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Microbiology and ImmunologyMolecular Bacteriology


We study on virulence factors and drag-resistance mechanisms of pathogenic bacteria, which cause healthcare-associated and community-acquired infections, such as Staphylococcus sp. including MRSA, Streptococcus sp., Bacillus sp., Enterococcus sp., Enterobacteriaceae sp. (Escherichia, Klebsiella etc.), Glucose non-fermenting sp. (Pseudomonas, Acinetobacter etc.), Haemophilus sp. and so on. We research to improve in diagnosis/prevention/treatment of bacterial infections through our analysis techniques for genome and proteome (LC-MS/MS etc.) besides basic bacteriological methods.

Research Projects

  1. Mechanisms of drag-resistance and molecular epidemiology in pathogenic bacteria
  2. Virulence factors and their expressions/regulations
  3. Analyses of genome, proteome, and metabolome for regulation of bacterial infections.

Faculty Members

SHIBAYAMA keigo Professor & Chair Bacteriology / Drug Resistance and Pathogenesis
KIMURA Kouji Associate Professor Bacteriology / Drug Resistance and Pathogenesis
WACHINO Jun-ichi Lecturer Bacteriology / Drug Resistance and Pathogenesis
Wanchun JIN Assistant Professor Bacteriology / Drug Resistance and Pathogenesis
Anupriya KUMAR Assistant Professor Bacteriology / Drug Resistance and Pathogenesis


  • 2016
    1. Cao XL, Shen H, Xu YY, Xu XJ, Zhang ZF, Cheng L, Chen JH, Arakawa Y.High prevalence of fosfomycin resistance gene fosA3 in bla CTX-M-harbouring Escherichia coli from urine in a Chinese tertiary hospital during 2010-2014. Epidemiol Infect, 2016; 12:1-7.
    2. Ohno H, J. Wachino,. Saito R, Jin W, Yamada K, Kimura K, Arakawa Y.A highly macrolide-resistant Campylobacter jejuni strain with rare A2074T mutations in 23S rRNA genes. Antimicrob Agents Chemother, 2016; 60(4):2580-2581.
    3. Nakane K, Kawamura K, Goto K, Arakawa Y.Long-term colonization of blaCTX-M-harboring Escherichia coli found in ordinary Japanese people engaged in food handling in community. Appl Environ.Microbiol, 2016; 82(6):1818-1827.
    4. Fukigai S¶, Morimoto M¶, Kimura K, Doyama Y, Miyazaki A, Kamiya C, Banno H, Morishima E, Onoda T, Nagano N, Jin W, Wachino J, Yamada K, Arakawa Y.Effectual detection of group B streptococci with reduced penicillin susceptibility (PRGBS) by commercially available methicillin-resistant-Staphylococcus aureus (MRSA)-selective agar. Diagn Microbiol Infect Dis, 2016; 85(3):309-312.¶ Equally contribution Taniguchi R, Kimura K*, Miyazaki A, Banno, H Jin W, Yamada K., Wachino J, Arakawa Y.
    5. High rate of slowly-killed-by-ampicillin phenotype among group B streptococci with reduced penicillin susceptibility (PRGBS).
    6. Antimicrob Agents Chemother in press.
    7. Inaba M, Matsuda N, Banno H, Jin W, Wachino J, Yamada K, Kimura K, Y. Arakawa .In vitro reduction of antibacterial activity of tigecycline against multidrug-resistant Acinetobacter baumannii with host stress hormone norepinephrine.Int J Antimicrob Agents 2016 ;48(6):680-689.
    8. Wachino J,Yamaguchi Y, Mori S , Jin W,Kimura K, Kurosaki H, Y. Arakawa Structural insights into recognition of hydrolyzed carbapenems and inhibitors by subclass B3 metallo-β-lactamase SMB-1. Antimicrob Agents Chemother 2016; 60(7): 4274-4282
  • 2015
    1. Fujita A,Kimura K,Yokoyama S,Jin W,Wachino J,Yamada K, Suematsu H,Yamagishi Y,Mikamo H,Arakawa Y. Characterization of piperacillin/tazobactam-resistant Klebsiella oxytoca recovered from a nosocomial outbreak. PLOS ONE, 2015;10(11):e0142366.
