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Yoshiaki Kawamura - One of the best experts on this subject based on the ideXlab platform.

  • Multi-step genomic dissection of a suspected intra-hospital Helicobacter Cinaedi outbreak.
    Microbial Genomics, 2019
    Co-Authors: Yasuhiro Gotoh, Junko Tomida, Takako Taniguchi, Dai Yoshimura, Keisuke Katsura, Yuji Saeki, Yasutoshi Hirabara, Mayumi Fukuda, Ichiro Takajo, Yoshiaki Kawamura
    Abstract:

    Helicobacter Cinaedi is an emerging pathogen causing bacteraemia and cellulitis. Nosocomial transmission of this microbe has been described, but detailed molecular-epidemiological analyses have not been performed. Here, we describe the results of a multi-step genome-wide phylogenetic analysis of a suspected intra-hospital outbreak of H. Cinaedi that occurred in a hospital in Japan. The outbreak was recognized by the infectious control team (ICT) of the hospital as a sudden increase in H. Cinaedi bacteraemia. ICT defined this outbreak case based on 16S rRNA sequence data and epidemiological information, but were unable to determine the source and route of the infections. We therefore re-investigated this case using whole-genome sequencing (WGS). We first performed a species-wide analysis using publicly available genome sequences to understand the level of genomic diversity of this under-studied species. The clusters identified were then separately analysed using the genome sequence of a representative strain in each cluster as a reference. These analyses provided a high-level phylogenetic resolution of each cluster, identified a confident set of outbreak isolates, and discriminated them from other closely related but distinct clones, which were locally circulating and invaded the hospital during the same period. By considering the epidemiological data, possible strain transmission chains were inferred, which highlighted the role of asymptomatic carriers or environmental contamination. The emergence of a subclone with increased resistance to fluoroquinolones in the outbreak was also recognized. Our results demonstrate the impact of the use of a closely related genome as a reference to maximize the power of WGS.

  • Diversity and microevolution of CRISPR loci in Helicobacter Cinaedi.
    PloS one, 2017
    Co-Authors: Junko Tomida, Tomohiro Sawa, Keigo Shibayama, Yuji Morita, Takaaki Akaike, Ken Kikuchi, Yoshiaki Kawamura
    Abstract:

    Helicobacter Cinaedi is associated with nosocomial infections. The CRISPR-Cas system provides adaptive immunity against foreign genetic elements. We investigated the CRISPR-Cas system in H. Cinaedi to assess the potential of the CRISPR-based microevolution of H. Cinaedi strains. A genotyping method based on CRISPR spacer organization was carried out using 42 H. Cinaedi strains. The results of sequence analysis showed that the H. Cinaedi strains used in this study had two CRISPR loci (CRISPR1 and CRISPR2). The lengths of the consensus direct repeat sequences in CRISPR1 and CRISPR2 were both 36 bp-long, and 224 spacers were found in the 42 H. Cinaedi strains. Analysis of the organization and sequence similarity of the spacers of the H. Cinaedi strains showed that CRISPR arrays could be divided into 7 different genotypes. Each genotype had a different ancestral spacer, and spacer acquisition/deletion events occurred while isolates were spreading. Spacer polymorphisms of conserved arrays across the strains were instrumental for differentiating closely-related strains collected from the same hospital. MLST had little variability, while the CRISPR sequences showed remarkable diversity. Our data revealed the structural features of H. Cinaedi CRISPR loci for the first time. CRISPR sequences constitute a valuable basis for genotyping, provide insights into the divergence and relatedness between closely-related strains, and reflect the microevolutionary process of H. Cinaedi.

