizing soil from Motobu-town, Okinawa, Japan.

A novel bacterial strain, MC10(T), was isolated from a compost sample produced in a composting machine utilizing soil from Motobu-town, Okinawa, Japan. The isolate was Gram-negative, but produced endospores. These conflicting characters prompted a taxonomic study of the isolate. The isolate was examined using a combination of phenotypic characterization, cellular fatty acid analysis, DNA base composition determination and 16S rRNA gene sequence analysis. Phylogenetic analysis, based on 16S rRNA gene sequence comparisons, placed strain MC10(T) within the genus Paenibacillus. As in other Paenibacillus species, the isolate contained anteiso-C(15:0) as the major fatty acid and the DNA G+C content was 47.0 mol%. However, 16S rRNA gene sequence similarity values of less than 95.6% were found between this isolate and all members of the genus Paenibacillus. Based upon these results, strain MC10(T) (=GTC 1835(T)=JCM 12774(T)=CCUG 50090(T)) should be designated as the type strain of a novel species within the genus Paenibacillus, Paenibacillus motobuensis sp. nov.

Bacterial Typing Techniques↗

PubMed2005

Quantitative microarray-based DNA-DNA hybridization assay for measuring genetic distances among bacterial species and its application to the identification of family Enterobacteriaceae.

Quantitative DNA-DNA hybridization to measure the genetic distances among bacterial species is indispensable for taxonomical determination. In the current studies, we developed a method to determine bacterial DNA relatedness on a glass microarray. Reference DNAs representing a total 93 species of Enterobacteriaceae were arrayed on a glass microplate, and signal intensities were measured after 2 hr of hybridization with Cy3-labeled bacterial DNAs. All immobilized DNAs from members of the family Enterobacteriaceae were identified by this method except for DNAs from Yersinia pseudotuberculosis and Y. pestis. These results suggest that quantitative microarray hybridization could be an alternative to conventional DNA-DNA hybridization for measuring chromosome relatedness among bacterial species.

DNA, Bacterial↗