    2. Seki T, Kimura K, Reid M.E, Miyazaki A, Banno H, Jin W, Wachino J, Yamada K, Arakawa Y.High isolation rate of multi-drug resistant group B streptococci with reduced penicillin susceptibility in Japan. Antimicrob Agents Chemother 2015;70(10):2725-2728.
    3. Kasama T, Ikami M, Jin W, Yamada K, Kaji N, Atsumi Y. Mizutani M, Okamoto A, Namikawa T, Ohta M, Tokeshi M, Baba Y.Rapid, highly sensitive, and simultaneous detection of staphylococcal enterotoxins in milk by using immuno-pillar devices. Anal Methods, 2015; 82(4):269-273.
    4. Kimura K, Nagano N, Arakawa Y.Classification of Group B Streptococci with Reduced β-Lactam Susceptibility (GBS-RBS) Based on the Amino Acid Substitutions in Penicillin-binding Proteins (PBPs). Antimicrob Agents Chemother,2015; 70(6):1601-1603.
    5. Jin W, Wachino J, Kimura K, Yamada K, Arakawa Y.New plasmid-mediated aminoglycoside 6'-N-acetyltransferase, AAC(6')-Ian, and extended-spectrum β-lactamase, TLA-3, from Serratia marcescens clinical isolate.J Antimicrob Chemother,2015;70(5):1331-1337.
    6. Yamada R, Kimura K, Nagano N, Nagano Y, Suzuki S, Jin W, Wachino J, Yamada K, Shibayama K, Arakawa Y. Comparative Analysis of Penicillin-Susceptible and Non-Susceptible Isolates in Group B Streptococci by Multilocus Sequence Typing. Jpn J Infect Dis, 2015; 68(4):326-329.
    7. Yamaguchi Y, Matsueda S, Matsunaga K, Takashio N, Toma-Fukai S, Yamagata Y, Shibata N, Wachino J, Shibayama K, Arakawa Y, Kurosaki H.Crystal structure of IMP-2 metallo-β-lactamase from Acinetobacter spp.: Comparison of active-Site loop structures between IMP-1 and IMP-2. Biol Pharm Bull, 2015; 38(1):96-101,.
    8. Suzuki T, Kimura K, Suzuki H, Banno H, Jin W, Wachino J, Yamada K, Arakawa Y.Have group A streptococci with reduced penicillin susceptibility emerged?J Antimicrob Chemother, 2015; 70(4):1258-1259.
    9. Nagasaka Y, Kimura K, Yamada K, Wachino J, Jin W, Notake S, Yanagisawa H, Arakawa Y.Genetic profiles of fluoroquinolone-nonsusceptible Klebsiella pneumoniae among cephalosporin-resistant K. pneumoniae.Microb Drug Resist ,2015;(2):224-233.
    10. Ito R, Shindo Y, Kobayashi D, Ando M, Jin W, Wachino J, Yamada K, Kimura K, Yagi T, Hasegawa Y, Arakawa Y.Molecular Epidemiological Characteristics of Klebsiella pneumoniae Associated with Bacteremia among Patients with Pneumonia.J Clin Microbiol, 2015; 53(3):879-886.
    11. Umene YD, Wong LK, Satoh T,Yamane K,Matsui M,Riley LW, Arakawa Y,Suzuki S.Molecular epidemiological characterization of uropathogenic Escherichia coli from an outpatient urology clinic in rural Japan.J Clin Microbiol,2015; 3(2):681-683.