  • unusual manifestation of Helicobacter Cinaedi infection a case report of intracranial subdural empyema and bacteremia
    BMC Infectious Diseases, 2017
    Co-Authors: Toshimasa Hayashi, Junko Tomida, Yoshiaki Kawamura, Masakazu Yoshida, Ikuyo Yokozawa, Shingaku Kaneko
    Abstract:

    There have been various reports concerning Helicobacter Cinaedi infections. However, few reports have examined central nervous system infections. A 52-year-old man was transferred from the local hospital because of a persistent headache and suspected intracranial subdural empyema. Neurosurgical drainage was performed via burr holes. Gram staining and results from abscess cultures were negative. The blood culture yielded H. Cinaedi. He was given an antibiotic regimen consisting of 2 g of ceftriaxone twice a day, but the size of the abscess was not reduced in size at all after 3 weeks of treatment. Neurosurgical drainage was performed again, and the antimicrobial regimen was switched to 2 g of meropenem 3 times a day. The size of the abscess was reduced after 2 weeks of the second drainage and antimicrobial drug change to meropenem. After 4 weeks treatment with meropenem, the patient was discharged, and his symptoms had completely resolved. H. Cinaedi infection should be considered in the differential diagnosis of subdural empyema cases for which Gram staining and abscess culture results are negative. Meropenem can be a first-line drug of choice or an effective alternative treatment for H. Cinaedi central nervous system infections.

  • Proposal of Helicobacter canicola sp. nov., previously identified as Helicobacter Cinaedi, isolated from canines
    Systematic and applied microbiology, 2016
    Co-Authors: Yoshiaki Kawamura, Peter Vandamme, Tatsuya Okamoto, Tohru Miyoshi-akiyama, Yuji Morita, Junko Tomida, Masashi Narita, Katsuhiko Hashimoto, Margo Cnockaert, Tomohiro Sawa
    Abstract:

    During the course of our taxonomic investigation of Helicobacter Cinaedi, it was realized that the strains isolated from dogs, which have been identified as H. Cinaedi, showed different biochemical traits than did the isolates obtained from humans. None of the three dog isolates could reduce nitrate to nitrite, whereas all of the human H. Cinaedi isolates could do so. The dog isolates showed a strong positive alkaline phosphatase reaction and could grow at 42°C, however the human isolates showed negative to very weak responses to those tests. The GyrA protein based phylogenetic analysis showed that the three isolates from dogs formed a slightly distinct cluster from the human isolate cluster. Phylogenetic analysis of the 16S rRNA, 23S rRNA, gyrB, and hsp60 gene sequences further confirmed that the dog isolates differed from the human H. Cinaedi isolate cluster. The whole-genome in silico DNA similarities of each isolate based on their full genome sequences revealed that the isolates from dogs shared more than 94.9% ANIb (average nucleotide identity based on BLAST), while 94.0% ANIb were found between the isolates from dogs and the humans, including the H. Cinaedi type strain ATCC BAA-847(T) (=CCUG 18818(T)). From these data, we propose a new species, 'H. canicola' sp. nov., for the isolates from dogs. The type strain is PAGU 1410(T) (CCUG 33887(T)=LMG 29580(T)).

  • Helicobacter Cinaedi bacteremia resulting from antimicrobial resistance acquired during treatment for X-linked agammaglobulinemia
    Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy, 2016
    Co-Authors: Meiwa Toyofuku, Junko Tomida, Yoshiaki Kawamura, Ippei Miyata, Yuki Yuza, Yuho Horikoshi
    Abstract:

    This is the first report of penicillin/cephalosporin-resistant Helicobacter Cinaedi arising from prolonged treatment. H. Cinaedi, common among immunocompromised patients, caused recurrent bacteremia and cellulitis in a 19-year-old Japanese man with X-linked agammaglobulinemia. The minimal inhibitory concentration of these drugs was raised, which subsequently resulted in clinical failure. Prolonged suboptimal treatment may cause bacterial resistance to β-lactam antibiotics in H. Cinaedi. It is possible that this resistance may have contributed to the treatment failure.

Tohru Miyoshi-akiyama - One of the best experts on this subject based on the ideXlab platform.

