Atsushi Hase

Nagasaki University, Nagasaki, Nagasaki, Japan

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Publications (38)63.84 Total impact

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    ABSTRACT: Intra-species phylogeny of Mycobacterium tuberculosis has been regarded as a clue to estimate its potential risk to develop drug-resistance and various epidemiological tendencies. Genotypic characterization of variable number of tandem repeats (VNTR), a standard tool to ascertain transmission routes, has been improving as a public health effort, but determining phylogenetic information from those efforts alone is difficult. We present a platform based on maximum a posteriori (MAP) estimation to estimate phylogenetic information for M. tuberculosis clinical isolates from individual profiles of VNTR types. This study used 1245 M. tuberculosis clinical isolates obtained throughout Japan for construction of an MAP estimation formula. Two MAP estimation formulae, classification of Beijing family and other lineages, and classification of five Beijing sublineages (ST11/26, STK, ST3, and ST25/19 belonging to the ancient Beijing subfamily and modern Beijing subfamily), were created based on 24 loci VNTR (24Beijing-VNTR) profiles and phylogenetic information of the isolates. Recursive estimation based on the formulae showed high concordance with their authentic phylogeny by multi-locus sequence typing (MLST) of the isolates. The formulae might further support phylogenetic estimation of the Beijing lineage M. tuberculosis from the VNTR genotype with various geographic backgrounds. These results suggest that MAP estimation can function as a reliable probabilistic process to append phylogenetic information to VNTR genotypes of M. tuberculosis independently, which might improve the usage of genotyping data for control, understanding, prevention, and treatment of TB. Copyright © 2015. Published by Elsevier B.V.
    No preview · Article · Jul 2015 · Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases

  • No preview · Article · Jan 2015
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    Full-text · Dataset · Nov 2014
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    ABSTRACT: Viruses are the major etiological agents of acute respiratory infections (ARIs) in young children. Although respiratory virus co-detections are common, analysis of combinations of co-detected viruses has never been conducted in Japan. Nineteen respiratory viruses or subtypes were surveyed using multiplex real-time PCR on 1,044 pediatric (patient age < 6 years) ARI specimens collected in Osaka City, Japan between January 2010 and December 2011. In total, 891 specimens (85.3%) were virus positive (1,414 viruses were detected), and 388 of the virus-positive specimens (43.5%, 388/891) were positive for multiple viruses. The ratio of multiple/total respiratory virus-positive specimens was high in children aged 0-35 months. Statistical analyses revealed that human bocavirus 1 and human adenovirus were synchronously co-detected. On the other hand, co-detections of human parainfluenza virus type 1 (HPIV-1) with HPIV-3, HPIV-3 with human metapneumovirus (hMPV), hMPV with respiratory syncytial virus A (RSV A), hMPV with influenza virus A (H1N1) 2009 (FLUA (H1N1) 2009), RSV A with RSV B, and human rhinovirus and FLUA (H1N1) 2009 were exclusive. These results suggest that young children (<3 years) are highly susceptible to respiratory viruses, and some combinations of viruses are synchronously or exclusively co-detected.
    Full-text · Article · Nov 2014 · Japanese journal of infectious diseases
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    ABSTRACT: Introduction: Viruses are major aetiological agents of acute respiratory infection in young children. Although many studies have reported detection and analysis of respiratory viruses in sporadic cases, there have been few follow-up studies of individuals. The purpose of this study was to investigate the frequency of respiratory viral infections in a young child and to examine the duration of viral genome detection in clinical specimens. Case presentation: A total of 284 nasal swabs were collected during symptomatic (196 specimens) and asymptomatic (88 specimens) periods of respiratory symptoms from a young female child (from 4 months to 31 months of age, who was admitted to a nursery school at 9 months). Multiplex real-time PCR for 19 respiratory viruses or subtypes was performed. One hundred and ninety-eight of the tested specimens were virus positive (69.7 %) (symptomatic periods, 149/196, 76.0 %; asymptomatic periods, 49/88, 55.7 %). Rhinovirus was the most frequently detected (26 times). Long durations of detection were observed for human coronavirus NL63 (30 days), rhinovirus (28 days) and human bocavirus 1 (22 days). Conclusion: Young children living in a group context have a high risk of respiratory virus infections, especially rhinovirus. In some instances, viral genomes were detectable for about 1 month by PCR.