    12. Asai K,Yamada K,Yagi T,Baba H,Kawamura I,Ohta M.Effect of incubation atmosphere on the production and composition of staphylococcal. biofilms J Infect Chemother, 2015 21(1):55–61,
  • 2014
    1. Nagasawa M, Kaku M, Kamachi K, Shibayama K, Arakawa Y, Yamaguchi K, Ishii Y.Loop-mediated isothermal amplification assay for 16S rRNA methylase genes in Gram-negative bacteria.J Infect Chemother, 2014;20:635-638,.
    2. Mori S, Kim H, Rimbara E, Arakawa Y, Shibayama K.Roles of Ala-149 in the catalytic activity of diadenosine tetraphosphate phosphorylase from Mycobacterium tuberculosis H37Rv.Biosci Biotechnol Biochem, 2014; 28:1-3,.
    3. Wachino J, Kimura K, Yamada K, Jin W, Arakawa Y.Evaluation of disk potentiation test using KB disks containing high dosage fosfomycin and glucose-6-phosphate to detect the production of glutathione S-transferase responsible for fosfomycin resistance.J Clin Microbiol, 2014;(10):3827-3828,.
    4. Kitanaka H, Sasano M, Yokoyama S, Suzuki M, Jin W, Inayoshi M, Hori M, Wachino J, Kimura K, Yamada K, Arakawa Y.Carbapenem-resistant Acinetobacter soli as a newly emerging invasive pathogen.Emerg Infect Dis. 2014 ;20(9):1574-1576.
    5. Nakamura G, Wachino J, Sato N, Kimura K, Yamada K, Jin W, Shibayama K, Yagi T , Kawamura K, Arakawa Y. Practical agar-based disk potentiation test to detect fosfomycin−non-susceptible Escherichia coli clinical isolates producing glutathione S-transferases.J Clin Microbiol, 2014; 52(9):3175-3179.
    6. Nagano N, Nagano Y, Toyama M, Kimura K, Shibayama K, Arakawa Y.Penicillin-susceptible group B streptococcal clinical isolates with reduced cephalosporin susceptibility. J Clin Microbial, 2014;52(9):3406-3410.
    7. Suzuki M, Hosoba E, Matsui M, Arakawa Y.New PCR-based genotyping method for easy, rapid and reliable identification of Acinetobacter baumannii international epidemic clones without performing MLST.J. Clin. Microbiol, 2014; 58(8):2925-2932.
    8. Kitanaka H, Wachino J, Jin W, Yokoyama S, Sasano M, Hori M, Yamada K, Kimura K, Arakawa Y.Novel integron-mediated fosfomycin-resistance genetic determinant, fosK.Antimicrob Agents Chemother, 2014;58(8):4978-4979.
    9. Okamoto A, Lee H, Yabutani M, Yamada K, Ohta M. Draft genome sequence of a Legionella pneumophila serogroup 4 strain causing legionellosis. Genome Announc, 2014;2(3):602-614.
    10. Banno H, Kimura K, Tanaka Y, Kitanaka H, Jin W, Wachino J, Yamada K, Shibayama K, Arakawa Y.Characterization of multi-drug-resistant group b streptococci with reduced penicillin susceptibility (PRGBS) forming small non-β-hemolytic colonies on sheep blood agar plates.J Clin Microbiol, 2014;52(6):2169-2171.
    11. Matsui M, Suzuki S, Yamane K, Suzuki M, Konda T, Arakawa Y, Shibayama K.Distribution of carbapenem resistance determinants among epidemic and non-epidemic types of Acinetobacter species in Japan.J Med Microbiol, 2014;63(pt 6):870-877.
    12. Bart MJ, Harris SR, Advani A, Arakawa Y, Bottero D, Bouchez V, Cassiday PK, Chiang CS, Dalby T, Fry NK, Gaillard ME, van Gent M, Guiso N, Hallander HO, Harvill ET, He Q, van der Heide HG, Heuvelman K, Hozbor DF, Kamachi K, Karataev GI, Lan R, LutyR,ev A, Maharjan RP, Mertsola J, Miyamura T, Octavia S, Preston A, Quail MA, Sintchenko V, Stefanelli P, Tondella ML, Tsang RS, Xu Y, Yao SM, Zhang S, Parkhill J, Mooi FR.Global population structure and evolution of Bordetella pertussis and their relationship with vaccination.MBio, 2014;5(2):e01074.
