サイキン ゲノム シークエンス

Bacteria exhibit unique biological characteristics at species or strain levels, and it has become possible to understand their diversities by analyzing whole genome sequences. Almost ２００ bacterial genome sequences have so far been published, and determination of the complete genomes of nearly５００bacteria is now in progress. Developments in sequencing technology and improvements in automated sequencers have contributed to the rapid accumulation of genome sequence data. Comparative analysis of bacterial genomes has revealed that there are extensive diversities in their structures such as linear chromosomes of Borrelia burgdorferi and two chromosomes of the genus Vibrio. The diversities have been established by a combination of horizontal gene transfer, gene duplication, deletion, and/or genomic rearrangements during the process of adaptation over a long period to each environment. These changes in bacterial genomes, especially in pathogenic bacteria, are related to the occurrence of novel types of infection or multi‐drug resistance. On the other hand, genomic analysis of a gut commensal, Bacteroides fragilis, has revealed that this species dynamically changes the genomic structure within a short period of time by multiple DNA inversions that create diverse surface antigenicities to evade the host immune system. Thus, whole genome sequencing provides important information on adaptation strategies of each bacterium. However, in an environmental ecosystem such as soil, water, and human microflora, a large number of bacteria interact with each other and comprise a functional unit. Community genomics, which targets all of the bacterial genome sequences included in a particular environmental ecosystem, is expected to provide novel insights into microbe‐microbe and hostmicrobe interactions

Infectious conjunctivitis caused by Pseudomonas aeruginosa isolated from a bathroom

Background: The elucidation of the routes of transmission of a pathogen is crucial for the prevention of infectious diseases caused by bacteria that are not a resident in human tissue. The purpose of this report is to describe a case of suture-related conjunctivitis caused by Pseudomonas aeruginosa for which we identified the transmission route using pulsed-field gel electrophoresis (PFGE). Case presentation: A 38-year-old man, who had undergone surgery for glaucoma 2 years ago previously, presented with redness, discomfort, and mucopurulent discharge in the right eye. A 9–0 silk suture had been left on the conjunctiva. A strain of P. aeruginosa was isolated from a culture obtained from the suture, and the patient was therefore diagnosed with suture-related conjunctivitis caused by P. aeruginosa. The conjunctivitis was cured by the application of an antimicrobial ophthalmic solution and removal of the suture. We used PFGE to survey of the indoor and outdoor environments around the patient’s house and office in order to elucidate the route of transmission of the infection. Three strains of P. aeruginosa were isolated from the patient’s indoor environment, and the isolate obtained from the patient’s bathroom was identical to that from the suture. Conclusion: The case highlights the fact that an indoor environmental strain of P. aeruginosa can cause ocular infections

Achromobacter buckle infection diagnosed by a 16S rDNA clone library analysis : a case report

Background: In clinical settings, bacterial infections are usually diagnosed by isolation of colonies after laboratory cultivation followed by species identification with biochemical tests. However, biochemical tests result in misidentification due to similar phenotypes of closely related species. In such cases, 16S rDNA sequence analysis is useful. Herein, we report the first case of an Achromobacter-associated buckle infection that was diagnosed by 16S rDNA sequence analysis. This report highlights the significance of Achromobacter spp. in device-related ophthalmic infections. Case presentation: A 56-year-old woman, who had received buckling surgery using a silicone solid tire for retinal detachment eighteen years prior to this study, presented purulent eye discharge and conjunctival hyperemia in her right eye. Buckle infection was suspected and the buckle material was removed. Isolates from cultures of preoperative discharge and from deposits on the operatively removed buckle material were initially identified as Alcaligenes and Corynebacterium species. However, sequence analysis of a 16S rDNA clone library using the DNA extracted from the deposits on the buckle material demonstrated that all of the 16S rDNA sequences most closely matched those of Achromobacter spp. We concluded that the initial misdiagnosis of this case as an Alcaligenes buckle infection was due to the unreliability of the biochemical test in discriminating Achromobacter and Alcaligenes species due to their close taxonomic positions and similar phenotypes. Corynebacterium species were found to be contaminants from the ocular surface. Conclusions: Achromobacter spp. should be recognized as causative agents for device-related ophthalmic infections. Molecular species identification by 16S rDNA sequence analysis should be combined with conventional cultivation techniques to investigate the significance of Achromobacter spp. in ophthalmic infections