    Full-text · Article · Oct 2014
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    ABSTRACT: Capnocytophaga canimorsus, which is often found in the oral cavities of dogs and cats, is sometimes transmitted to humans, causing severe infection. To elucidate the risk of C. canimorsus in humans and animals, this study was undertaken to characterize this bacterium epidemiologically and genetically. We examined the distribution of C. canimorsus in dogs and cats, and analyzed the correlation between the presence of bacteria and individual factors statistically. We also compared C. canimorsus isolates genetically using 16S rRNA gene sequence analysis and pulsed-field gel electrophoresis (PFGE). C. canimorsus was detected in 76 of 109 dogs (69.7%) and 57 of 104 cats (54.8%). A relation between C. canimorsus presence and some individual factors was detected both in dogs and cats, but the predictive factors of carrying the bacterium differed between dogs and cats. 16S rRNA gene sequences from C. canimorsus isolates in this study were combined with previously published sequences to assess their intra-specific phylogeny. Results show that C. canimorsus is classifiable into two main groups (I and II) with differing γ-glutamyl aminopeptidase activity. Strains from human patients belonged unevenly to group I, possibility suggesting that group I can be transmitted to humans and group II is indigenous only to the oral cavities of dogs and cats. PFGE genotyping showed high discriminatory power, and the dendrogram accorded with genetic segregation between isolates of group I and II. Sma I-digest PFGE developed for this study is useful as a molecular typing method for additional epidemiological and phylogenetic studies of C. canimorsus.
    No preview · Article · Jun 2014 · Veterinary Microbiology
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    ABSTRACT: To ascertain the effectiveness of variable number of tandem repeat (VNTR) analysis in areas with a low incidence of tuberculosis (TB), we examined the combination of comprehensive VNTR analyses and field epidemiological investigation results in Yamagata Prefecture, Japan, where estimated incidence of new TB cases per 100,000 population was 11.3 in 2011. We collected Mycobacterium tuberculosis isolates from 184 (69.2%) of 266 pulmonary TB patients across the whole of Yamagata Prefecture between 2009 and 2011. Next, 24 loci [JATA (12), QUB-11a, ETR A, QUB-18, QUB3232, v3820, v4120, MIRU04, MIRU16, MIRU40, ETR C, Mtub30, Mtub39] in VNTR genotypes were determined. The relationships among TB patients derived from the respective clusters were surveyed using field epidemiological investigation results provided by the Public Health Center. Seventeen clusters were formed by 49 (26.6%) of the 184 isolates. We found 3 hospital infection cases, 3 family infection cases, and 1 nursing home infection case forming 6 clusters. Among these cases, two relationships among patients were revealed after additional epidemiological investigation at the Public Health Center. The VNTR pattern of the largest cluster, which was formed by 12 isolates, was identical with that of an incipient patient of a TB mass infection that occurred in 2007. In areas with a low incidence of TB, a combination of comprehensive VNTR analysis and field epidemiological investigation is useful to find unknown transmission routes, identify for new risk groups, and trace mass infections.
    No preview · Article · Jun 2013 · Kekkaku: [Tuberculosis]
  • Aki Tamaru · Takayuki Wada · Tomotada Iwamoto · Atsushi Hase
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    ABSTRACT: To evaluate the usefulness of the JATA (12)-variable number of tandem repeats (VNTR) system for identifying the source of Mycobacterium tuberculosis outbreaks. DESIGN; JATA(12)-VNTR genotyping was performed on M. tuberculosis isolates from a total of 206 patients in whom group infection was confirmed by epidemiological studies ("group infection"), as well as from 64 patient clusters in whom group infection was suspected but not confirmed ("non-group infection"). The patients were diagnosed in Osaka Prefecture from April 1999 to December 2011. All isolates from the "non-group infection" patients showed a unique VNTR pattern, whereas isolates from 185 (89.9%) "group infection" patients showed a common and group-specific JATA (12)-VNTR pattern. However, single-locus variants were observed in 1 (1.6%) "non-group infection" case and in 21 (10.2%) "group infection" cases. Tuberculosis in 248 (91.9%) of the 270 study patients could be correctly identified based on the genotyping of the isolates by using the JATA (12)-VNTR. If proper attention is paid to the single-locus variant, the JATA (12)-VNTR system would be a useful tool for identification of sources of tuberculosis outbreaks.