    13. Kawamura K, Goto K, Nakane K, Arakawa Y.Molecular epidemiology of extended-spectrum β-lactamases and Escherichia coli iso lated from retail foods including chicken meat in Japan.Foodborne Pathog Dis. 2014;11(2):104-110.
  • 2013
    1. Matsui M, Suzuki S, Suzuki M, Arakawa Y, Shibayama K.Rapid discrimination of Acinetobacter baumannii international clone II lineage by pyrosequencing SNP analyses of bla(OXA-51-like) genes.J Microbiol Methods, 2013;94(2):121-124.
    2. Ato M, Takahashi Y, Fujii H, Hashimoto S, Kaji T, Itamura S, Horiuchi Y, Arakawa Y, Tashiro M,Takemori T.Influenza A whole virion vaccine induces a rapid reduction of peripheral blood leukocytes via interferon-α-dependent apoptosis.Vaccine,2013; 31(17):2184-2190.
    3. Kimura K, Yanagisawa H, Wachino J, Shibayama K, Arakawa Y.Rapid and reliable loop-mediated isothermal amplification method for detecting Streptococcus agalactiae.Jpn J Infect Dis, 2013; 66(6): 546-548.
    4. Nagano N, Endoh Y, Nagano Y, Toyama M, Matsui M, Shibayama K, Arakawa Y.First report of oxa-48 carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in Japan from a patient returned from Southeast Asia.Jpn J Infect Dis, 2013; 201; 66:79-81.
    5. Matsuoka M, Sasaki T, Seki N, Kobayashi M, Sawabe K, Sasaki Y, Shibayama K, Sasaki T, Arakawa Y.Hemin-binding proteins as potent marker for serological diagnosis of infections with Bartonella quintana.Clin Vaccine Immunol, 2013; 20(4):620-626.
    6. Wachino J, Yamaguchi Y, Mori S, Kurosaki H, Arakawa Y, Shibayama K.Structural insights into the subclass B3 metallo-β-lactamase SMB-1 and the mode of inhibition by the common metallo-β-lactamase inhibitor mercaptoacetate.Antimicrob Agents Chemother, 2013; 57:101-109.
    7. Jin W, Yamada K, Ikami M, Kaji N, Tokeshi M, Atsumi Y, Mizutani M, Murai A, Okamoto A, Namikawa T, Baba Y, Ohta M. Application of IgY to sandwich enzyme-linked immunosorbent assays, lateral flow devices, and immunopillar chips for detecting staphylococcal enterotoxins in milk and dairy products. J Microbiol Methods, 2013; 92:323–331.
    8. Kimura K, Wachino J, Kurokawa H, Matsui M, Suzuki S, Yamane K, Nagano N, Shibayama K, Arakawa Y.High cephalosporin resistance due to amino acid substitutions in PBP1A and PBP2X in a clinical isolate of group B streptococcus.J Antimicrob Chemother , 2013; 68(7):1533-1536.
    9. Kimura K, Nishiyama Y, Shimizu S, Wachino J, Matsui M, Suzuki S, Yamane K, Shibayama K, Arakawa Y.Screening for group B streptococci with reduced penicillin. susceptibility in clinical isolates obtained between 1977 and 2005. Jpn J Infect Dis, 2013; 66(3):222-225.
    10. Kimura K, Matsubara K, Yamamoto G, Shibayama K, Arakawa Y.Active screening of group B streptococci with reduced penicillin susceptibility and altered serotype distribution, isolated from pregnant women in Kobe, Japan. Jpn J Infect Dis,2013; 66(2):158-160.
