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Okubo Torahiko

Faculty of Health Sciences　Health Sciences　Medical Laboratory ScienceLecturer

【研究対象】
(1) 原生生物と細菌の相互作用：野外環境中では、多くの微生物同士が相互作用しながら棲息していると考えられます。そうした中で、病原性細菌や薬剤耐性菌などの医療上重要な細菌の生存・拡散に寄与する可能性を検証します。実施例；アメーバによる細菌運搬現象、繊毛虫による薬剤耐性プラスミド接合伝達促進作用
(2) バイオエアロゾル：都市環境の空気中に浮遊する細菌叢の解析を行なっています。
(3) 薬剤耐性菌：大学病院検査室と協力し、薬剤耐性菌の解析を行なっています。
(4) 海外研究：アフリカ ウガンダ共和国における家畜由来薬剤耐性菌の調査を行なっています。（中部大学他との共同研究）

Researcher basic information

■ Degree
  • 博士(獣医学), 酪農学園大学大学院
■ URL
researchmap URLホームページURL■ Various IDs
Researcher number
  • 90762196
J-Global ID■ Research Keywords and Fields
Research Keyword
  • Desiccation tolerance
  • Chlamydia trachomatis
  • Legionella pneumophila
  • Protozoa
  • bio-aerosol
  • Antimicrobial Resistant Bacteria
  • Veterinary Medicine
  • Bacteriology
Research Field
  • Life Science, Hygiene and public health: excluding laboratory approach
  • Life Science, Hygiene and public health: excluding laboratory approach
  • Life Science, Hygiene and public health: including laboratory approach
  • Others, Others, Laboratory medicine
  • Life Science, Bacteriology
  • Life Science, Ecology and environment
■ Educational Organization

Career

■ Career
Career
  • Apr. 2018 - Present
    Faculty of Health Sciences, Hokkaido University, Department of Medical Laboratory Sciences, Lecturer
  • May 2015 - Mar. 2018
    Faculty of Health Sciences, Hokkaido University, Department of Medical Laboratory Science, Research associate
Educational Background
  • Apr. 2011 - Mar. 2015, Rakuno Gakuen University Graduate School, Faculty of Veterinary Medicine, Department of Veterinary Medicine
  • Apr. 2005 - Mar. 2011, Rakuno Gakuen University, Faculty of Veterinary Medicine, Department of Veterinary Medicine
  • Apr. 2002 - Mar. 2005, 東京都立国立高等学校

Research activity information

■ Awards
  • Aug. 2017, 第84回日本細菌学会北海道支部学術総会, 優秀賞
    札幌地下歩行空間での空気中浮遊細菌の菌叢解析
    大久保寅彦;松尾淳司;大崎敬子;神谷茂;山口博之
  • Sep. 2016, 第83回日本細菌学会北海道支部学術総会, 優秀賞
    北海道大学病院にて分離されたニューデリー・メタロβラクタマーゼNDM-5産生大腸菌の性状解析
    大久保寅彦;松尾淳司;山口博之
  • Sep. 2015, 第82回日本細菌学会北海道支部学術総会, 最優秀賞
    繊毛虫との共培養で大腸菌から漏れ出す クオラムセンシング分子 autoinducer-2 について
    大久保寅彦;松尾淳司;山﨑智拡;花輪智子;中村眞二;神谷茂;山口博之
■ Papers
  • Exploring potential targets of Chlamydia trachomatis required for cellular adaptation through screening approved-drug libraries
    Ruiyu Li; Saicheng Zhang; Satoko Otsuguro; Akira Matsuda; Sora Kuroiwa; Tsubasa Tatsumiya; Jeewan Thapa; Torahiko Okubo; Katsumi Maenaka; Yuichi Takizawa; Hideaki Higashi; Hiroyuki Yamaguchi
    Next Research, 5, 101318, 101318, Elsevier BV, Mar. 2026
    Scientific journal
  • Symbiont- and Bacterial Cell Size-dependent Backpacking and Grazing of Acanthamoeba.
    Nana Tanaka; Kotoka Kuriki; Torahiko Okubo; Yoshiaki Enoeda; Ayano Konno; Shinji Nakamura; Toyotaka Sato; Shin-Ichi Yokota; Hiroyuki Yamaguchi
    Microbes and environments, 41, 1, 2026, [Domestic magazines]
    English, Scientific journal, On solid media, Acanthamoeba harboring the endosymbiotic bacterium (Neochlamydia) carries live Escherichia coli on its cell surface without phagocytosing this bacterium, and defends against infection by Legionella pneumophila of a small size in an endosymbiotic bacterium-dependent manner. This implies the presence of an unknown protective mechanism. Therefore, we exami-ned the physical properties of the carried bacteria using transposon insertion mutants that had lost the "backpack" on solid media. A mutant was selected from a library in which the nhaA gene, encoding a Na+/H+ antiporter, was disrupted. The knockout mutant was longer than the parental strain and was gradually consumed by symbiotic amoebae. Similarly, the NhaA-knockout mutant strain was longer and lacked the backpack. The complementation of nhaA restored bacterial cells to their normal size, and the backpack phenomenon reappeared. Using E. coli elongated by a treatment with mitomycin C, the backpack was not evident, and enlarged bacteria were consumed by symbiotic amoebae. Therefore, symbiotic amoebae protected themselves from intruders by not engulfing small bacteria in an endosymbiosis-dependent manner. The present results propose a novel countermeasure by phagocytic cells against intruders that involves the recognition of bacterial sizes and is dependent on endosymbiosis.
  • Chlamydia trachomatis L2 434/Bu readily activates glycolysis under hypoxia for efficient metabolism
    Ruiyu Li; Saicheng Zhang; Satoko Otsuguro; Manabu Nagao; Akira Matsuda; Jeewan Thapa; Torahiko Okubo; Katsumi Maenaka; Hideaki Higashi; Hiroyuki Yamaguchi
    Biochemical and Biophysical Research Communications, 150461, 150461, Elsevier BV, Aug. 2024
    Scientific journal
  • Differential impact of environmental factors on airborne live bacteria and inorganic particles in an underground walkway.
    Hiroyuki Yamaguchi; Torahiko Okubo; Eriko Nozaki; Takako Osaki
    PloS one, 19, 3, e0300920, 2024, [International Magazine]
    English, Scientific journal, We previously reported that variations in the number and type of bacteria found in public spaces are influenced by environmental factors. However, based on field survey data alone, whether the dynamics of bacteria in the air change as a result of a single environmental factor or multiple factors working together remains unclear. To address this, mathematical modeling may be applied. We therefore conducted a reanalysis of the previously acquired data using principal component analysis (PCA) in conjunction with a generalized linear model (Glm2) and a statistical analysis of variance (ANOVA) test employing the χ2 distribution. The data used for the analysis were reused from a previous public environmental survey conducted at 8:00-20:00 on May 2, June 1, and July 5, 2016 (regular sampling) and at 5:50-7:50 and 20:15-24:15 on July 17, 2017 (baseline sampling) in the Sapporo underground walking space, a 520-meter-long underground walkway. The dataset consisted of 60 samples (22 samples for "bacterial flora"), including variables such as "temperature (T)," "humidity (H)," "atmospheric pressure (A)," "traffic pedestrians (TP)," "number of inorganic particles (Δ5: 1-5 μm)," "number of live airborne bacteria," and "bacterial flora." Our PCA with these environmental factors (T, H, A, and TP) revealed that the 60 samples could be categorized into four groups (G1 to G4), primarily based on variations in PC1 [Loadings: T(-0.62), H(-0.647), TP(0.399), A(0.196)] and PC2 [Loadings: A(-0.825), TP(0.501), H(0.209), T(-0.155)]. Notably, the number of inorganic particles significantly increased from G4 to G1, but the count of live bacteria was highest in G2, with no other clear pattern. Further analysis with Glm2 indicated that changes in inorganic particles could largely be explained by two variables (H/TP), while live bacteria levels were influenced by all explanatory variables (TP/A/H/T). ANOVA tests confirmed that inorganic particles and live bacteria were influenced by different factors. Moreover, there were minimal changes in bacterial flora observed among the groups (G1-G4). In conclusion, our findings suggest that the dynamics of live bacteria in the underground walkway differ from those of inorganic particles and are regulated in a complex manner by multiple environmental factors. This discovery may contribute to improving public health in urban settings.
  • Mastitis on selected farms in Wakiso district, Uganda: Burden, pathogens and predictors of infectivity of antimicrobial resistant bacteria in dairy herds.
    Steven Kakooza; Francis Mutebi; Paul Ssajjakambwe; Eddie Wampande; Esther Nabatta; Collins Atuheire; Sayaka Tsuchida; Torahiko Okubo; Kazunari Ushida; John Baligwamunsi Kaneene
    Veterinary medicine and science, 9, 5, 2376, 2385, Sep. 2023, [International Magazine]
    English, Scientific journal, BACKGROUND: Mastitis and associated antimicrobial resistance (AMR) are major challenges to the dairy industry worldwide. OBJECTIVE: This study aimed to expose the mastitis burden, causative bacteria and drivers for mastitis-causing multi-drug-resistant (MDR) Staphylococci infectivity in cows on dairy farms in Wakiso district, Uganda. METHODS: On 22 farms, practices were documented using questionnaires, and 175 cows were screened by the California mastitis test. Composite milk samples from the positive reactors were submitted to the laboratory for bacterial culture testing. Antimicrobial sensitivity testing by the Kirby Bauer disc diffusion method was done only on Staphylococci with a panel of 10 antimicrobials of clinical relevance. RESULTS: Mastitis was detected in 80.6% (n = 141) of the 175 sampled cows, of which sub-clinical mastitis (76.0%: n = 133) was predominant. The Chi-squared analysis hypothesized that cow age (p = 0.017), sub-county (p = 0.013), parity (p < 0.0001), sex of farm owner (p = 0.003), farm duration in dairy production (p = 0.048) and the use of milking salve (p = 0.006) were associated with mastitis. Coagulase-negative Staphylococci were the most prevalent (71.4%; n = 95), followed by Staphylococcus aureus (30.1%, n = 40). Staphylococci (76.3%; n = 135) were majorly resistant to penicillin and tetracycline. Only one isolate was phenotyped as a methicillin-resistant Staphylococcus specie (MRSS). The prevalences of MDR strains at cow and isolate level were 6.3% and 8.3%. The major MDR phenotype identified was penicillin-tetracycline-trimethoprim-sulphamethoxazole. The isolate detected as an MRSS exhibited the broadest MDR pattern. Cow parity was identified as a predictor of infectivity of mastitis-causing MDR Staphylococci in dairy herds. CONCLUSION: The high prevalence of mastitis and associated pathogen AMR found exposes possibilities of economic losses for the dairy sector warranting the need for farmer sensitization on the institution of proper mastitis prevention and control programs, with emphasis on milking hygiene practices and routine disease monitoring.
  • Chlamydia trachomatis relies on the scavenger role of aryl hydrocarbon receptor with detyrosinated tubulin for its intracellular growth, but this is impaired by excess indole
    Saicheng Zhang; Yuki Funahashi; Satoho Tanaka; Torahiko Okubo; Jeewan Thapa; Shinji Nakamura; Hideaki Higashi; Hiroyuki Yamaguchi
    Microbes and Infection, 25, 5, 105097, 105097, Elsevier BV, Jun. 2023
    Scientific journal
  • The fecal microbiomes analysis of Marabou storks (Leptoptilos crumenifer) reveals their acclimatization to the feeding environment in the Kampala urban areas, Uganda.