    No preview · Article · Apr 2013 · Kekkaku: [Tuberculosis]
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    ABSTRACT: Japan Anti-Tuberculosis Association (JATA) (12)-variable numbers of tandem repeats (VNTR) is a standard method for genotyping of clinical isolates of Mycobacterium tuberculosis in Japan. As a model study for nationwide surveillance, this study aimed to describe the tendency and frequency of genotypes of M. tuberculosis in a large number of clinical samples. Clinical isolates of M. tuberculosis (n = 1,778) were obtained from patients with tuberculosis in 3 areas, i.e., Osaka City, Osaka Prefecture, and Kobe City, during 2007 and 2008. The samples were analyzed using JATA (12)-VNTR. All genotypes were subjected to clustering analysis. In total, 1,086 (61.1%) isolates showed clustering. The most common clusters were composed of 3 members. Such clusters were considered to reflect either actual transmission or low discriminatory power of JATA (12)-VNTR. Several prevalent JATA(12)-VNTR genotypes formed large clusters and were discussed in relation with epidemiological findings of other studies. The findings of this study will aid in the construction of an effective genotyping-based surveillance system of M. tuberculosis, through improvement of interpretation of VNTR types, observation of certain particular strains in an area, and efficient detection of unidentified outbreaks.
    No preview · Article · Apr 2013 · Kekkaku: [Tuberculosis]
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    ABSTRACT: Many viruses have been reported to be associated with rash development. Multiplex real-time PCR was used to investigate the presence of 5 viruses associated with rashes: measles virus (MV), rubella virus (RV), human parvovirus B19 (PVB19), human herpes virus 6 (HHV-6), and HHV-7. A total of 187 clinical specimens from 169 patients with erythema were collected between January 2006 and December 2011. Virus-positive specimens were as follows: MV (n = 23), PVB19 (n = 8), RV (n = 2), HHV-6 (n = 5), HHV-7 (n = 1), MV and PVB19 (n = 1), and HHV-6 and HHV-7 (n = 1). All of the MV-positive specimens were collected in 2007 and the strains whose sequence were available (21/24, 87.5%) were of genotype D5. The results indicate that multiplex real-time PCR might be a useful screening method for detecting and differentiating rash-associated viruses in clinical specimens.
    Full-text · Article · Sep 2012
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    ABSTRACT: The Beijing family is an endemic lineage of Mycobacterium tuberculosis in eastern Asia. In Japan, five evolutionarily sequential sublineages composing the lineage have predominated. Comparative genomic sequencing based on a microarray technique was conducted for five representative strains of those respective sublineages. Results revealed approximately 200 point mutations specific to each strain. Subsequently, to investigate the genetic diversity of each sublineage, we analysed the phylogenetic divergence of 103 domestic strains belonging to them using genetic markers derived from the mutation information. Results show that the five sublineages have comprised smaller lineages which had diverged at various points. The smaller sub-sublineages have emerged with respective bottlenecks, which are reflected in the excessive monophyletic evolution of the species. Our data provide necessary information to grasp a comprehensive picture of genetic diversity of the lineage constructed in its evolution.
    No preview · Article · May 2012 · Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases
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    ABSTRACT: TO THE EDITOR: Human enterovirus (HEV) C (family Picornaviridae, genus Enterovirus) consists of 3 types of poliovirus (1, 2, and 3), 9 types of coxsackievirus A (CV-A1, 11, 13, 17, 19, 20, 21, 22, and 24), and 9 types of enterovirus (EV) (95, 96, 99, 102, 104, 105, 109, 113, and 116) (www.picornaviridae.com/enterovirus/hev-c/hev-c.htm). EV-104 was first identified in 2009 in Switzerland in 8 children who had pneumonia or acute otitis media (1). To our knowledge, there has been only 1 other report of EV-104, detected in Italy in 3 adults and 2 children who had upper respiratory tract infection (RTI) (2). We report the detection of a novel EV-104 strain in an adult with upper RTI in Japan.