    11. Kimura K, Nagano N, Nagano Y, Wachino J, Shibayama K, Arakawa Y.Ability of the VITEK® 2 system to detect group B streptococci with reduced penicillin susceptibility. J Antimicrob Chemother, 2013; 68(6):1442-1444.
    12. Yamada K, Jin W, Ohkura T, Murai A, Hayakawa R, Kinoshita K, Mizutani M, Okamoto A, Namikawa T, Ohta M. Detection of methicillin-resistant Staphylococcus aureus using specific anti-pbp2a chicken igY antibody. Jpn J Infect Dis, 2013; 66(2):103-108.
    13. Kimura K, Nagano N, Nagano Y,Suzuki S, Wachino J, Shibayama K, Arakawa Y.High frequency of fluoroquinolone- and macrolide-resistant streptococci among clinically isolated group B streptococci with reduced penicillin susceptibility.J Antimicrob Chemother , 2013; 68(3): 539-542.
  • 2012
    1. Nomura T, Tanimoto K, Shibayama K, Arakawa Y, Fujimoto S, Ike Y, Tomita H.Identification of VanN-type vancomycin resistance in an Enterococcus faecium isolate from chicken meat in Japan.Antimicrob Agents Chemother, 2012; 56: 6389-6392.
    2. Wachino J, Arakawa Y.Exogenously acquired 16S rRNA methyltransferases found in aminoglycoside-resistant pathogenic Gram-negative bacteria:an update.Drug Resist Updat, 2012; 15:133-148.
    3. Wachino J, Yamaguchi Y, Mori S, Yamagata Y, Arakawa Y, Shibayama K.Crystallization and preliminary X-ray analysis of the subclass B3 metallo-β-lactamase SMB-1 that confers carbapenem resistance.Acta Crystallogr Sect F Struct Biol Cryst Commun, 2012; 68: 343-346.
    4. Otsuka N, Han HJ, Toyoizumi-Ajisaka H, Nakamura Y, Arakawa Y, Shibayama K, Kamachi K.Prevalence and genetic characterization of pertactin-deficient Bordetella pertussis in Japan.PLoS One, 2012; 7(2):e31985.
    5. Nagano N, Nagano Y, Toyama M, Kimura K, Tamura T, Shibayama K, Arakawa Y.Nosocomial spread of multidrug-resistant group B streptococci with reduced penicillin susceptibility belonging to clonal complex 1.J Antimicrob Chemother, 2012; 67:849-856.
    6. Lee SY, Park YJ, Yu JK, Jung S, Kim Y, Jeong SH, Arakawa Y,Prevalence of acquired fosfomycin resistance among extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae clinical isolates in Korea and IS26-composite transposon surrounding fosA3.J Antimicrob Chemother, 2012; 67:2843-2847.
    7. Takeno A, Okamoto A, Torii K, Oshima K, Hirakawa H, Toh H, Agata N, Yamada K, Ogasawara N, Hayashi T, Shimizu T, Kuhara S, Hattori M, and Ohta M, complete genome sequence of Bacillus cereus NC7401, which produces high levels of the emetic toxin cereulide. J Bacteriol, 2012;194(17):4767-4768.
  • 2011
    1. Sekizuka T, Matsui M, Yamane K, Takeuchi F, Ohnishi M, Hishinuma A, Arakawa Y, Kuroda M,Complete sequencing of the bla(NDM-1)-positive IncA/C plasmid from Escherichia coli ST38 isolate suggests a possible origin from plant pathogens.PLoS One, 2011; 6(9):e25334.
    2. Mori S, Shibayama K, Wachino J, Arakawa Y.Structural insights into the novel diadenosine 5',5‴-P¹,P⁴-tetraphosphate phosphorylase from Mycobacterium tuberculosis H37Rv.J Mol Biol, 2011; 410:93-104.