    Sayaka Tsuchida; Atsushi Ueda; Steven Kakooza; Torahiko Okubo; Eddie M Wampande; Takuji Yamada; Kazunari Ushida
    The Journal of veterinary medical science, 85, 4, 450, 458, 30 Mar. 2023, [Domestic magazines]
    English, Scientific journal, The Marabou stork (Leptoptilos crumenifer) is a typical scavenging bird and adapted to the Savannah environment, where they show a carnivorous feeding style. However, Marabou stork recently penetrated into the city areas and acclimatized to the urban environment, where they modified their feeding habits to an omnivorous type toward more carbohydrate. To reveal their adaptation to the variable feeding customs, this study compared the gut microbiomes and chemical compositions of feces of Marabou storks inhabiting two different locations in peri urban Kampala: one is a slaughter house floc that predicted their original carnivorous feeding, and the other is a landfill floc that adapted more to the omnivorous feeding. 16S rRNA gene sequencing analysis revealed more diverse gut microbiome, more enriched Lactobacilli, and less abundant Peptostreptococci in the landfill flock comparing to the slaughter house flock. Isolation work and predicted metagenome analysis confirmed more diverse Lactobacilli and more enriched functions for carbohydrate metabolism in the landfill flock. In addition, chemical composition of feces revealed higher ammonia in the former, which is consisting with higher Peptostreptococci and their practice of carnivorous feeding. These results highlighted their adaptation to the variable feeding environment, which presumably protects their health and ensure survival of species.
  • Human pathogenic bacteria on high-touch dry surfaces can be controlled by warming to human-skin temperature under moderate humidity.
    Ayano Konno; Torahiko Okubo; Yoshiaki Enoeda; Tomoko Uno; Toyotaka Sato; Shin-Ichi Yokota; Rika Yano; Hiroyuki Yamaguchi
    PloS one, 18, 9, e0291765, 2023, [International Magazine]
    English, Scientific journal, Healthcare-associated infections have become a major health issue worldwide. One route of transmission of pathogenic bacteria is through contact with "high-touch" dry surfaces, such as handrails. Regular cleaning of surfaces with disinfectant chemicals is insufficient against pathogenic bacteria and alternative control methods are therefore required. We previously showed that warming to human-skin temperature affected the survival of pathogenic bacteria on dry surfaces, but humidity was not considered in that study. Here, we investigated environmental factors that affect the number of live bacteria on dry surfaces in hospitals by principal component analysis of previously-collected data (n = 576, for CFU counts), and experimentally verified the effect of warming to human-skin temperature on the survival of pathogenic bacteria on dry surfaces under humidity control. The results revealed that PCA divided hospital dry surfaces into four groups (Group 1~4) and hospital dry surfaces at low temperature and low humidity (Group 3) had much higher bacterial counts as compared to the others (Group 1 and 4) (p<0.05). Experimentally, warming to human-skin temperature (37°C with 90% humidity) for 18~72h significantly suppressed the survival of pathogenic bacteria on dry surfaces, such as plastic surfaces [p<0.05 vs. 15°C (Escherichia coli DH5α, Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, and blaNDM-5 E. coli)] or handrails [p<0.05 vs. 15~25°C (E. coli DH5α, S. aureus, P. aeruginosa, A. baumannii)], under moderate 55% humidity. Furthermore, intermittent heating to human-skin temperature reduced the survival of spore-forming bacteria (Bacillus subtilis) (p<0.01 vs. continuous heating to human-skin temperature). NhaA, an Na+/H+ antiporter, was found to regulate the survival of bacteria on dry surfaces, and the inhibitor 2-aminoperimidine enhanced the effect of warming at human-skin temperature on the survival of pathogenic bacteria (E. coli DH5α, S. aureus, A. baumannii) on dry surfaces. Thus, warming to human-skin temperature under moderate humidity is a useful method for impairing live pathogenic bacteria on high-touch surfaces, thereby helping to prevent the spread of healthcare-associated infections.
  • One Health Approachに基づいたフルオロキノロン耐性大腸菌の市中内拡散・定着様式の解明
    佐藤 豊孝; 立花 徹; 玉井 聡; 星野 祐治; 鳥越 慎吾; 榊原 啓一郎; 前谷 茂樹; 福田 昭; 大久保 寅彦; 臼井 優; 高橋 聡; 横田 伸一; 田村 豊; 堀内 基広
    日本獣医学会学術集会講演要旨集, 165回, [F2A, 10], (公社)日本獣医学会, Sep. 2022
    Japanese
  • Chlamydia trachomatis L2/434/Bu Favors Hypoxia for its Growth in Human Lymphoid Jurkat Cells While Maintaining Production of Proinflammatory Cytokines
    Ryoya Tsujikawa; Jeewan Thapa; Torahiko Okubo; Shinji Nakamura; Saicheng Zhang; Yoshikazu Furuta; Hideaki Higashi; Hiroyuki Yamaguchi
    Current Microbiology, 79, 9, Springer Science and Business Media LLC, Sep. 2022
    Scientific journal
  • Chlamydia trachomatis Requires Functional Host-Cell Mitochondria and NADPH Oxidase 4/p38MAPK Signaling for Growth in Normoxia
    Jeewan Thapa; Gen Yoshiiri; Koki Ito; Torahiko Okubo; Shinji Nakamura; Yoshikazu Furuta; Hideaki Higashi; Hiroyuki Yamaguchi
    Frontiers in Cellular and Infection Microbiology, 12, Frontiers Media SA, 26 May 2022
    Scientific journal, Chlamydia trachomatis (Ct) is an intracellular energy-parasitic bacterium that requires ATP derived from infected cells for its growth. Meanwhile, depending on the O2 concentration, the host cells change their mode of ATP production between oxidative phosphorylation in mitochondria (Mt) and glycolysis; this change depends on signaling via reactive oxygen species (ROS) produced by NADPH oxidases (NOXs) as well as Mt. It has been proposed that Ct correspondingly switches its source of acquisition of ATP between host-cell Mt and glycolysis, but this has not been verified experimentally. In the present study, we assessed the roles of host-cell NOXs and Mt in the intracellular growth of CtL2 (L2 434/Bu) under normoxia (21% O2) and hypoxia (2% O2) by using several inhibitors of NOXs (or the downstream molecule) and Mt-dysfunctional (Mtd) HEp-2 cells. Under normoxia, diphenyleneiodonium, an inhibitor of ROS diffusion, abolished the growth of CtL2 and other Chlamydiae (CtD and C. pneumoniae). Both ML171 (a pan-NOX inhibitor) and GLX351322 (a NOX4-specific inhibitor) impaired the growth of CtL2 under normoxia, but not hypoxia. NOX4-knockdown cells diminished the bacterial growth. SB203580, an inhibitor of the NOX4-downstream molecule p38MAPK, also inhibited the growth of CtL2 under normoxia but not hypoxia. Furthermore, CtL2 failed to grow in Mtd cells under normoxia, but no effect was observed under hypoxia. We conclude that under normoxia, Ct requires functional Mt in its host cells as an ATP source, and that this process requires NOX4/p38MAPK signaling in the host cells. In contrast to hypoxia, crosstalk between NOX4 and Mt via p38MAPK may be crucial for the growth of Ct under normoxia.
  • アメーバによる共生細菌依存的な細菌運搬現象のメカニズムの検証
    大久保 寅彦; 佐藤 豊孝; 横田 伸一; 中村 眞二; 山口 博之; 田中 菜那
    日本細菌学雑誌, 77, 1, 64, 64, 日本細菌学会, Feb. 2022
    Japanese
  • Wild ciliates differ in susceptibility to Legionella pneumophila JR32.
    Airi Kawashiro; Torahiko Okubo; Shinji Nakamura; Jeewan Thapa; Masaki Miyake; Hiroyuki Yamaguchi
    Microbiology (Reading, England), 167, 8, Aug. 2021, [Peer-reviewed], [International Magazine]
    English, Scientific journal, We investigated how Legionella pneumophila (Lp) JR32 interacts with Anteglaucoma CS11A and Colpoda E6, two ciliates that we isolated from sewage and sink trap sludge, respectively, using a handmade maze device containing a 96-well crafting plate. Our 18S rDNA-based phylogenetic analysis showed that Anteglaucoma CS11A and Colpoda E6 formed distinct clades. Scanning electron microscopy showed that Anteglaucoma CS11A had a bigger-sized body than Colpoda E6 and, unlike Tetrahymena IB (the reference strain), neither ciliate produced pellets, which are extracellular vacuoles. Fluorescence microscopic observations revealed that although the intake amounts differed, all three ciliates rapidly ingested LpJR32 regardless of the presence or absence of the icm/dot virulence genes, indicating that they all interacted with LpJR32. In co-cultures with Anteglaucoma CS11A, the LpJR32 levels were maintained but fell dramatically when the co-culture contained the LpJR32 icm/dot deletion mutant instead. Anteglaucoma CS11A died within 2 days of co-culture with LpJR32, but survived co-culture with the deletion mutant. In co-cultures with Colpoda E6, LpJR32 levels were maintained but temporarily decreased independently of the virulence gene. Concurrently, the Colpoda E6 ciliates survived by forming cysts, which may enable them to resist harsh environments, and by diminishing the sensitivity of trophozoites to Lp. In the Tetrahymena IB co-cultures with LpJR32 or Δicm/dot, the Lp levels were maintained, albeit with temporal decreases, and the Tetrahymena IB levels were also maintained. We conclude that unlike Tetrahymena IB with pellet production, Anteglaucoma CS11A can be killed by LpJR32 infection, and Colpoda E6 can resist LpJR32 infection through cyst formation and the low sensitivity of trophozoites to Lp. Thus, the two ciliates that we isolated had different susceptibilities to LpJR32 infection.
  • Usefulness of a 3D-printing air sampler for capturing live airborne bacteria and exploring the environmental factors that can influence bacterial dynamics.
    Saaya Mori; Sakura Ishiguro; Satoru Miyazaki; Torahiko Okubo; Ryosuke Omori; Ayako Kai; Kyohei Sugiyama; Airi Kawashiro; Masato Sumi; Jeewan Thapa; Shinji Nakamura; Chietsugu Katoh; Hiroyuki Yamaguchi
    Research in microbiology, 172, 6, 103864, 103864, 14 Jul. 2021, [Peer-reviewed], [International Magazine]
    English, Scientific journal, We created a handmade 3D-printed air sampler to effectively collect live airborne bacteria, and determined which environmental factors influenced the bacteria. Bacterial colony forming units (CFUs) in the air samples (n=37) were monitored by recording the environmental changes occurring over time, then determining the presence/absence of correlations among such changes. The bacterial CFUs changed sharply and were significantly correlated with the DNA concentrations, indicating that the captured bacteria made up most of the airborne bacteria. Spearman's rank correlation analysis revealed significant correlations between the bacterial CFU values and some environmental factors (humidity, wind speed, insolation, and 24-h rainfall). Similarly the significant associations of CFU with humidity and wind speed were also found by multiple regression analysis with box-cox transformation. Among our panel of airborne bacteria (952 strains), 70 strains were identified as soil-derived Bacillus via the production of Escherichia coli- and Staphylococcus aureus-growth inhibiting antibiotics and by 16S rDNA typing. Soil-derived protozoa were also isolated from the air samples. We conclude that the airborne bacteria mainly derived from soil can alter in number according to environmental changes. Our sampler, which was created by easy-to-customize 3D printing, is a useful device for understanding the dynamics of live airborne bacteria.
  • A retrospective analysis of antimicrobial resistance in pathogenic Escherichia coli and Salmonella spp. isolates from poultry in Uganda.
    Steven Kakooza; Adrian Muwonge; Esther Nabatta; Wilfred Eneku; Dickson Ndoboli; Eddie Wampande; Damian Munyiirwa; Edrine Kayaga; Maria Agnes Tumwebaze; Mathias Afayoa; Paul Ssajjakambwe; Dickson Stuart Tayebwa; Sayaka Tsuchida; Torahiko Okubo; Kazunari Ushida; Ken'ichi Sakurai; Francis Mutebi
    International journal of veterinary science and medicine, 9, 1, 11, 21, 19 May 2021, [Peer-reviewed], [International Magazine]
    English, Scientific journal, There are increasing reports of antimicrobial treatment failures for bacterial diseases of poultry in Uganda. The paucity of data on antimicrobial resistance (AMR) of pathogenic bacteria in Uganda is a major setback to AMR control. This study investigated the occurrence of fowl typhoid, colibacillosis, and AMR in associated pathogens from 2012 to 2018. Laboratory records from the Central Diagnostic Laboratory (CDL), a National Veterinary Diagnostic Facility located at Makerere University, were reviewed. Archived isolates of the causative bacteria for the two diseases were also evaluated for AMR. The frequencies of the two disease conditions, their clinical and necropsy presentations and the demographic data of the diagnostic samples were summarized from the records. Archived bacterial isolates were revived before antimicrobial susceptibility testing. This was done on Mueller Hinton agar using the disk diffusion method, against 16 antimicrobials of medical and veterinary importance according to the Clinical Laboratory Standards Institute guidelines. A total of 697 poultry cases were presented for bacteriological investigations in the review period. Colibacillosis and salmonellosis had prevalence rates of 39.7% (277/697) and 16.2% (113/697), respectively. A total of 63 and 92 isolates of Escherichia coli and Salmonella spp., respectively, were archived but 43 (68.3%) E. coli and 47 (51.1%) Salmonella spp. isolates were recovered and evaluated for AMR. Multidrug resistance was more frequent in E. coli (38; 88.4%) than salmonellae (25; 53.2%), (p < 0.001). The high prevalence of colibacillosis, salmonellosis and the AMR of associated pathogens warrants immediate institution of appropriate disease control measures.