ジアエンソサンナトリウムエキ ノ ユウコウ リヨウ ニ カンスル ケントウ

Sodium hypochlorite solution is cheap and powerful disinfectant widely used in hospitals and food industries. The bactericidal activity of chlorine solution is considered to depend on the amount of dissociated hypochlorite (HClO) in the solutions. The most important factor affecting the amount of HClO in the chroline solution is pH, and the decrease in pH increases the concentration of dissociated HClO. Alkaline solutions of both sodium and calcium hypochlorite contain only small amount (about 10% of free available chroline in these solution) of HClO. Recently, there are several reports showing the effectiveness of “acidic hypochlorite solution”, which is adjusted pH with hydrochloric acid (HCl) to 5.0, as a powerful disinfectant. However, special attention must be paid to handling and storage of HCl, and the increase of chlorine content in the solution by the addition of HCl might possibly induce toxic chlorine gas production. In this study, the bactericidal activity of acidic hypochlorite solutions, which have been adjusted to pH 5.0 with hydrochloric acid, acetic acid, citrate, lactate, formate, phosphate or sulphate, was investigated using various bacterial strains. The acidic hypochlorite solution prepared with acetic acid showed the equivalent bactericidal activity to that with hydrochloric acid and killed all of the Bacillus subtilis spores within 10 min. In addition, the acidic hypochlorite solution with acetic acid killed all of bacterial cells of Escherichia coli O157 : H 7, Legionella pneumophila, Pseudomonas aeruginosa, Salmonella Typhimurium and methicillin-resistant Staphylococcus aureus within 30 sec. On the other hand, the solutions prepared with citrate and lactate showed no bactericidal activity against any bacterial strains tested in this study despite of low pH. We proposed that acetic acid is a desirable acid to safely and easily prepare the acidic hypochlorite solution with the equivalent bactericidal activity to the solution prepared by HCl

Role of unbalanced growth of Gram-negative bacteria in ileal ulcer formation in rats treated with a nonsteroidal antiinflammatory drug

Nonsteroidal anti-inflammatory drugs (NSAIDs) induced formation of intestinal ulcers as side effects, in which an unbalanced increase in the number of Gram-negative bacteria in the small intestine plays an important role. To clarify how intestinal microflora are influenced by NSAIDs, we examined the effects of 5-bromo-2-(4-fluorophenyl)-3-(4-methylsulfonylphenyl) thiophene (BFMeT), an NSAID, on intestinal motility and on the growth of Escherichia coli and Lactobacillus acidophilus. Transit index, a marker of peristalsis, was not different in BFMeT-treated and solvent-treated rats, indicating that BFMeT increased the number of Gram-negative bacteria without suppression of peristalsis. The factors that affect the growth of intestinal bacteria were not found in intestinal contents of BFMeT-treated rats, because the growth of E. coli and that of L. acidophilus in the supernatants of small intestinal contents of BFMeT-treated rats and solvent-treated rats were not different. The mechanism of the increase in the number of Gram-negative bacteria is still unclear, but heat-killed E. coli cells and their purified lipopolysaccharide (LPS) caused deterioration of BFMeT-induced ileal ulcers, while they could not cause the ulcers by themselves without the NSAID. Concentration of LPS and myeloperoxidase activity level were elevated correlatively in the intestinal mucosa of rats treated with LPS and BFMeT. These results suggest that an increase in the number of Gramnegative bacteria and their LPS in the mucosa induces activation of neutrophils together with the help of NSAID action and causes ulcer formation

Activation of 1-nitropyrene by nitroreductase increases the DNA adduct level and mutagenicity

1-Nitropyrene (1-NP) is a mutagenic nitro compound in the environment. We studied correlations between the mutagenicity of 1-NP for three strains of Salmonella typhimurium, the activity of bacterial nitroreductases and the amount of 1-NP-derived DNA adducts. Bacterial strains used in this study were S. typhimurium strains TA98, nitroreductase-less mutant TA98NR and YG1021 carrying a nitroreductase-producing plasmid. The mutagenicity of 1-NP was measured using the Ames assay, and the nitroreductase activities of these strains were assayed by quantification of 1-aminopyrene produced from 1-NP. The DNA adducts were measured by the 32P-postlabeling method. Among the three bacterial strains, strain YG1021 was the highest in mutagenicity of 1-NP, the nitroreductase activity and the DNA adduct level. However, S. typhimurium strain TA98NR had the lowest values of these three parameters. Nitroreductase activity, DNA adduct level and mutagenicity were strongly correlated with each other. These results indicate that bacterial nitroreductase plays an important role in forming the DNA adducts, and that the higher the adduct level the higher the level of mutagenicity

Utilization of titanium oxide-like compound as an inorganic phosphate adsorbent for the control of serum phosphate level in chronic renal failure

Hyperphosphatemia adversely affects the prognosis of patients with chronic renal failure (CRF). We synthesized a titanium oxide-like compound (TAP) as a phosphate adsorbent for treatment of hyperphosphatemia in CFR patients. We evaluated the ability of TAP to adsorb inorganic phosphate in vitro and in vivo. TAP was shown to contain sulfate and hydroxyl groups by thermal analysis, which probably involved in phosphate adsorption through an ionic exchange mechanism. TAP constantly adsorbed phosphate (66.20-72.84 mg/g TAP) over a wide pH range (1.22-7.27) in vitro. To evaluate the phosphate binding potential of TAP in vivo, adenine-induced CRF rats were fed AIN-76 diet containing 3% TAP, 10% TAP, 3% sevelamer hydrochloride (clinical phosphate adsorbent), or 3% calcium carbonate, and serum levels of phosphate and calcium and urinary phosphate were compared with those in untreated CRF rats. Orally administered TAP showed the inhibitory effect on serum phosphate level in adenine-induced CRF rats, which was equivalent to that of sevelamer hydrochloride. These results indicate that TAP is a useful alternative phosphate-binder with fewer side effects than sevelamer hydrochloride and calcium carbonate