    3. Han HJ, Kuwae A, Abe A, Arakawa Y, Kamachi K,Differential expression of type III effector BteA protein due to IS481 insertion in Bordetella pertussis.PLoS One, 2011; 6(3):e17797.
    4. Shibayama K, Takeuchi H, Wachino J, Mori S, Arakawa Y.Biochemical and pathophysiological characterization of Helicobacter pylori asparaginase.Microbiol Immunol, 2011; 55:408-417.
    5. Okamoto A, Yamada K.Proteome driven re-evaluation and functional annotation of the Streptococcus pyogenes SF370 genome. BMC Microbiol,2011;11:249.
    6. Okamoto A, Hasegawa T, Yamada K, and Ohta M. Application of both high-performance liquid chromatography combined with tandem mass spectrometry shotgun and 2-D polyacrylamide gel electrophoresis for streptococcal exoproteins gave reliable proteomic data. Microbiol Immunol, 2011; 55(2):84-94.
    7. Tomita Y, Ohta M, Yamada K, Okamoto A, Yagi T, and Hasegawa Y. A new microarray system to detect Streptococcus pneumoniae serotypes. J Biomed Biotech, 2011; 352736.
    8. Kimura K, Nagano N, Nagano Y, Wachino J, Suzuki S, Shibayama K, Arakawa Y.Predominance of sequence type 1group with serotype VI among group B streptococci with reduced penicillin susceptibility identified in Japan.J Antimicrob Chemother, 2011; 66:2460-2464.
    9. Wachino J, Yoshida H, Yamane K, Suzuki S, Matsui M, Yamagishi T, Tsutsui A, Konda T, Shibayama K, Arakawa Y.SMB-1, a novel subclass B3metallo-β-lactamase, associated with ISCR1 and a class 1 integron,from a carbapenem-resistant Serratia marcescens clinical isolate. Antimicrob Agents Chemother, 2011; 55:5143-5149.
    10. Wachino J, Yamane K, Arakawa Y. Practical disk-based method for detection of Escherichia coli clinical isolates producing the fluoroquinolon e-modifying enzyme AAC(6')-Ib-cr. J Clin Microbiol, 2011; 49:2378-2379.
    11. Tsutsui A ,Suzuki S, Yamane K ,Matsui M , Konda T, Marui E, Takahashi K , Arakawa Y. Genotypes and infection sites in an outbreak of multidrug-resistant Pseudomonas aeruginosa. J Hosp Infect, 2011; 78:317-322.
    12. Yamaguchi Y, Imamura K,Sasao A, Murakami E,Arakawa Y, Kurosaki H. Metal Preference of Zn(II)and Co(II) for DinuclearMetal Binding Site of IMP-1Metallo-β-lactamase and of Co(II)-substituted IMP-1 with Mercaptoacetic acid.Med Chem Commun, 2011; 2:720-725.
    13. Yamaguchi Y, Ding S, Murakami E, Imamura K, Fuchigami S, Hashiguchi R, Yutani K, Mori H, Suzuki S, Arakawa Y, Kurosaki H . A demetallation method for imp-1metallo-β-lactamase that has restored enzymatic activity upon addition of metal Ion(s). ChemBioChem, 2011; 12:1979-1983.

Call for graduate students

※ We welcome passionate graduate students who are interested in the mechanisms of infectious diseases and antibiotic resistance. In our laboratory, there are students with a background in biology, graduating from a medical, pharmacological or agricultural department etc, though the background is not strictly asked to enter the lab. After completing the course, they work as clinicians, pharmacists, nurses, clinical laboratory technicians, national/local government officers, or university faculties etc.

We also welcome undergraduate students who are interested in basic research. Students continue and develop their research after finishing the course for medical student (''KISOIGAKU seminor''), and they have opportunities of conference presentations inside and outside the country. Since the study on infectious diseases is closely linked to clinical practice, the knowledge and technique obtained through research experience in this laboratory will be greatly valuable for the career in future.