  • Distribution of amoebal endosymbiotic environmental chlamydia Neochlamydia S13 via amoebal cytokinesis.
    Miho Okude; Junji Matsuo; Tomohiro Yamazaki; Kentaro Saito; Yoshikazu Furuta; Shinji Nakamura; Jeewan Thapa; Torahiko Okubo; Hideaki Higashi; Hiroyuki Yamaguchi
    Microbiology and immunology, 65, 3, 115, 124, Mar. 2021, [Peer-reviewed], [International Magazine]
    English, Scientific journal, We previously isolated a symbiotic environmental amoeba, harboring an environmental chlamydia, Neochlamydia S13. Interestingly, this bacterium failed to survive outside of host cells and was immediately digested inside other amoebae, indicating bacterial distribution via cytokinesis. This may provide a model for understanding organelle development and chlamydial pathogenesis and evolution; therefore, we assessed our hypothesis of Neochlamydia S13 distribution via cytokinesis by comparative analysis with other environmental Chlamydiae (Protochlamydia R18 and Parachlamydia Bn9 ). Dual staining with 4',6-diamidino-2-phenylindole and phalloidin revealed that the progeny of Neochlamydia S13 and Protochlamydia R18 existed in both daughter cells with a contractile ring on the verge of separation. However, in contrast to other environmental Chlamydiae, little Neochlamydia S13 16S ribosomal DNA was amplified from the culture supernatant. Interestingly, Neochlamydia S13 failed to infect aposymbiotic amoebae, indicating an intimate interaction with the host cells. Furthermore, its infectious rates in cultures expanded from a single amoeba were always maintained at 100%, indicating distribution via cytokinesis. We concluded that unlike other environmental Chlamydiae, Neochlamydia S13 has a unique ability to divide its progeny only via host amoebal cytokinesis. This may be a suitable model to elucidate the mechanism of cell organelle distribution and of chlamydial pathogenesis and evolution.
  • 共生細菌依存的にアメーバに起こる細菌運搬現象には運ばれる細菌のNa+/H+アンチポーターNhaAが関与する
    田中 菜那; 大久保 寅彦; 佐藤 豊孝; 横田 伸一; タパ・ジーワン; 山口 博之
    日本細菌学雑誌, 76, 1, 68, 68, 日本細菌学会, Feb. 2021
    Japanese
  • Na+/H+アンチポーター(NhaA)は大腸菌の乾燥抵抗性を規定する
    榎枝 秀朗; 田中 菜那; 大久保 寅彦; 佐藤 豊孝; 横田 伸一; タパ・ジーワン; 山口 博之
    日本細菌学雑誌, 76, 1, 71, 71, 日本細菌学会, Feb. 2021
    Japanese
  • Isolation and Characterization of Antimicrobial-Resistant Escherichia coli from Retail Meats from Roadside Butcheries in Uganda.
    Torahiko Okubo; Montira Yossapol; Shiori Ikushima; Steven Kakooza; Eddie M Wampande; Tetsuo Asai; Sayaka Tsuchida; Kenji Ohya; Fumito Maruyama; John D Kabasa; Kazunari Ushida
    Foodborne pathogens and disease, 17, 11, 666, 671, Nov. 2020, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Retail meats are one of the main routes for spreading antimicrobial-resistant bacteria (ARB) from livestock to humans through the food chain. In African countries, retail meats are often sold at roadside butcheries without chilling or refrigeration. Retail meats in those butcheries are suspected to be contaminated by ARB, but it was not clear. In this study, we tested for the presence of antimicrobial-resistant Escherichia coli from retail meats (n = 64) from roadside butcheries in Kampala, Uganda. The meat surfaces were swabbed and inoculated on PetriFilm SEC agar to isolate E. coli. We successfully isolated E. coli from 90.6% of these retail meat samples. We identified the phylogenetic type, antimicrobial susceptibility, and antimicrobial resistance genes prevalence between retail meat isolates (n = 89). Phylogenetic type B1 was identified from 70.8% of the retail meat isolates, suggesting that the isolates originated primarily from fecal contamination during meat processing. Tetracycline (TET)-resistant isolates with tetA and/or tetB gene(s) were the most frequently detected (28.1%), followed by ampicillin (AMP) resistance genes with blaTEM (15.7%,) and sulfamethoxazole-trimethoprim (SXT) resistance genes with sul2 (15.7%). No extended-spectrum beta-lactamase-producing isolates were detected. A conjugation assay showed that resistance to AMP, TET, and SXT could be simultaneously transferred to recipients. These findings suggest that antimicrobial-resistant E. coli can easily be transferred from farms to tables from retail meats obtained from roadside butcheries.
  • Hypoxia promotes Chlamydia trachomatis L2/434/Bu growth in immortal human epithelial cells via activation of the PI3K-AKT pathway and maintenance of a balanced NAD+/NADH ratio.
    Jeewan Thapa; Kent Hashimoto; Saori Sugawara; Ryoya Tsujikawa; Torahiko Okubo; Shinji Nakamura; Hiroyuki Yamaguchi
    Microbes and infection, 22, 9, 441, 450, 19 May 2020, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Chlamydia trachomatis LGV (CtL2) causes systemic infection and proliferates in lymph nodes as well as genital tract or rectum producing a robust inflammatory response, presumably leading to a low oxygen environment. We therefore assessed how CtL2 growth in immortal human epithelial cells adapts to hypoxic conditions. Assessment of inclusion forming units, the quantity of chlamydial 16S rDNA, and inclusion size showed that hypoxia promotes CtL2 growth. Under hypoxia, HIF-1α was stabilized and p53 was degraded in infected cells. Moreover, AKT was strongly phosphorylated at S473 by CtL2 infection. This activation was significantly diminished by LY-294002, a PI3K-AKT inhibitor, which decreased the number of CtL2 progeny. HIF-1α stabilizers (CoCl2, desferrioxamine) had no effect on increasing CtL2 growth, indicating no autocrine impact of growth factors produced by HIF-1α stabilization. Furthermore, in normoxia, CtL2 infection changed the NAD+/NADH ratio of cells with increased gapdh expression; in contrast, under hypoxia, the NAD+/NADH ratio was the same in infected and uninfected cells with high and stable expression of gapdh, suggesting that CtL2-infected cells adapted better to hypoxia. Together, these data indicate that hypoxia promotes CtL2 growth in immortal human epithelial cells by activating the PI3K-AKT pathway and maintaining the NAD+/NADH ratio with stably activated glycolysis.
  • Chlamydia trachomatis isolated from cervicovaginal samples in Sapporo, Japan, reveals the circulation of genetically diverse strains.
    Jeewan Thapa; Takanori Watanabe; Mana Isoba; Torahiko Okubo; Kiyotake Abe; Kunihiro Minami; Hiroyuki Yamaguchi
    BMC infectious diseases, 20, 1, 53, 53, 16 Jan. 2020, [Peer-reviewed], [International Magazine]
    English, Scientific journal, BACKGROUND: This study was conducted to understand the molecular epidemiology of circulating Chlamydia trachomatis (Ct) strains in Sapporo, Japan. METHODS: A total of 713 endocervical samples collected from April 2016 to March 2019 were screened for Ct. The obtained Ct positive samples were analyzed by ompA genotyping and multilocus sequence analysis (MLSA). RESULTS: Eighty-three (11.6%) samples were positive for Ct plasmid DNA. Sequence analysis of the ompA gene from the 61 positive cases revealed eight genotypes: F (40.9%), E (19.6%), D (14.7%), G (9.8%), H (6.5%), I (3.2%), K (3.2%), and J (1.6%). The globally dominant genotype E and F strains were highly conserved with 13 ompA genetic variants being detected, whereas genotype D strains were the most diverse. Genetic characterization of D strains revealed that D1 genetic variants may be potentially specific to Sapporo. MLSA revealed 13 unique sequence types (STs) including four novel STs from 53 positive samples, with the globally dominant STs 39 and 19 being predominant. STs 39, 34, and 21 were exclusively associated with genotypes E and F indicating their global dominance. Novel ST70 and ST30 were specifically associated with genotype D. CONCLUSION: Our study has revealed the circulation of genetically diverse Ct strains in the women population of Sapporo, Japan. We suggest identifying a transmission network of those successful strains and implementing public health prevention strategies to control the spread of Ct in Sapporo.
  • Effect of thermal control of dry fomites on regulating the survival of human pathogenic bacteria responsible for nosocomial infections.
    Tomoko Shimoda; Torahiko Okubo; Yoshiki Enoeda; Rika Yano; Shinji Nakamura; Jeewan Thapa; Hiroyuki Yamaguchi
    PloS one, e0226952, 12, e0226952, Dec. 2019, [Peer-reviewed], [International Magazine]
    English, Scientific journal, We monitored the survival of human pathogenic bacteria [Escherichia coli (ATCC), extended-spectrum β-lactamase-producing E. coli (Clinical isolate), New Delhi metallo-β-lactamase-producing E. coli (clinical isolate), Staphylococcus aureus (ATCC)] on dry materials (vinyl chloride, aluminum, plastic, stainless steel) at distinct temperatures (room temperature or 15°C-37°C). These bacteria favored a lower temperature for their prolonged survival on the dry fomites, regardless of the material type. Interestingly, when mixed with S. aureus, E. coli survived for a longer time at a lower temperature. Cardiolipin, which can promote the survival of S. aureus in harsh environments, had no effect on maintaining the survival of E. coli. Although the trends remained unchanged, adjusting the humidity from 40% to 60% affected the survival of bacteria on dry surfaces. Scanning electron microscopic analysis revealed no morphological differences in these bacteria immediately before or after one day of dry conditions. In addition, ATP assessment, a method used to visualize high-touch surfaces in hospitals, was not effective at monitoring bacterial dynamics. A specialized handrail device fitted with a heater, which was maintained at normal human body core temperature, successfully prohibited the prolonged survival of bacteria [Enterococcus faecalis (ATCC), E. coli (ATCC), Pseudomonas aeruginosa (ATCC), S. aureus (ATCC), Acinetobacter baumannii (clinical isolate), and Serratia marcescens (clinical isolate)], with the exception of spore-forming Bacillus subtilis (from our laboratory collection) and the yeast-like fungus Candida albicans (from our laboratory collection)] on dry surfaces. Taken together, we concluded that the tested bacteria favor lower temperatures for their survival in dry environments. Therefore, the thermal control of dry fomites has the potential to control bacterial survival on high-touch surfaces in hospitals.
  • Screening of hospital-manhole sewages using MacConkey agar with cefotaxime reveals extended-spectrum β-lactamase-producing Escherichia coli
    Torahiko Okubo; Takaki Hasegawa; Akira Fukuda; Jeewan Thapa; Masaru Usui; Yutaka Tamura; Hiroyuki Yamaguchi
    International Journal of Antimicrobial Agents, 54, 6, 831, 833, Dec. 2019, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Complete genome and bimodal genomic structure of the amoebal symbiont Neochlamydia strain S13 revealed by ultra-long reads obtained from MinION.