    Full-text · Article · May 2012 · Emerging Infectious Diseases
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    Full-text · Article · Nov 2011
  • Takayuki Wada · Atsushi Hase
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    ABSTRACT: The methodological establishment of variable number of tandem repeat(s) (VNTR) genotyping of Mycobacterium tuberculosis has opened a new era of molecular epidemiology against tuberculosis (TB). The method can provide simple, rapid and accurate identification of clinical isolates from TB patients that makes it possible to compare the isolates among different laboratories. Such advantages of VNTR not only help us certify the identification of isolates in putative outbreaks easily but also promote the reasonable estimation of unidentified transmissions in surveillance studies. Recently, the Japan Anti-Tuberculosis Association (JATA) (12)-VNTR has become a standard genotyping method of M. tuberculosis, and its spread has been expected in Japan. In Osaka City, located in the western part of the country, JATA (12)-VNTR has been applied to molecular epidemiological study of TB. Moreover, the additional 12 VNTR loci have been analyzed for various purposes, such as to enhance the discriminatory power (public health needs) or to further analyze the population genetic structure (research needs). As the nationwide findings of VNTR genotyping of M. tuberculosis are accumulated, this technology will be increasingly useful for detecting transmission of any specific strain in large geographic areas that could not be recognized by conventional epidemiological methods. The needs for the VNTR genotyping of M. tuberculosis and its practical uses are expected to expand drastically in the future.
    No preview · Article · Dec 2010 · Kekkaku: [Tuberculosis]
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    ABSTRACT: The etiological roles of diarrheagenic Escherichia coli (DEC), including enteroaggregative E. coli (EAggEC), diffusely adherent E. coli (DAEC) and EAST1EC--a strain of E. coli that possesses no diarrheagenic characteristics other than the EAggEC heat-stable toxin 1 (EAST1) gene--remain controversial. To clarify the prevalence of DEC among healthy individuals in Osaka City, Japan, and to compare the virulence properties of strains previously isolated from diarrheal patients, fecal specimens were examined for DEC. Isolation rates of Shiga toxin-producing E. coli, enterotoxigenic E. coli, and EAggEC were significantly lower among healthy adults than sporadic adult patients. There were no differences in enteropathogenic E. coli (EPEC), DAEC and EAST1EC between patients and healthy carriers. Subtyping of the intimin gene (eae) of EPEC, and measuring the IL-8 inductivity of DAEC on epithelial cells could provide criteria to distinguish strains in diarrheal patients from those in healthy carriers. Proper criteria should be established in order to diagnose subtypes of DEC as causative agents.
    Full-text · Article · Aug 2009 · Japanese journal of infectious diseases
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    ABSTRACT: A population-based study of Mycobacterium tuberculosis isolated from homeless tuberculosis patients was performed during 2002-2004 in Osaka City, Japan. The data show that the ancient Beijing subfamily was predominant, whereas clustered isolates based on refined variable number of tandem repeats genotyping (19 loci) mainly belonged to the modern Beijing subfamily, suggesting its increased transmissibility.
    No preview · Article · Jul 2009 · Tuberculosis (Edinburgh, Scotland)
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    ABSTRACT: Aims: The source and routes of diarrhoeagenic Escherichia coli (DEC) have not been clarified because it is difficult to detect these organisms in samples with numerous coliform bacteria. We have developed multiplex real-time PCR assays for exhaustive detection of DEC. Methods and Results: Primers and TaqMan probes were designed to amplify and quantify one gene (eae, stx1, stx2, elt, est, virB, aggR, astA, and afaB) from each of seven pathotypes of DEC, in duplex or triplex reactions under the same PCR cycling conditions. Specificity was confirmed using 860 strains including 88 DEC strains. The fluorescence threshold cycle and DNA concentrations correlated with decision coefficients of more than 0.99. Subsequently, meat samples and enrichment broths were spiked with DEC and the assays used to detect the genes. The detection limits varied from 7.1 x 10(2) to 1.1 x 10(4) CFU ml(-1), depending on the target genes. All meat samples spiked with a variety of DEC (more than 10 CFU 10 g(-1)) were found to be positive by the method. Conclusions: The present system allows for the efficient and simultaneous determination of various DEC pathotypes. Significance and Impact of the Study: This system makes epidemiological investigations for DEC sensitive and quick, and is a useful tool to clarify the source and routes of DEC.