PCR-dot blot hybridization based on the neuraminidase-encoding gene is useful for detection of Bacteroides fragilis

Bacteroides fragilis is a Gram-negative obligate anaerobe frequently isolated from clinical specimens and sometimes causes severe septicemia in compromised hosts. Increasing interest has been shown in the enterotoxigenicity and drug resistance of B. fragilis in the field of medical microbiology. We previously reported rapid detection of this anaerobe by nested PCR targeting a neuraminidase-encoding gene nanH. In the present study, we synthesized a digoxigenin-labeled oligonucleotide probe, NH1,which is specific for nanH of B. fragilis, and we combined the hybridization assay using NH1with the nanH-PCR to detect this anaerobe in a bacteremia model mice. In the specificity test, the oligonucleotide probe, NH1, hybridized only to amplification products from B. fragilis. PCR-dot blot hybridization based on nanH enabled detection of cells of B. fragilis in blood samples even when the number was as low as 2x103colony-forming units/ml. These findings suggest that PCR-dot blot hybridization targeting nanH is a useful procedure for diagnosis of septicemia caused by B. fragilis when viable cells in blood cannot be detected by the traditional culture techniques

Porphyromonas gingivalis Outer Membrane Vesicles Stimulate Gingival Epithelial Cells to Induce Pro-Inflammatory Cytokines via the MAPK and STING Pathways

Porphyromonas gingivalis (Pg) is a keystone pathogen associated with chronic periodontitis and produces outer membrane vesicles (OMVs) that contain lipopolysaccharide (LPS), gingipains, and pathogen-derived DNA and RNA. Pg-OMVs are involved in the pathogenesis of periodontitis. Pg-OMV-activated pathways that induce the production of the pro-inflammatory cytokines, interleukin (IL)-6, and IL-8 in the human gingival epithelial cell line, OBA-9, were investigated. The role of mitogen-activated protein kinase (MAPK) and nuclear factor (NF)-κB in levels of Pg-OMV-induced pro-inflammatory cytokines was investigated using Western blot analysis and specific pathway inhibitors. Pg-OMVs induced IL-6 and IL-8 production via the extracellular signal-regulated kinase (Erk) 1/2, c-Jun N-terminal kinase (JNK), p38 MAPK, and NF-κB signaling pathways in OBA-9 cells. In addition, the stimulator of interferon genes (STING), an essential innate immune signaling molecule, was triggered by a cytosolic pathogen DNA. Pg-OMV-induced IL-6 and IL-8 mRNA expression and production were significantly suppressed by STING-specific small interfering RNA. Taken together, these results demonstrated that Pg-OMV-activated Erk1/2, JNK, p38 MAPK, STING, and NF-κB signaling pathways resulting in increased IL-6 and IL-8 expression in human gingival epithelial cells. These results suggest that Pg-OMVs may play important roles in periodontitis exacerbation by stimulating various pathways

D-Tagatose Effectively Reduces the Number of Streptococcus mutans and Oral Bacteria in Healthy Adult Subjects: A Chewing Gum Pilot Study and Randomized Clinical Trial

We examined the effect of D-Tagatose on the growth of oral bacteria including Streptococcus mutans (S. mutans). Saliva collected from 10 healthy volunteers was plated on BHI medium (to culture total oral bacteria) and MBS medium (to culture S. mutans, specifically). Agar plates of BHI or MBS containing xylitol or D-Tagatose were cultured under aerobic or anaerobic conditions. We then counted the number of colonies. In BHI plates containing D-Tagatose, a complete and significant reduction of bacteria occurred under both aerobic and anaerobic conditions. In MSB medium, significant reduction of S. mutans was also observed. We then performed a doubleblind parallel randomized trial with 19 healthy volunteers. They chewed gum containing xylitol, D-Tagatose, or both for 4 weeks, and their saliva was collected weekly and plated on BHI and MSB media. These plates were cultured under anaerobic conditions. Total bacteria and S. mutans were not effectively reduced in either the D-Tagatose or xylitol gum group. However, S. mutans was significantly reduced in volunteers chewing gum containing both D-Tagatose and xylitol. Thus, D-Tagatose inhibited the growth of S. mutans and many types of oral bacteria, indicating that D-Tagatose intake may help prevent dental caries, periodontitis, and many oral diseases