    Yamagishi J; Hayashida K; Matsuo J; Okubo T; Kuroda M; Nagai H; Sekizuka T; Yamaguchi H; Sugimoto C
    Journal of human genetics, 65, 1, 41, 48, Nov. 2019, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Neochlamydia strain S13 is an amoebal symbiont of an Acanthamoeba sp. The symbiont confers resistance to Legionella pneumophila on its host; however, the molecular mechanism underlying this resistance is not completely understood. Genome analyses have been crucial for understanding the complicated host-symbiont relationship but segregating the host's genome DNA from the symbiont's DNA is often challenging. In this study, we successfully identified a bimodal genomic structure in Neochlamydia strain S13 using PacBio RS II supported by ultra-long reads derived from MinION. One mode consisted of circular sequences of 2,586,667 and 231,307 bp; the other was an integrated sequence of the two via long homologous regions. They encoded 2175 protein-coding regions, some of which were implied to be acquired via horizontal gene transfer. They were specifically conserved in the genus Neochlamydia and formed a cluster in the genome, presumably by multiplication through genome replication. Moreover, it was notable that the sequenced DNA was obtained without segregating the symbiont DNA from the host. This is an easy and versatile technique that facilitates the characterization of diverse hosts and symbionts in nature.
  • Detection of the sul2-strA-strB gene cluster in an ice core from Dome Fuji Station, East Antarctica.
    Torahiko Okubo; Rieko Ae; Jun Noda; Yoshinori Iizuka; Masaru Usui; Yutaka Tamura
    Journal of global antimicrobial resistance, 17, 72, 78, Jun. 2019, [Peer-reviewed], [International Magazine]
    English, Scientific journal, OBJECTIVES: Bacteria harbouring antimicrobial resistance genes (ARGs) have been isolated from various locations, including ancient microbiomes, indicating that these genes pre-date the discovery of antibiotics. To gain further information regarding ARGs in the pre-antibiotic era, ice samples derived from Dome Fuji Station, Eastern Antarctica, were examined. METHODS: DNA was extracted from firn or ice core samples (n=3; 1200-1400ybp, 1700-2100ybp and 2200-2800ybp, respectively) under sterile conditions. Whole-genome amplification and PCR analyses were utilised to detect ARGs. RESULTS: A 2764-bp gene cluster containing the type II dihydropteroate synthase gene sul2 and the aminoglycoside phosphotransferase genes strA and strB was detected in the 1200-1400-year-old Antarctic ice core (DF-63.5). The sul2-strA-strB gene cluster is frequently associated with plasmid RSF1010 and transposon Tn5393; however, these elements were not detected in sample DF-63.5. The gene cluster exhibited a high level of sequence identity to sequences harboured in present-day bacteria, although there were sequence polymorphisms in the strA gene. Furthermore, expression of this gene cluster in Escherichia coli resulted in reduced susceptibility to dihydrostreptomycin and sulfamethoxazole. CONCLUSION: The results of this study provide further evidence that certain ARGs existed in the pre-antibiotic era. Because the sul2 gene confers resistance to the synthetic compound sulfamethoxazole, these findings suggest that ARGs against synthetic antimicrobials emerged in bacteria during the pre-antibiotic era.
  • A simple and short microbiology practical improves undergraduate nursing students' awareness of bacterial traits and ability to avoid spreading infections
    RIKA YANO; Torahiko Okubo; Tomoko Shimoda; Junji Matsuo; Hiroyuki Yamaguchi
    BMC Medical Education, 19, 53, https://doi.org/10.1186/s12909, 53, Feb. 2019, [Peer-reviewed], [International Magazine]
    English, Scientific journal, BACKGROUND: Nurses are responsible for implementing appropriate measures to reduce hospital infections, especially with multidrug resistant bacteria, so nursing students should learn about microbiology. This helps them to understand bacterial dissemination and infectious disease control. Because of tight schedules, however, its teaching is limited in undergraduate nursing classes in Japan. We therefore tested whether a simple short practical session in a microbiology class could help to improve undergraduate nursing students' awareness of bacterial traits and how to prevent infections. METHODS: This study involved second-grade nursing students (n = 76). Two short practical sessions (a total of 3 h, across 2 days) were used to assess the effectiveness of washing or disinfection on hand bacteria in a 16-class microbiology course (total class time was 24 h, plus an exam). Hand bacteria were sampled on LB agar plates with orientation during the first half-day, and the plates examined for colonies with distinct color or morphological traits, and discussed, in the second session, a week later. Questionnaires before and after the exercise were used to assess changes in awareness of unseen bacteria inhabiting around us connecting bacterial traits and how to prevent infections. RESULTS: The results showed that the practical increased the nursing students' awareness of fomites (utensils) (p = 0.0115), fomites (contact-based) (p = 0.0016), habitats (body surface) (p = 0.0127), action facilitating hospital infection (p = 0.0166), and changes in physical condition caused by bacterial infections (p = 0.0136). There were no changes in word associations (p = 0.627) or habitats (inside body) (p = 0.308). Difficulty score, which is an element in questionnaire psychometric properties, tended to be close to the expected score through the practical, but not statistical significant. In addition, regardless of before or after practical, Cronbach α score, which is an indicator of the reliability among items of multi-choice questions, showed > 0.8, indicating validity of evaluation items. Thus, the student's awareness of unseen bacteria inhabiting around us was significantly increased as compared to those before practical in microbiology class. CONCLUSIONS: The simple short practical effectively improved nursing students' awareness of unseen bacteria inhabiting around us in microbiology course, useful for even tight teaching schedules.
  • Activation of caspase-3 during Chlamydia trachomatis-induced apoptosis at a late stage.
    Matsuo J; Haga S; Hashimoto K; Okubo T; Ozawa T; Ozaki M; Yamaguchi H
    Canadian journal of microbiology, 65, 2, 135, 143, Feb. 2019, [Peer-reviewed], [International Magazine]
    English, Scientific journal, The obligate intracellular bacterium Chlamydia trachomatis activates the host cell apoptosis pathway at a late stage of its developmental cycle. However, whether caspase-3, which is a key enzyme of apoptosis, is activated in Chlamydia-infected cells remains unknown. Here, we established HEp-2 cells stably expressing cFluc-DEVD, which is a caspase-3 substrate sequence inserted into cyclic firefly luciferase, and then monitored the dynamics of caspase-3 activity in cells infected with Chlamydia. Transfected cells without infection showed a significant increase in luciferase activity due to stimulation with staurosporine, an inducer of apoptosis. Activation was significantly blocked by addition of caspase inhibitor z-VAD-fmk. Furthermore, as expected, Chlamydia infection caused a significant increase in luciferase activation at 36-48 h postinfection with a contrastive decrease at 24 h postinfection, which is already well known. Such activation caused by the infection was much stronger when the amount of bacteria was increased. Thus, caspase-3 activation was accurately monitored by the luciferase activity in HEp-2 cells constitutively expressing the cFluc-DEVD probe. Furthermore, our data showed that C. trachomatis activates caspase-3 in host cells at a late stage of infection.
  • Phenotypic and genotypic analyses of antimicrobial resistant bacteria in livestock in Uganda
    Torahiko Okubo; Montira Yossapol; Fumito Maruyama; Eddie M. Wampande; Steven Kakooza; Kenji Ohya; Sayaka Tsuchida; Tetsuo Asai; John D. Kabasa; Kazunari Ushida
    Transboundary and Emerging Diseases, 66, 1, 317, 326, Jan. 2019, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Chlamydia pneumoniae enhances IL-8 production with reduced azithromycin sensitivity under hypoxia
    Junji Matsuo; Kohei Sakai; Torahiko Okubo; Hiroyuki Yamaguchi
    APMIS : acta pathologica, microbiologica, et immunologica Scandinavica, in press, 3, 131, 138, Dec. 2018, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Obligate intracellular bacterium Chlamydia pneumoniae causes respiratory tract infections such as community-acquired pneumonia. During infection, C. pneumoniae induces inflammatory responses in host cells and the oxygen concentration at the infection sites subsequently decreases. Because hypoxic conditions influence further inflammatory responses and reduced antibacterial effects, this may exacerbate the C. pneumoniae infection. Here, we show inflammatory responses and drug sensitivity in C. pneumoniae-infected cells under hypoxic conditions. First, we confirmed the enhanced growth of C. pneumoniae under hypoxia, which indicates that the hypoxic condition we used could adequately reproduce past reports. We then demonstrated a significant increase in production of the pro-inflammatory cytokine Interleukin 8 (IL-8) in C. pneumoniae-infected cells under hypoxic conditions. Furthermore, hypoxia decreased the antibacterial effects of azithromycin against C. pneumoniae compared with normoxic conditions. Together, our data suggest that inflammatory responses and drug sensitivity may have been underestimated in C. pneumoniae infection in previous studies. Thus, to accurately understand the Chlamydia infection, it may be necessary to perform in vitro experiments under hypoxic conditions.
  • Tetrahymena promotes interactive transfer of carbapenemase gene encoded in plasmid between fecal Escherichia coli and environmental Aeromonas caviae.
    Matsushita M; Okubo T; Hasegawa T; Matsuo J; Watanabe T; Iwasaki S; Fukumoto T; Hayasaka K; Akizawa K; Shimizu C; Yamaguchi H
    Microbiology and immunology, 62, 11, 720, 728, Oct. 2018, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Tetrahymena can facilitate plasmid transfer among Escherichia coli or from E. coli to Salmonella Enteritidis via vesicle accumulation. In this study, whether ciliates promote the interactive transfer of plasmids encoding blaIMP-1 between fecal E. coli and environmental Aeromonas caviae was investigated. Both bacteria were mixed with or without ciliates and incubated overnight at 30°C. The frequency of plasmid-acquired bacteria was estimated by colony counts using an agar plate containing ceftazidim (CAZ) followed by determination of the minimum inhibitory concentration (MIC). Cultures containing ciliates interactively transferred the plasmid between E. coli and Aeromonas with a frequency of 10-4 to 10-5 . All plasmid-acquired bacteria showed a MIC against CAZ of >128 μg/mL and the plasmid transfer was confirmed by PCR amplification of the blaIMP-1 gene. Fluorescent observation showed that both bacteria accumulated in the same vesicle and that transwell sequestering significantly decreased the transfer frequency. Although ciliates preferentially ingested E. coli rather than A. caviae, both bacteria were co-localized into the same vesicles of ciliates, indicating that their meeting is associated with the gene transfer. Thus, ciliates interactively promote plasmid transfer between E. coli and A. caviae. The results of this study will facilitate control of the spread of multiple-antibiotic resistant bacteria.
  • Co-harboring of cephalosporin (bla)/colistin (mcr) resistance genes among Enterobacteriaceae from flies in Thailand
    Akira Fukuda; Masaru Usui; Torahiko Okubo; Chie Tagaki; Nop Sukpanyatham; Yutaka Tamura
    FEMS Microbiology Letters, 365, 16, fny178, Aug. 2018, [Peer-reviewed], [International Magazine]
    English, Scientific journal, The spreading of antimicrobial-resistant Enterobacteriaceae, especially those co-harboring plasmid-mediated cephalosporin (bla) and colistin (mcr) resistance genes, is becoming increasingly problematic. As a vector, flies carry antimicrobial-resistant bacteria (ARB) into human and livestock habitats. To investigate ARB in flies, we collected 235 flies from 27 sites (18 urban areas, five pig farms and four chicken farms) in Thailand during 2013-2015. Cefotaxime-resistant Enterobacteriaceae (CtxRE) and bla-positive CtxRE were isolated from 70 (29.8%) and 48 (20.4%) flies, respectively. In 93 bla-positive CtxRE isolates that included Escherichia coli, Enterobacter spp., and Klebsiella pneumoniae from 48 flies, the most frequent bla gene was TEM (n = 62), followed by CTX-M-55 (n = 31), CTX-M-14 (n = 26), CMY-2 (n = 24) and SHV (n = 10), and 58 isolates harbored multiple types of these genes. In addition, we detected the mcr-1 (n = 1) and mcr-3 (n = 19) genes in bla-positive CtxRE isolates from 16 flies. In conjugation experiments, 10 mcr-3- and bla-positive isolates exhibited co-transfer of mcr-3 and blaTEM-1 genes. These results suggest that a relatively high proportion of flies in Thailand carries cephalosporin-resistant Enterobacteriaceae harboring co-transmissible cephalosporin and colistin resistance genes.