    Preview · Article · Mar 2009 · Journal of Applied Microbiology
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    Full-text · Article · Jun 2008 · Japanese journal of infectious diseases
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    ABSTRACT: Colicins are proteins produced by and active against several strains of Escherichia coli. Previously we reported that colicinogenic bacteria seemed beneficial in preventing the clinical manifestations of infectious disease caused by enterohemorrhagic E. coli O157 in humans. The inhibitory effects could be due to a decrease in O157 levels and/or pathogenicity. This study investigated the effects of colicinogenic E. coli on the production of Shiga toxin (Stx) by O157. Standard strains of colicinogenic bacteria carrying plasmids for each type of colicin (E3/5/8/9) were used for the study. The O157 strains were cultured in the presence of colicinogenic bacteria or extracted colicins. Compared with results for controls, DNase colicins (E8/9) facilitated an 8- to 64-fold increase in production of Stx2, while RNase colicins (E3/5) suppressed Stx production in only two strains. Stx prophages were induced in synchrony with Stx production. Semiquantitative real-time reverse transcription-PCR (RT-PCR) was then performed to examine SOS gene expression. The RT-PCR results clearly indicated a marked increase in mRNA levels of SOS reaction-associated genes after the addition of DNase colicins. We believe that Stx prophages are induced by the SOS response to DNA damage caused by DNase colicins, thus leading to higher Stx production. These findings suggest that while colicinogenic bacteria can be antagonistic to O157 infection, DNase colicins may enhance Stx production. Thus, colicinogenic flora is likely to be involved in the complex pathogenic pathways of O157 infection, and further investigation should be performed before the use of colicinogenic bacteria as an intervention method.
    Preview · Article · Jan 2008 · Applied and Environmental Microbiology
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    ABSTRACT: Using 243 Mycobacterium tuberculosis isolates obtained in 2001 in Osaka City, Japan, the discriminatory power of variable numbers of tandem repeats (VNTRs) of 12 standard mycobacterial interspersed repetitive units (MIRUs) was assessed. The biggest cluster defined by MIRU-VNTRs consisted of 57 (23.5 %) isolates and they belonged to the Beijing family based on spoligotyping. When additional VNTR loci were included in the MIRU-VNTR analysis, the 57 originally clustered strains were further differentiated by the addition of Queen's University Belfast (QUB)-VNTRs, but not exact tandem repeat-VNTR. The allelic diversity of additional VNTR loci such as VNTR 3232 (QUB-3232), VNTR 2163a (QUB-11a), VNTR 2163b (QUB-11b) and VNTR 1982 (QUB-18) was high in the 57 strains. When the 243 M. tuberculosis isolates were analysed using 16-locus VNTR (the 12 standard MIRUs and the 4 QUB loci) and IS6110 RFLP, the respective Hunter-Gaston discriminatory indexes were 0.9966 and 0.9971. The discrimination power of 16-locus VNTR was equal to that of IS6110 RFLP analysis. If appropriate loci are added to the standard MIRU analysis, VNTR genotyping could be a valuable tool for strain typing and epidemiological research of M. tuberculosis in Japan.
    Full-text · Article · Sep 2007 · Journal of Medical Microbiology

Publication Stats

513 Citations
63.84 Total Impact Points

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Institutions

  • 2013
    • Nagasaki University
      • Department of International Health
      Nagasaki, Nagasaki, Japan
    • Osaka Prefectural Institute of Public Health
      Ōsaka, Ōsaka, Japan
  • 2008
    • The University of Tokyo
      • Department of Biotechnology
      Edo, Tōkyō, Japan
  • 2004
    • Osaka City University
      • Department of Host Defense
      Ōsaka, Ōsaka, Japan