  • Complete Genome Sequence of Helicobacter Cinaedi Type Strain ATCC BAA-847
    2016
    Co-Authors: Tohru Miyoshi-akiyama, Nozomi A Takeshita, Norio B Ohmagari, Teruo Kirikaea
    Abstract:

    Here we report the completely annotated genome sequence of theHelicobacter Cinaedi type strain (ATCC BAA-847), which is an emerging pathogen that causes cellulitis and bacteremia. The genome sequence will provide new insights into the diagnosis, pathogenic mechanisms, and drug resistance ofH. Cinaedi. The type strain of Helicobacter Cinaedi, ATCC BAA-847 (CDCDO148), was isolated in the 1980s (February 1980 to June 1983) from a rectal swab taken from a homosexual man who had attended the Sexually Transmitted Disease Clinic at Harborview Medical Center, Seattle,WA, and it was identified as a novelCam-pylobacter species (7). When the Campylobacter genus underwent reclassification in 1991, it was moved into the Helicobacter genus (8). H. Cinaedi causes cellulitis and bacteremia in immunocom-promised patients (3), as well as in immunocompetent hosts (4). NosocomialH. Cinaedi infections have recently been reported (5). However, the pathogenicity and etiological properties of H. Cinaedi are poorly understood. Recently, the genome sequence of H. Cinaedi strain PAGU611, isolated from a case of human bacte-remia in Japan, was reported (2). Here, an8-kbpaired-end libraryof theH. CinaediATCCBAA-847 genome was prepared and used for sequence analysis with a GS FLX titanium sequencer (Roche). This generated 567,221 reads, covering 171,999,544bp(68.8-fold coverage),whichwereassembled into scaf-folds and contigs. Gap filling was then performed by conventional Sanger sequencing of the PCR fragments based on brute force PCR among the contigs and scaffolds. Finally, the Illumina MiSeq 2 150-bp 110,730 paired-end reads were added to the draft genome sequence. Primary coding sequence extraction was performed us-ing MetaGeneAnnotator (6). Initial functional assignment and manual correctionwere carriedoutby comparing thegenomesequence data of H. Cinaedi PAGU611 (AP012344 and AP012345) and CCUG18818(ABQT01000001.1 toABQT01000096.1)by in silicomo

  • Proposal of Helicobacter canicola sp. nov., previously identified as Helicobacter Cinaedi, isolated from canines
    Systematic and applied microbiology, 2016
    Co-Authors: Yoshiaki Kawamura, Peter Vandamme, Tatsuya Okamoto, Tohru Miyoshi-akiyama, Yuji Morita, Junko Tomida, Masashi Narita, Katsuhiko Hashimoto, Margo Cnockaert, Tomohiro Sawa
    Abstract:

    During the course of our taxonomic investigation of Helicobacter Cinaedi, it was realized that the strains isolated from dogs, which have been identified as H. Cinaedi, showed different biochemical traits than did the isolates obtained from humans. None of the three dog isolates could reduce nitrate to nitrite, whereas all of the human H. Cinaedi isolates could do so. The dog isolates showed a strong positive alkaline phosphatase reaction and could grow at 42°C, however the human isolates showed negative to very weak responses to those tests. The GyrA protein based phylogenetic analysis showed that the three isolates from dogs formed a slightly distinct cluster from the human isolate cluster. Phylogenetic analysis of the 16S rRNA, 23S rRNA, gyrB, and hsp60 gene sequences further confirmed that the dog isolates differed from the human H. Cinaedi isolate cluster. The whole-genome in silico DNA similarities of each isolate based on their full genome sequences revealed that the isolates from dogs shared more than 94.9% ANIb (average nucleotide identity based on BLAST), while 94.0% ANIb were found between the isolates from dogs and the humans, including the H. Cinaedi type strain ATCC BAA-847(T) (=CCUG 18818(T)). From these data, we propose a new species, 'H. canicola' sp. nov., for the isolates from dogs. The type strain is PAGU 1410(T) (CCUG 33887(T)=LMG 29580(T)).

  • Complete Genome Sequence of Helicobacter Cinaedi Type Strain ATCC BAA-847
    Journal of bacteriology, 2012
    Co-Authors: Tohru Miyoshi-akiyama, Norio Ohmagari, Nozomi Takeshita, Teruo Kirikae
    Abstract:

    ABSTRACT Here we report the completely annotated genome sequence of the Helicobacter Cinaedi type strain (ATCC BAA-847), which is an emerging pathogen that causes cellulitis and bacteremia. The genome sequence will provide new insights into the diagnosis, pathogenic mechanisms, and drug resistance of H. Cinaedi.