  • Acanthamoeba S13WT relies on its bacterial endosymbiont to backpack human pathogenic bacteria and resist Legionella infection on solid media
    Torahiko Okubo; Mizue Matsushita; Shinji Nakamura; Junji Matsuo; Hiroki Nagai; Hiroyuki Yamaguchi
    Environmental Microbiology Reports, 10, 3, 344, 354, Wiley-Blackwell, 01 Jun. 2018, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Amoebal endosymbiont Neochlamydia protects host amoebae against Legionella pneumophila infection by preventing Legionella entry
    Chinatsu Maita; Mizue Matsushita; Masahiro Miyoshi; Torahiko Okubo; Shinji Nakamura; Junji Matsuo; Masaharu Takemura; Masaki Miyake; Hiroki Nagai; Hiroyuki Yamaguchi
    Microbes and Infection, 20, 4, 236, 244, Elsevier Masson SAS, 01 Apr. 2018, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Long-term survival of Naegleria polaris from Antarctica after 10 years of storage at 4 A degrees C
    Junji Matsuo; Shinji Nakamura; Torahiko Okubo; Manabu Fukui; Hiroyuki Yamaguchi
    PARASITOLOGY RESEARCH, 117, 3, 937, 941, Mar. 2018, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Impact of capsaicin, an active component of chili pepper, on pathogenic chlamydial growth (Chlamydia trachomatis and Chlamydia pneumoniae) in immortal human epithelial HeLa cells
    Kazuya Yamakawa; Junji Matsuo; Torahiko Okubo; Shinji Nakamura; Hiroyuki Yamaguchi
    Journal of Infection and Chemotherapy, 24, 2, 83, 87, Elsevier B.V., 01 Feb. 2018, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Subtle changes in host cell density cause a serious error in monitoring of the intracellular growth of Chlamydia trachomatis in a low-oxygen environment: Proposal for a standardized culture method
    Sakai K; Matsuo J; Watanabe T; Okubo T; Nakamura S; Yamaguchi H
    Journal of Microbiological Methods, 153, 84, 91, 2018, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Impact of bacterial traces belonging to the Enterobacteriaceae on the prevalence of Chlamydia trachomatis in women visiting a community hospital in Japan
    Taki K; Watanabe T; Matsuo J; Sakai K; Okubo T; Matsushita M; Abe K; Minami K; Yamaguchi H
    Journal of Infection and Chemotherapy, 24, 10, 815, 821, 2018, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Analysis of adult damselfly fecal material aids in the estimation of antibiotic-resistant Enterobacterales contamination of the local environment.
    Yamaguchi Y; Okubo T; Matsushita M; Wataji M; Iwasaki S; Hayasaka K; Akizawa K; Matsuo J; Shimizu C; Yamaguchi H
    PeerJ, 6, e5755, 2018, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Because damselflies are ubiquitously but focally present in natural environments and play a critical role as predators of other insect species, the fecal matter of damselflies may be useful for investigating antibiotic-resistant bacterial populations, including human pathogens, in local environments. We therefore examined the prevalence of antibiotic-resistant bacteria, including Enterobacterales, in fecal material from 383 damselflies (adults and larvae) collected from seven locations around Sapporo City, Japan, in 2016 and 2017. Fecal samples were plated on soybean casein digest (SCD) agar plates with and without antibiotics (SCD-A and SCD-w/o, respectively) to identify environmental bacteria and gut bacteria, respectively, and on MacConkey agar plates with antibiotics (MacConkey-A) to select for Gram-negative bacteria, including human pathogenic Enterobacterales species. The prevalence of colonies on each of the plates was compared, and representative colonies on MacConkey-A plates were identified to the species level using an API 20E kit and the MALDI Biotyper system. Overall, SCD-w/o plates showed a gut bacterial load of approximately 108 colony-forming units per adult damselfly or larva. There was a significant difference between the prevalence of colonies on the SCD-A and MacConkey-A plates, and a significantly increased prevalence of antibiotic-resistant bacteria on MacConkey-A plates was observed in samples collected from Shinoroshinkawa. Cluster analysis based on minimum inhibitory concentration values of 59 representative isolates from MacConkey-A agar plates revealed that samples from Shinoroshinkawa contained a higher prevalence of Enterobacterales than those from other sampling locations. Thus, fecal materials discharged by adult damselflies could be used in future studies as a simple tool for estimating antibiotic-resistant bacteria, including Enterobacterales species, in the local environment.
  • Lateral Gene Transfer Between Protozoa-Related Giant Viruses of Family Mimiviridae and Chlamydiae.
    Watanabe T; Yamazaki S; Maita C; Matushita M; Matsuo J; Okubo T; Yamaguchi H
    Evolutionary bioinformatics online, 14, 1176934318788337, 1176934318788337, 2018, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Obligate intracellular chlamydiae diverged into pathogenic and environmental chlamydiae 0.7-1.4 billion years ago. While pathogenic chlamydiae have adapted to a wide range of vertebrates, environmental chlamydiae inhabit unicellular amoebae, the free-living Acanthamoeba. However, how and why this divergence occurred remains unclear. Meanwhile, giant viruses consisting of protozoa-related and protozoa-unrelated viruses have been discovered, with the former group being suggested to have more influenced environmental chlamydiae during their evolution while cohabiting host amoebae. Against this background, we attempted to visualize genes of giant viruses in chlamydial genomes by bioinformatic analysis mainly with comparative genome and phylogenic analysis, seeking genes present in chlamydiae that are specifically shared with protozoa-related giant viruses. As a result, in contrast to protozoa-unrelated giant viruses, the genes of protozoa-related giant viruses were significantly shared in both the chlamydia genomes depending on the giant virus type. In particular, the prevalence of Mimiviridae genes among the protozoa-related giant virus genes in chlamydial genomes was significantly high. Meanwhile, the prevalence of protozoa-related giant virus genes in pathogenic chlamydia genomes was consistently higher than those of environmental chlamydiae; the actual number of sequences similar to giant virus was also significantly predominant compared with those in the environmental chlamydial genomes. Among them, the most prevalent of giant virus was in the case of chlamydiae with Megavirus chiliensis; total of 1338 genes of the chlamydiae were found to be shared with the virus (444 genes specific to environmental chlamydiae, 892 genes shared between both chlamydiae, only two genes in the pathogenic chlamydiae). Phylogenic analysis with most prevalent sets (Megavirus chiliensis and Protochlamydia EI2 or Chlamydia trachomatis L2 434Bu) showed the presence of orthologs between these with several clustered. In addition, Pearson's single regression analysis revealed that almost the prevalence of the genes from the giant viruses in chlamydial genomes was negatively and specifically correlated with the number of chlamydial open reading frames (ORFs). Thus, these results indicated the trace of lateral gene transfer between protozoa-related giant viruses of family Mimiviridae and chlamydiae. This is the first demonstration of a putative linkage between chlamydiae and the giant viruses, providing us with a hint to understand chlamydial evolution.
  • Walker occupancy has an impact on changing airborne bacterial communities in an underground pedestrian space, as small-dust particles increased with raising both temperature and humidity
    Torahiko Okubo; Takako Osaki; Eriko Nozaki; Akira Uemura; Kouhei Sakai; Mizue Matushita; Junji Matsuo; Shinji Nakamura; Shigeru Kamiya; Hiroyuki Yamaguchi
    PLOS ONE, 12, 9, e0184980, Sep. 2017, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Diversity changes of microbial communities into hospital surface environments
    Rika Yano; Tomoko Shimoda; Reina Watanabe; Yasutoshi Kuroki; Torahiko Okubo; Shinji Nakamura; Junji Matsuo; Sadako Yoshimura; Hiroyuki Yamaguchi
    JOURNAL OF INFECTION AND CHEMOTHERAPY, 23, 7, 439, 445, Jul. 2017, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Ciliates promote the transfer of a plasmid encoding bla(NDM)-5 from Escherichia coli, isolated from a hospital in Japan, to other human pathogens
    Torahiko Okubo; Mizue Matushita; Yukiko Ohara; Junji Matsuo; Satoshi Oguri; Tatsuya Fukumoto; Kasumi Hayasaka; Kouzi Akizawa; Hitoshi Shibuya; Chikara Shimizu; Hiroyuki Yamaguchi
    INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS, 49, 3, 387, 388, Mar. 2017, [Peer-reviewed], [International Magazine]
    English
  • Acanthamoeba containing endosymbiotic chlamydia isolated from hospital environments and its potential role in inflammatory exacerbation
    Tatsuya Fukumoto; Junji Matsuo; Torahiko Okubo; Shinji Nakamura; Kentaro Miyamoto; Kentaro Oka; Motomichi Takahashi; Kouji Akizawa; Hitoshi Shibuya; Chikara Shimizu; Hiroyuki Yamaguchi
    BMC MICROBIOLOGY, 16, 1, 292, 8, Dec. 2016, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Horizontal Transfer of Plasmid-Mediated Cephalosporin Resistance Genes in the Intestine of Houseflies (Musca domestica)
    Akira Fukuda; Masaru Usui; Torahiko Okubo; Yutaka Tamura
    MICROBIAL DRUG RESISTANCE, 22, 4, 336, 341, Jun. 2016, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Use of Aeromonas spp. as General Indicators of Antimicrobial Susceptibility among Bacteria in Aquatic Environments in Thailand
    Masaru Usui; Chie Tagaki; Akira Fukuda; Torahiko Okubo; Chanchai Boonla; Satoru Suzuki; Kanako Seki; Hideshige Takada; Yutaka Tamura
    FRONTIERS IN MICROBIOLOGY, 7, 710, 710, May 2016, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • 犬由来菌に対するフルオロキノロン系抗菌薬の殺菌能力評価
    大久保 寅彦; 臼井 優; 福田 昭; 佐藤 友美; 田村 豊
    Journal of the veterinary medicine, 69, 1, 39, 42, 文永堂出版, Jan. 2016, [Peer-reviewed]
    Japanese, Scientific journal
  • Draft genome sequences of Legionella pneumophila JR32 and Lp01 laboratory strains domesticated in Japan
    Chinatsu Maita; Mizue Matushita; Torahiko Okubo; Junji Matsuo; Masaki Miyake; Hiroki Nagai; Hiroyuki Yamaguchi
    Genome Announcements, 4, 4, American Society for Microbiology, 2016, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Isolation of multiple drug-resistant enteric bacteria from feces of wild Western Lowland Gorilla (Gorilla gorilla gorilla) in Gabon
    Pierre Philippe Mbehang Nguema; Torahiko Okubo; Sayaka Tsuchida; Shiho Fujita; Juichi Yamagiwa; Yutaka Tamura; Kazunari Ushida
    JOURNAL OF VETERINARY MEDICAL SCIENCE, 77, 5, 619, 623, May 2015, [Peer-reviewed], [Domestic magazines]
    English, Scientific journal
  • Draft genome sequence of Chlamydia trachomatis strain 54, isolated from the urogenital tract of a male in Japan
    Tomohiro Yamazaki; Junji Matsuo; Momoka Kikuchi; Kentaro Miyamoto; Kentaro Oka; Motomichi Takahashi; Satoshi Takahashi; Torahiko Okubo; Hiroyuki Yamaguchi
    Genome Announcements, 3, 5, American Society for Microbiology, 2015, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Protozoal ciliate promotes bacterial autoinducer-2 accumulation in mixed culture with Escherichia coli
    Satoshi Oguri; Tomoko Hanawa; Junji Matsuo; Kasumi Ishida; Tomohiro Yamazaki; Shinji Nakamura; Torahiko Okubo; Tatsuya Fukumoto; Kouzi Akizawa; Chikara Shimizu; Shigeru Kamiya; Hiroyuki Yamaguchi
    JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY, 61, 5, 203, 210, 2015, [Peer-reviewed], [Domestic magazines]
    English, Scientific journal
  • Bacterial Diversity in Sea Ice from the Southern Ocean and the Sea of Okhotsk
    Torahiko Okubo; Yuika Tosaka; Toyotaka Sato; Masaru Usui; Chie Nakajima; Yasuhiko Suzuki; Satoshi Imura; Yutaka Tamura
    Journal of Applied & Environmental Microbiology, 2, 6, 266, 272, Oct. 2014, [Peer-reviewed]
    English, Scientific journal
  • Isolation of Escherichia coli Strains with AcrAB-TolC Efflux Pump-Associated Intermediate Interpretation or Resistance to Fluoroquinolone, Chloramphenicol and Aminopenicillin from Dogs Admitted to a University Veterinary Hospital
    Toyotaka Sato; Shin-ichi Yokota; Risa Ichihashi; Tomoka Miyauchi; Torahiko Okubo; Masaru Usui; Nobuhiro Fujii; Yutaka Tamura
    JOURNAL OF VETERINARY MEDICAL SCIENCE, 76, 7, 937, 945, Jul. 2014, [Peer-reviewed], [Domestic magazines]
    English, Scientific journal
  • 北海道で分離された大腸菌におけるキノロン、アミノグリコシド、セフェム交叉耐性株に関する検討
    横田 伸一; 大越 康雄; 大久保 寅彦; 佐藤 豊孝; 田村 豊; 塚本 尚行; 桑原 理
    日本化学療法学会雑誌, 62, Suppl.A, 403, 403, (公社)日本化学療法学会, May 2014
    Japanese
  • Association of Veterinary Third-Generation Cephalosporin Use with the Risk of Emergence of Extended-Spectrum-Cephalosporin Resistance in Escherichia coli from Dairy Cattle in Japan
    Toyotaka Sato; Torahiko Okubo; Masaru Usui; Shin-ichi Yokota; Satoshi Izumiyama; Yutaka Tamura
    PLOS ONE, 9, 4, e96101, Apr. 2014, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Comparison of broad-spectrum cephalosporin-resistant Escherichia coli isolated from dogs and humans in Hokkaido, Japan
    Torahiko Okubo; Toyotaka Sato; Shin-ichi Yokota; Masaru Usui; Yutaka Tamura
    JOURNAL OF INFECTION AND CHEMOTHERAPY, 20, 3-4, 243, 249, Mar. 2014, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Phylogenetic association of fluoroquinolone and cephalosporin resistance of D-O1-ST648 Escherichia coli carrying bla(CMY-2) from faecal samples of dogs in Japan
    Toyotaka Sato; Shin-ichi Yokota; Torahiko Okubo; Masaru Usui; Nobuhiro Fujii; Yutaka Tamura
    JOURNAL OF MEDICAL MICROBIOLOGY, 63, Pt 2, 263, 270, Feb. 2014, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • The Role of Flies in Spreading the Extended-Spectrum beta-lactamase Gene from Cattle
    Masaru Usui; Tomohiro Iwasa; Akira Fukuda; Toyotaka Sato; Torahiko Okubo; Yutaka Tamura
    MICROBIAL DRUG RESISTANCE, 19, 5, 415, 420, Oct. 2013, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • 豚疣贅性心内膜炎から分離したStreptococcus suisの薬剤感受性及び分子疫学的解析
    ONO YUTA; YANAGISAWA RISA; YOKOYAMA MITSUE; FURUSAKI YOJI; OKUBO TORAHIKO; IKEDA TETSUYA; SHIMIZU SHUN'ICHI
    獣医公衆衛生研究, 16, 1, 33, 36, Sep. 2013
    Japanese
  • 動物病院来院猫からのセファロスポリン耐性およびフルオロキノロン耐性大腸菌の検出
    大久保 寅彦; 小野 匡; 佐藤 豊孝; 臼井 優; 田村 豊
    北海道獣医師会雑誌, 57, 8, 411, 411, (公社)北海道獣医師会, Aug. 2013
    Japanese
  • 犬由来大腸菌におけるフルオロキノロン耐性及びセファロスポリン耐性の関連
    佐藤 豊孝; 横田 伸一; 大久保 寅彦; 臼井 優; 藤井 暢弘; 田村 豊
    日本獣医師会雑誌, 66, 5, 350, 350, (公社)日本獣医師会, May 2013
    Japanese
  • 伴侶動物由来細菌へのフルオロキノロン剤曝露による耐性菌出現リスク
    臼井 優; 佐藤 豊孝; 大久保 寅彦; 田村 豊
    獣医畜産新報, 66, 4, 279, 282, 文永堂出版(株), Apr. 2013
    Japanese
  • Contribution of the AcrAB-TolC efflux pump to high-level fluoroquinolone resistance in Escherichia coli isolated from dogs and humans
    Toyotaka Sato; Shin-Ichi Yokota; Torahiko Okubo; Kanako Ishihara; Hiroshi Ueno; Yasukazu Muramatsu; Nobuhiro Fujii; Yutaka Tamura
    Journal of Veterinary Medical Science, 75, 4, 407, 414, 2013, [Peer-reviewed], [Domestic magazines]
    English, Scientific journal
  • Amino acid substitutions in gyrA and parC are associated with fluoroquinolone resistance in mycoplasma bovis isolates from Japanese dairy calves
    Toyotaka Sato; Torahiko Okubo; Masaru Usui; Hidetoshi Higuchi; Yutaka Tamura
    Journal of Veterinary Medical Science, 75, 8, 1063, 1065, 2013, [Peer-reviewed], [Domestic magazines]
    English, Scientific journal
  • Fluoroquinolone resistance mechanisms in an Escherichia coli isolate, HUE1, without quinolone resistance-determining region mutations
    Toyotaka Sato; Shin-Ichi Yokota; Ikuo Uchida; Torahiko Okubo; Masaru Usui; Masahiro Kusumoto; Masato Akiba; Nobuhiro Fujii; Yutaka Tamura
    Frontiers in Microbiology, 4, MAY, 125, 125, Frontiers Research Foundation, 2013, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • High Prevalence of Cross-Resistance to Aminoglycosides in Fluoroquinolone-Resistant Escherichia coli Clinical Isolates
    Naoyuki Tsukamoto; Yasuo Ohkoshi; Torahiko Okubo; Toyotaka Sato; Osamu Kuwahara; Nobuhiro Fujii; Yutaka Tamura; Shin-ichi Yokot
    CHEMOTHERAPY, 59, 5, 379, 384, 2013, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • 市販鶏肉由来薬剤耐性サルモネラ属菌における耐性遺伝子の解析
    小川 紋; 佐藤 豊孝; 大久保 寅彦; 臼井 優; 田村 豊
    北海道獣医師会雑誌, 56, 8, 436, 436, (公社)北海道獣医師会, Aug. 2012
    Japanese
  • 薬剤耐性大腸菌の畜舎内伝播におけるハエの役割
    臼井 優; 岩佐 友寛; 佐藤 豊孝; 大久保 寅彦; 田村 豊
    北海道獣医師会雑誌, 56, 8, 437, 437, (公社)北海道獣医師会, Aug. 2012
    Japanese
  • 犬由来大腸菌におけるフルオロキノロン耐性およびセファロスポリン耐性の関連
    佐藤 豊孝; 横田 伸一; 大久保 寅彦; 臼井 優; 藤井 暢弘; 田村 豊
    北海道獣医師会雑誌, 56, 8, 438, 438, (公社)北海道獣医師会, Aug. 2012
    Japanese
  • 牛呼吸器由来Mycoplasma bovisにおけるフルオロキノロン系抗菌薬耐性機構
    佐藤 豊孝; 大久保 寅彦; 臼井 優; 樋口 豪紀; 永幡 肇; 田村 豊
    日本獣医学会学術集会講演要旨集, 154回, 226, 226, (公社)日本獣医学会, Aug. 2012
    Japanese
  • 南極の氷中に含まれていた細菌叢の解析
    大久保 寅彦; 佐藤 豊孝; 中村 昇太; 飯田 哲也; 臼井 優; 能田 淳; 萩原 克郎; 田村 豊
    日本獣医学会学術集会講演要旨集, 154回, 229, 229, (公社)日本獣医学会, Aug. 2012
    Japanese
  • 薬剤耐性大腸菌の畜舎内伝播におけるハエの役割
    臼井 優; 岩佐 友寛; 佐藤 豊孝; 大久保 寅彦; 田村 豊
    日本獣医学会学術集会講演要旨集, 154回, 273, 273, (公社)日本獣医学会, Aug. 2012
    Japanese
  • 市販鶏肉由来薬剤耐性サルモネラ属菌における耐性遺伝子の解析
    小川 紋; 佐藤 豊孝; 大久保 寅彦; 臼井 優; 田村 豊
    日本獣医学会学術集会講演要旨集, 154回, 276, 276, (公社)日本獣医学会, Aug. 2012
    Japanese
  • Prevalence of Fluoroquinolone-Resistant Escherichia coli O25:H4-ST131 (CTX-M-15-Nonproducing) Strains Isolated in Japan
    Shin-ichi Yokota; Toyotaka Sato; Torahiko Okubo; Yasuo Ohkoshi; Tamaki Okabayashi; Osamu Kuwahara; Yutaka Tamura; Nobuhiro Fujii
    CHEMOTHERAPY, 58, 1, 52, 59, 2012, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • 犬及び人由来フルオロキノロン耐性大腸菌におけるプラスミド介在性キノロン耐性遺伝子oqxABの検出
    佐藤 豊孝; 横田 伸一; 内田 郁夫; 大久保 寅彦; 石原 加奈子; 岡林 環樹; 藤井 暢弘; 田村 豊
    感染症学雑誌, 85, 5, 557, 557, (一社)日本感染症学会, Sep. 2011
    Japanese
  • 犬および人由来フルオロキノロン耐性大腸菌の性状比較
    佐藤 豊孝; 横田 伸一; 大久保 寅彦; 石原 加奈子; 藤井 暢弘; 田村 豊
    北海道獣医師会雑誌, 55, 8, 417, 417, (公社)北海道獣医師会, Aug. 2011
    Japanese
  • ヒト及びイヌ由来大腸菌におけるプラスミド介在性キノロン耐性遺伝子aac(6')-Ib-crの検出
    北原 尚英; 佐藤 豊孝; 大久保 寅彦; 石原 加奈子; 田村 豊
    北海道獣医師会雑誌, 55, 8, 418, 418, (公社)北海道獣医師会, Aug. 2011
    Japanese
  • 牛における第三世代セファロスポリン使用による薬剤耐性菌の発生評価試験
    佐藤 豊孝; 大久保 寅彦; 石原 加奈子; 泉山 諭; 田村 豊
    日本獣医学会学術集会講演要旨集, 152回, 215, 215, (公社)日本獣医学会, Aug. 2011
    Japanese
  • 牛呼吸器由来マイコプラズマにおけるマクロライド系抗菌薬の薬剤感受性調査
    佐藤 豊孝; 樋口 豪紀; 大久保 寅彦; 石原 加奈子; 永幡 肇; 田村 豊
    日本獣医学会学術集会講演要旨集, 152回, 217, 217, (公社)日本獣医学会, Aug. 2011
    Japanese
  • ヒト及びイヌ由来大腸菌におけるプラスミド介在性キノロン耐性遺伝子aac(6')-Ib-crの検出
    北原 尚英; 佐藤 豊孝; 大久保 寅彦; 石原 加奈子; 田村 豊
    日本獣医学会学術集会講演要旨集, 152回, 262, 262, (公社)日本獣医学会, Aug. 2011
    Japanese
  • A Fluoroquinolone-Resistant Escherichia coli Clinical Isolate without Quinolone Resistance-Determining Region Mutations Found in Japan
    Toyotaka Sato; Shin-ichi Yokota; Ikuo Uchida; Torahiko Okubo; Kanako Ishihara; Nobuhiro Fujii; Yutaka Tamura
    ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 55, 8, 3964, 3965, Aug. 2011, [Peer-reviewed], [International Magazine]
    English
  • 犬及び人由来フルオロキノロン耐性大腸菌におけるプラスミド介在性キノロン耐性遺伝子oqxABの検出
    佐藤 豊孝; 横田 伸一; 内田 郁夫; 大久保 寅彦; 石原 加奈子; 岡林 環樹; 藤井 暢弘; 田村 豊
    感染症学雑誌, 85, 臨増, 191, 191, (一社)日本感染症学会, Mar. 2011
    Japanese
  • 犬および人から分離されたセファロスポリン耐性大腸菌における耐性性状の比較
    大久保 寅彦; 佐藤 豊孝; 石井 良和; 横田 伸一; 石原 加奈子; 田村 豊
    感染症学雑誌, 85, 臨増, 301, 301, (一社)日本感染症学会, Mar. 2011
    Japanese
  • 犬由来フルオロキノロン-セファロスポリン多剤耐性大腸菌の系統発生分類による解析
    佐藤 豊孝; 横田 伸一; 大久保 寅彦; 石原 加奈子; 岡林 環樹; 藤井 暢弘; 田村 豊
    日本獣医学会学術集会講演要旨集, 150回, 253, 253, (公社)日本獣医学会, Sep. 2010
    Japanese
  • 犬および人由来セファロスポリン耐性大腸菌における耐性因子の比較
    大久保 寅彦; 佐藤 豊孝; 石原 加奈子; 石井 良和; 田村 豊
    日本獣医学会学術集会講演要旨集, 150回, 254, 254, (公社)日本獣医学会, Sep. 2010
    Japanese
■ Other Activities and Achievements
■ Lectures, oral presentations, etc.