Teruo Kirikae - One of the best experts on this subject based on the ideXlab platform.

Junko Tomida - One of the best experts on this subject based on the ideXlab platform.

  • Multi-step genomic dissection of a suspected intra-hospital Helicobacter Cinaedi outbreak.
    Microbial Genomics, 2019
    Co-Authors: Yasuhiro Gotoh, Junko Tomida, Takako Taniguchi, Dai Yoshimura, Keisuke Katsura, Yuji Saeki, Yasutoshi Hirabara, Mayumi Fukuda, Ichiro Takajo, Yoshiaki Kawamura
    Abstract:

    Helicobacter Cinaedi is an emerging pathogen causing bacteraemia and cellulitis. Nosocomial transmission of this microbe has been described, but detailed molecular-epidemiological analyses have not been performed. Here, we describe the results of a multi-step genome-wide phylogenetic analysis of a suspected intra-hospital outbreak of H. Cinaedi that occurred in a hospital in Japan. The outbreak was recognized by the infectious control team (ICT) of the hospital as a sudden increase in H. Cinaedi bacteraemia. ICT defined this outbreak case based on 16S rRNA sequence data and epidemiological information, but were unable to determine the source and route of the infections. We therefore re-investigated this case using whole-genome sequencing (WGS). We first performed a species-wide analysis using publicly available genome sequences to understand the level of genomic diversity of this under-studied species. The clusters identified were then separately analysed using the genome sequence of a representative strain in each cluster as a reference. These analyses provided a high-level phylogenetic resolution of each cluster, identified a confident set of outbreak isolates, and discriminated them from other closely related but distinct clones, which were locally circulating and invaded the hospital during the same period. By considering the epidemiological data, possible strain transmission chains were inferred, which highlighted the role of asymptomatic carriers or environmental contamination. The emergence of a subclone with increased resistance to fluoroquinolones in the outbreak was also recognized. Our results demonstrate the impact of the use of a closely related genome as a reference to maximize the power of WGS.

  • Diversity and microevolution of CRISPR loci in Helicobacter Cinaedi.
    PloS one, 2017
    Co-Authors: Junko Tomida, Tomohiro Sawa, Keigo Shibayama, Yuji Morita, Takaaki Akaike, Ken Kikuchi, Yoshiaki Kawamura
    Abstract:

    Helicobacter Cinaedi is associated with nosocomial infections. The CRISPR-Cas system provides adaptive immunity against foreign genetic elements. We investigated the CRISPR-Cas system in H. Cinaedi to assess the potential of the CRISPR-based microevolution of H. Cinaedi strains. A genotyping method based on CRISPR spacer organization was carried out using 42 H. Cinaedi strains. The results of sequence analysis showed that the H. Cinaedi strains used in this study had two CRISPR loci (CRISPR1 and CRISPR2). The lengths of the consensus direct repeat sequences in CRISPR1 and CRISPR2 were both 36 bp-long, and 224 spacers were found in the 42 H. Cinaedi strains. Analysis of the organization and sequence similarity of the spacers of the H. Cinaedi strains showed that CRISPR arrays could be divided into 7 different genotypes. Each genotype had a different ancestral spacer, and spacer acquisition/deletion events occurred while isolates were spreading. Spacer polymorphisms of conserved arrays across the strains were instrumental for differentiating closely-related strains collected from the same hospital. MLST had little variability, while the CRISPR sequences showed remarkable diversity. Our data revealed the structural features of H. Cinaedi CRISPR loci for the first time. CRISPR sequences constitute a valuable basis for genotyping, provide insights into the divergence and relatedness between closely-related strains, and reflect the microevolutionary process of H. Cinaedi.