■ Syllabus
  • 先端検査医学特論, 2024年, 修士課程, 保健科学院
  • 公衆衛生学実習, 2024年, 学士課程, 医学部
  • 技能修得到達度評価, 2024年, 学士課程, 医学部
  • 臨地実習（検体・病理検査）, 2024年, 学士課程, 医学部
  • 医動物学, 2024年, 学士課程, 医学部
  • 医動物学, 2024年, 学士課程, 医学部
  • 医動物学演習, 2024年, 学士課程, 医学部
  • 検査管理学Ⅱ, 2024年, 学士課程, 医学部
  • 検査総合管理学Ⅱ, 2024年, 学士課程, 医学部
  • 医学概論・関係法規, 2024年, 学士課程, 医学部
  • 関係法規, 2024年, 学士課程, 医学部
  • 医用工学概論実習, 2024年, 学士課程, 医学部
  • 検査総合管理学Ⅰ, 2024年, 学士課程, 医学部
  • 検査総合管理学Ⅲ, 2024年, 学士課程, 医学部
  • 英語演習, 2024年, 学士課程, 全学教育
  • 保健・医療概論, 2024年, 学士課程, 医学部
  • 臨床病態学Ⅰ, 2024年, 学士課程, 医学部
  • アドバンス微生物学Ⅰ, 2024年, 学士課程, 医学部
  • アドバンス微生物学Ⅱ, 2024年, 学士課程, 医学部
  • 微生物学実習Ⅰ, 2024年, 学士課程, 医学部
  • 微生物学実習Ⅱ, 2024年, 学士課程, 医学部
  • 微生物検査学実習, 2024年, 学士課程, 医学部
  • 臨床微生物学, 2024年, 学士課程, 医学部
  • ベーシック微生物学, 2024年, 学士課程, 医学部
  • 保健微生物学, 2024年, 学士課程, 医学部
  • 一般教育演習(ﾌﾚｯｼｭﾏﾝｾﾐﾅｰ), 2024年, 学士課程, 全学教育
  • 医療安全管理学Ⅱ, 2024年, 学士課程, 医学部
■ Affiliated academic society
  • JAPANESE SOCIETY FOR BACTERIOLOGY
■ Research Themes
  • Mechanisms of Hypoxia Adaptation and Cell Modification in Genital Chlamydia: Insights from Cancer Cell Parallels
    Grants-in-Aid for Scientific Research
    01 Apr. 2025 - 31 Mar. 2029
    山口 博之; 大久保 寅彦
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 25K02490
  • Study of the mechanism of desiccation resistance in clinical strains of Escherichia coli using the pandemic clone ST131 as a model
    Grants-in-Aid for Scientific Research
    01 Apr. 2025 - 31 Mar. 2028
    大久保 寅彦; 佐藤 豊孝; 山口 博之
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Hokkaido University, 25K10357
  • 日常生活動作レベルが高頻度接触面の細菌動態に与える影響と感染リスク判断への応用
    科学研究費助成事業
    01 Apr. 2024 - 31 Mar. 2028
    宇野 智子; 渡辺 玲奈; 山口 博之; 大久保 寅彦; 矢野 理香
    日本学術振興会, 基盤研究(C), 札幌医科大学, 24K13649
  • アジア諸国と協調して展開するAdvanced One Health Tricycle Project
    新興・再興感染症に対する革新的医薬品等開発推進研究事業
    Apr. 2023 - Mar. 2026
    菅井 基行; 岸井 こずゑ; 小松澤 均; 白川 利朗; 浅井 鉄夫; 春日 郁朗; 大久保 寅彦
    23809700
  • Functional elucidation of novel effectors of Legionella pneumophila approached through interactions with unique ciliate
    Grants-in-Aid for Scientific Research
    01 Apr. 2022 - 31 Mar. 2025
    大久保 寅彦; 中村 眞二; 山口 博之
    (1)未知エフェクターの検出：前年度に引き続き、作出済みのトランスポゾン挿入変異Legionella pneumophila (Lp) 菌株と繊毛虫Anteglaucomaの共培養実験を実施した。変異株全体(n=782)の共培養実験を完了し、56株(56/782, 7.2%)の病原性喪失株（繊毛虫が生残）を選抜した。AP-PCR法とシークエンスでトランスポゾン挿入部位を確認した結果、Ⅳ型分泌装置関連遺伝子(dot, icm等）の変異(n=17), 既知のエフェクタータンパク遺伝子の変異(n=6)、各種トランスポータータンパク遺伝子の変異(n=7)などを特定した。既報でヒト細胞または原生生物細胞への病原性が知られているものを除外し、まだ報告がない病原性遺伝子の候補として10遺伝子(lpg1859, lpg1343, lpg1206, lpg2856, lpg1828, lpg1013, lpg0077, lpg2345, DEAD/DEAH box helicase, hypothetical protein)を特定した。
    (2)ヒト細胞への影響：上記の10遺伝子が変異したLp菌株をHeLa細胞に感染させて48時間後の細胞生存性を確認した結果、7株で細胞が生残した。これらの7遺伝子がコードするタンパクは繊毛虫細胞とヒト細胞の双方に病原性を及ぼす未報告のエフェクターだと考えられる。研究調書に記載したTHP-1細胞とLpの共培養も開始したが、まだ結果が出揃っていない。
    (3)部位特異的変異株による再現実験：部位特異的変異によってLpの遺伝子を改変しても同様の結果が得られるかを検証するために、相同組換えによって上記の10遺伝子を欠損させた株の作出を試みたが、R5年度中には欠損株の樹立には至らなかった。
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Hokkaido University, 22K07051
  • New development of research to elucidate the intracellular adaptation mechanism of genital chlamydia unraveled from its similarity to cancer cells
    Grants-in-Aid for Scientific Research
    01 Apr. 2021 - 31 Mar. 2025
    山口 博之; 中村 眞二; THAPA JEEWAN; 大久保 寅彦
    性感染症の原因であるクラミジア(Chlamydia trachomatis)が、発癌の危険因子であることが明らかになってきた。それ故にクラミジアの細胞内への適応機構の分子機構の解明はそれら病態形成機序を明らかにする上で極めて重要である。しかしクラミジアは未だ遺伝子改変が困難なこともあってその詳細な分子機構は明らかになっていない。そこで本年度はクラミジアの生存性を指標に既存薬と阻害剤ライブラリーのスクリーニングを行いヒットした化合物の細胞標的分子の情報からクラミジアが細胞内で頼る新たな候補分子(Gab2、PKA、PKG、CREB)の同定に成功した。具体的には、以下の2つの点について明らかにした。
    1. 既存薬ライブラリー(約4,000)のスクリーニングでクラミジアの増殖を顕著に抑制した薬剤(抗菌薬を除く)のKEGG情報から標的分子候補を類推し、それら候補分子の阻害剤によるクラミジアの影響を精査することで、クラミジアの細胞内増殖が細胞の恒常性維持に重要なPKA、PKG、CREBを要求することを明らかにした。
    2. 細胞は解糖系に依存したATPを産生を促進し細胞死を回避するためにPPI3K-AKT経路を活性化する。私たちの以前の研究でクラミジア感染細胞においてAKTのリン酸化(Ser473)が促進することを明らかにした。そこでPI3K-AKT経路に関わる分子の阻害剤パネルを用いてクラミジアの感受性を元にスクリーニングを行い、その結果を元に主成分解析を行ったところ、クラミジアが細胞内で利用する分子としてアダプター分子が候補として同定された。そこで主要なアダプター分子の一つであるGabをノックダウンした細胞でクラミジアの動態を精査したところ、クラミジアがその細胞内での増殖にGabを要求することが明らかになった。
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 23K21378
  • New development of research to elucidate the intracellular adaptation mechanism of genital chlamydia unraveled from its similarity to cancer cells
    Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    01 Apr. 2021 - 31 Mar. 2025
    山口 博之; 中村 眞二; THAPA JEEWAN; 大久保 寅彦
    性感染症の主な原因である細胞内寄生性細菌クラミジア(Chlamydia trachomatis: Ct)の細胞内への適応機構は、未だ遺伝子改変ができないこともあって明らかになっていない。そこでCt感染細胞と癌細胞との類似性[1. PI3K-AKT経路を活性化、2. 通常酸素分圧下でミトコンドリアを要求する、3. 癌抑制因子として知られる芳香族炭素水素受容体転写因子(AHR)のリガンドであるインドールにてその発育が抑制される、4. 北大既存薬(3200剤)/オリジナル(2640剤)ライブラリーのスクリーニングで、癌の進行を促進するG蛋白共役胆汁酸受容体(TGR5)やHIVインテグラーゼの阻害剤などがクラミジアの増殖を完全に阻止した]から、Ctが細胞内で利用している新たな細胞内情報伝達経路とそれら修飾に関わる分泌エフェクター分子を同定すると共に、それら分子の中から癌治療の標的となりうる分子を探ることを目的とする。その結果、初年度の実験にて、以下の成果を得た。
    1. Ct感染細胞では低酸素状態にて感染後30分でAKT(Ser473)リン酸化が起こり、持続することを見いだした。
    2. インドールがCtが細胞内で増殖を抑制し、その機構として芳香族炭化水素受容体AhR分子が関与する可能性を示唆する結果を得た。
    3. Ctの通常酸素下でのミトコンドリアの要求性は、NOX4/p38MAPKと関連していることを明らかにした。4. 北大既存薬ライブラリーでヒットした12薬剤についてその有効性について検証し11薬剤がCtの細胞内発育を有意に抑制することを確認し、KEGG解析にてCtが利用すると予想される新規の22の情報伝達系を同定した。
    5. 北大オリジナルライブラリーでヒットした1薬剤についてその有効性について検証し、KEGG解析にてCtが利用すると予想される新規標的分子候補を同定した。
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 21H02726
  • Elucidation of colonization mechanism of an international high-risk pathogenic bacteria in the community
    Grants-in-Aid for Scientific Research
    01 Apr. 2021 - 31 Mar. 2024
    Sato Toyotaka
    In this study, using fluoroquinolone-resistant E. coli ST131 as a model, we clarified the mode of transmission and establishment of AMR infection, which is a problem in the "nosocomial" setting, from an "extra-hospital (community)" approach, in order to provide scientific knowledge that will contribute to next-generation (hospital-community integrated) AMR control measures that will fundamentally solve the international AMR problem for which the current AMR control measures have been unrewarding. To achieve this objective, we conducted a detailed analysis of ST131 transmission status, modes of transmission, and mechanisms of establishment (identification of establishment factors). This research project identified the molecular epidemiological characteristics of ST131 and factors that are likely to be involved in its in vivo establishment and survival, and led to the elucidation of a new mode of ST131 circulation and establishment mechanism in the community.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 21H03622
  • Understanding and application of microbiota in building environment: creation of pathogen control theory by temperature control
    Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Research (Pioneering)
    30 Jul. 2020 - 31 Mar. 2024
    Yamaguchi Hiroyuki
    This research has shown that by adjusting temperature, one of the universal environmental factors, to match human skin, it is possible to reduce the survivability of pathogenic bacteria on dry surfaces, something that had not been previously assumed. The molecular mechanism may be that when human skin is heated, the body length of pathogenic bacteria cannot be properly controlled on a dry surface. We also demonstrated that the flow of people and their density are related environmental factors that determine the number of bacteria floating in a space. Based on these research results, we are currently working with companies with which we have signed joint research agreements to continue developing a new device that is sustainable, will not select for resistant bacteria, and can suppress and control the number of pathogenic bacteria on frequently touched surfaces.
    Japan Society for the Promotion of Science, Grant-in-Aid for Challenging Research (Pioneering), Hokkaido University, 20K20613
  • 入院患者の日常生活動作レベルがベッド周辺環境の微生物汚染に及ぼす影響
    科学研究費助成事業 基盤研究(C)
    01 Apr. 2020 - 31 Mar. 2024
    下田 智子; 矢野 理香; 山口 博之; 大久保 寅彦
    本研究は、患者の周辺環境への接触とその接触面での細菌の生存を具体的な患者の日常生活動作レベルを精査し、適切な看護実践（環境整備）へ応用することを目指す。
    医療施設において、病原体は手指やその他の媒介物による接触を介して、感受性のある人に移動する可能性があるため病原体で汚染された環境表面の接触伝播経路に着目した。特に患者や医療従事者の手指が接触する機会が多い、ベッド柵やオーバーベッドテーブル等の患者周辺環境に着目した環境の調査研究を計画した。
    2020年度は、新型コロナウイルス感染症の影響を受け、患者が療養している環境での調査が困難となった。そこで、2021年度は新型コロナウイルス感染症が発生する前に調査した結果から交絡因子を検討し、患者周辺の環境微生物汚染度と日常生活動作レベルの差異との関連について、準実験研究を用いて検討する計画へ変更した。
    準実験研究の目的は、模擬病室内の患者周辺環境において、日常生活動作レベルの差異と模擬患者の手が触れる接触面積やアデノシン３リン酸（ATP）値との関連を検討した。模擬患者（12名）に先行研究で看護師の動作が分析されている車いすへの移乗を依頼した。その際のベッド周辺環境への接触面積やATP値を測定した。日常生活動作レベルの差異と模擬患者の手が触れる接触面積には相関関係がなかった。しかし、ATPで評価した環境微生物汚染度は、日常生活動作レベルが高くなるほど高値を示した。本結果は、模擬患者の日常生活動作レベルの差異とベッド周辺環境の汚染度に関連がある可能性を示唆したと考える。
    日本学術振興会, 基盤研究(C), 札幌医科大学, 20K10626
  • Dissemination of antimicrobial-resistant bacteria from hospital sewage to natural environments
    Grants-in-Aid for Scientific Research Grant-in-Aid for Early-Career Scientists
    01 Apr. 2019 - 31 Mar. 2022
    Okubo Torahiko
    In this study, extended-spectrum β-lactamase-producing E. coli (n=44) were isolated from manhole sewage. Although there was no significant difference in the frequency of resistance between general facility sewage and hospital sewage, the hospital sewage-derived strain was resistant to fluoroquinolones in addition to β-lactam resistance. These results indicate that sewage is an important pathway for the spread of drug-resistant bacteria into the environment, and that hospital sewage in particular contains drug-resistant bacteria that have become highly resistant. In addition, Anteglaucoma harbinensis and nine other strains of ciliates were isolated from sewage. Anteglaucoma showed a unique characterization of Legionella susceptibility, which provided a secondary ciliate useful as a tool in the search for virulence factors of Legionella.
    Japan Society for the Promotion of Science, Grant-in-Aid for Early-Career Scientists, Hokkaido University, 19K19403
  • The collaborative research project for drug resistance bacteria in animal agriculture of tropical Africa and finding the alternatives for drug use.
    Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (A)
    01 Apr. 2016 - 31 Mar. 2020
    USHIDA Kazunari
    Drug resistance bacteria (DRB) was emerged from human therapies and the animal agriculture. In a recent trend, prevalence of DRB decreased in developed countries. However, it is growing in developing countries. In this study we made a surveillance of DRB in Ugandan animal agriculture, where economic growth pushes the intensive animal production. We also collected potentially probiotic lactic acid bacteria from domestic birds under extensive feeding systems and wild birds for the future reduction of the antimicrobials in animal agriculture. We detected mostly tetracycline-resistant bacteria from feces and meet products of Ugandan livestock. However, we detected several multidrug-resistant ESBL Escherichia coli from feces of scavenging bird in abattoirs and dumping site of Capital city, which indicate the potential risk for transmission of ESBL by these wild birds. We have successfully isolated several potential probiotic lactobacilli from domestic and wild birds.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (A), 16H02767
  • 熱帯アフリカにおける畜産由来薬剤耐性菌発生の実態把握と対策の提案
    KAKENHI
    Apr. 2016 - Mar. 2020
    牛田一成
    JSPS, Competitive research funding
  • Exploring critical factors responsible for regulating the survival of Chlamydia trachomatis into cervical mucosa
    Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    01 Apr. 2016 - 31 Mar. 2019
    Yamaguchi Hiroyuki
    Chlamydia trachomatis is the leading cause of bacterial sexually transmitted infections, with an estimated 131 million new cases annually worldwide. Although IFN-γ is a critical defense factor against C. trachomatis genital infection that acts by depleting host cellular tryptophan pool, the presence of indole, which is a precursor for tryptophan, can rescue genital chlamydiae despite depletion of tryptophan in IFN-γ-exposed cells in vitro, presumably, the higher vaginal indole amount prolongs the survival of C. trachomatis in the vaginal tract. Here, using the 554 cervical swabs with the prevalence of C. trachomatis infection, we indicated that the flow of bacteria through the anogenital route along with gut indole, had a strong impact on the prevalence of C. trachomatis in the cervicogenital tract of women. We also established a standardized chlamydial culture method in hypoxia and the detection system of apoptosis with caspase-3 expressing HEp-2 cells into chlamydia-infecte cells.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 16H05225
  • The role of amoebal endosymbiont in predator-prey interactions
    Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory Research
    01 Apr. 2016 - 31 Mar. 2019
    Yamaguchi Hiroyuki
    We explored the role of the endosymbiont in predator‐prey interactions using symbiotic amoebae (Neochlamydia-symbiotic acanthamoeba: S13 amoebae). As a result, we found here for the first time as follows: 1. the presence of symbiotic Neochlamydia S13 inhabited in the S13 amoebae could be responsible for the restriction of phagocytic activity of Legionella in specific, resulting in the defense of the amoebae against Legionella infection. 2. S13 amoebae required the Neochlamydia endosymbiont to backpack human pathogenic bacteria and resist Legionella infection on solid agar. These findings might contribute not only to an understanding of the host-parasite relationship, but also to development of a novel strategy against complicated infectious diseases with intracellular parasites.
    Japan Society for the Promotion of Science, Grant-in-Aid for Challenging Exploratory Research, Hokkaido University, 16K15270
  • アメーバ共生細菌原始クラミジアのレジオネラ撃退に関わる分子マシナリーの探索
    KAKENHI
    Apr. 2016 - Mar. 2019
    山口博之
    JSPS, Competitive research funding
  • 腟菌叢とメタボローム: クラミジア卵管線維化機構とPID診断バイオマーカーの探索
    KAKENHI
    Apr. 2016 - Mar. 2019
    山口博之
    JSPS, Competitive research funding
  • Effect of bacterial signal molecule AI-2 on the metabolism and pathogenicity of protozoa
    Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)
    01 Apr. 2016 - 31 Mar. 2018
    Okubo Torahiko; YAMAGUCHI Hiroyuki; MATSUO Junji; NAKAMURA Shinji; MATSUSHITA Mizue; AKIZAWA Kouji; HAYASAKA Kasumi; FUKUMOTO Tatsuya; IWASAKI Sumio
    AI-2 is a bacterial signal molecule which is used for bacterial closs talk. In our previous studies, we reported that co-cultivation of bacteria and protozoa causes the raise of AI-2 concentration in the solution. However, the effect of AI-2 on protozoa was not reported. In this study, we compared phenotypic characteristics of protozoa under the presence or absence of AI-2. Our results showed that AI-2 causes the raise of mobility of amoeba cells in a concentraion dependent manner on solid agar surfaces. This suggests that amoeba can detect AI-2 concentration and control its mobility. We showed cross-Kingdom effect of AI-2 on protozoa for the first time.
    Japan Society for the Promotion of Science, Grant-in-Aid for Young Scientists (B), Hokkaido University, 16K19113
  • 細菌由来シグナル分離AI-2が原生生物の代謝及び病原性に与える影響の解明
    KAKENHI
    Apr. 2016 - Mar. 2018
    Torahiko Okubo
    JSPS, Principal investigator, Competitive research funding
  • 市販鶏肉の表面で繰り広げられる細菌と原生動物の相互作用の可視化と応用
    科学研究費助成事業 研究活動スタート支援
    28 Aug. 2015 - 31 Mar. 2016
    大久保 寅彦
    1. 市販鶏肉上で生じている細菌と原生動物の相互作用を可視化するという当初計画に基づき、予備試験、鶏肉サンプルの採材、微生物叢解析、原生動物の分離培養を実施した。
    2. 鶏肉とアメーバまたはアメーバDNAを用いた予備試験により、鶏肉からの原生動物の検出限界は、培養法で1,000cell/g、遺伝子検出法（PCR）で0.1cell/gであると求められた。
    3. 市販鶏肉を購入し、(1)当日 (2)4℃ 2days (3)4℃ 7days (4)15℃ 2days (5)15℃ 7daysの条件で静置後にDNAを抽出し、微生物叢解析を行なった。16S rDNAに基づく細菌叢解析の結果、当日サンプルではガンマプロテオバクテリアやバシルスなどが多く、細菌叢に多様性がみられたのに対し、4℃静置サンプルではガンマプロテオバクテリアが圧倒的多数となっていた。属レベルで見た場合、こうしたガンマプロテオバクテリアの多くはエロモナス、シュードモナスなどの水系細菌・低温発育菌であったことから、こうした細菌は冷蔵した鶏肉の上で増殖し続けていたと考えられた。一方、15℃静置サンプルにおいては、2days時点ではガンマプロテオバクテリアが優占化したが、7days時点ではバクテロイデスの大幅な増加がみられた。これは好気性菌の増殖によって鶏肉表面の酸素が消費されたことによるものと考えられる。
    4. 当初、18S rDNAにもとづく原生生物叢の解析を実施予定であったが、ニワトリ由来DNAが障害となって解析を実施できなかった。分離培養では、2サンプルから2種類の鞭毛虫(Parabodo sp., Sandona sp.)を得た。これらの鞭毛虫と食中毒菌(E.coli, Salmonella Enteritidis)の共培養を実施したが、鞭毛虫は細菌数の増減に有意な影響を与えなかった。
    5. 鶏肉表面で生じている細菌叢構成の劇的な変化、および鶏肉に付着する鞭毛虫を検出した。今回は食中毒菌と相互作用する原生動物は得られなかったが、今後の調査により細菌の生存性や病原性に影響する微生物の検出につなげたい。
    日本学術振興会, 研究活動スタート支援, 北海道大学, 15H05997
  • 市販鶏肉表面で繰り広げられる細菌と原生生物の相互作用の可視化と応用
    KAKENHI
    Sep. 2015 - Mar. 2016
    Torahiko Okubo
    JSPS, Principal investigator, Competitive research funding
■ Academic and Social Contribution Activities/Other
Industrial Property Rights
  • Editorial board member of Microbes and Environments
    Peer review
    Peer review etc
Social Contribution Activities
  • ウガンダ国絶滅危惧種ヨウム保全の地域連携モデルケース構築支援
    2021 - 2025
    Advisor, Report writing
    独立行政法人国際協力機構（JICA）
  • JICA short term volunteer
    01 Mar. 2012 - 31 May 2012
    Advisor
    torahiko
    短期派遣ボランティアとしてウガンダでの家畜疾病診断ラボ構築プロジェクトに参加。