  • unusual manifestation of Helicobacter Cinaedi infection a case report of intracranial subdural empyema and bacteremia
    BMC Infectious Diseases, 2017
    Co-Authors: Toshimasa Hayashi, Junko Tomida, Yoshiaki Kawamura, Masakazu Yoshida, Ikuyo Yokozawa, Shingaku Kaneko
    Abstract:

    There have been various reports concerning Helicobacter Cinaedi infections. However, few reports have examined central nervous system infections. A 52-year-old man was transferred from the local hospital because of a persistent headache and suspected intracranial subdural empyema. Neurosurgical drainage was performed via burr holes. Gram staining and results from abscess cultures were negative. The blood culture yielded H. Cinaedi. He was given an antibiotic regimen consisting of 2 g of ceftriaxone twice a day, but the size of the abscess was not reduced in size at all after 3 weeks of treatment. Neurosurgical drainage was performed again, and the antimicrobial regimen was switched to 2 g of meropenem 3 times a day. The size of the abscess was reduced after 2 weeks of the second drainage and antimicrobial drug change to meropenem. After 4 weeks treatment with meropenem, the patient was discharged, and his symptoms had completely resolved. H. Cinaedi infection should be considered in the differential diagnosis of subdural empyema cases for which Gram staining and abscess culture results are negative. Meropenem can be a first-line drug of choice or an effective alternative treatment for H. Cinaedi central nervous system infections.

  • Proposal of Helicobacter canicola sp. nov., previously identified as Helicobacter Cinaedi, isolated from canines
    Systematic and applied microbiology, 2016
    Co-Authors: Yoshiaki Kawamura, Peter Vandamme, Tatsuya Okamoto, Tohru Miyoshi-akiyama, Yuji Morita, Junko Tomida, Masashi Narita, Katsuhiko Hashimoto, Margo Cnockaert, Tomohiro Sawa
    Abstract:

    During the course of our taxonomic investigation of Helicobacter Cinaedi, it was realized that the strains isolated from dogs, which have been identified as H. Cinaedi, showed different biochemical traits than did the isolates obtained from humans. None of the three dog isolates could reduce nitrate to nitrite, whereas all of the human H. Cinaedi isolates could do so. The dog isolates showed a strong positive alkaline phosphatase reaction and could grow at 42°C, however the human isolates showed negative to very weak responses to those tests. The GyrA protein based phylogenetic analysis showed that the three isolates from dogs formed a slightly distinct cluster from the human isolate cluster. Phylogenetic analysis of the 16S rRNA, 23S rRNA, gyrB, and hsp60 gene sequences further confirmed that the dog isolates differed from the human H. Cinaedi isolate cluster. The whole-genome in silico DNA similarities of each isolate based on their full genome sequences revealed that the isolates from dogs shared more than 94.9% ANIb (average nucleotide identity based on BLAST), while 94.0% ANIb were found between the isolates from dogs and the humans, including the H. Cinaedi type strain ATCC BAA-847(T) (=CCUG 18818(T)). From these data, we propose a new species, 'H. canicola' sp. nov., for the isolates from dogs. The type strain is PAGU 1410(T) (CCUG 33887(T)=LMG 29580(T)).

  • Helicobacter Cinaedi bacteremia resulting from antimicrobial resistance acquired during treatment for X-linked agammaglobulinemia
    Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy, 2016
    Co-Authors: Meiwa Toyofuku, Junko Tomida, Yoshiaki Kawamura, Ippei Miyata, Yuki Yuza, Yuho Horikoshi
    Abstract:

    This is the first report of penicillin/cephalosporin-resistant Helicobacter Cinaedi arising from prolonged treatment. H. Cinaedi, common among immunocompromised patients, caused recurrent bacteremia and cellulitis in a 19-year-old Japanese man with X-linked agammaglobulinemia. The minimal inhibitory concentration of these drugs was raised, which subsequently resulted in clinical failure. Prolonged suboptimal treatment may cause bacterial resistance to β-lactam antibiotics in H. Cinaedi. It is possible that this resistance may have contributed to the treatment failure.

Hidefumi Koh - One of the best experts on this subject based on the ideXlab platform.

  • first case report of thyroid abscess caused by Helicobacter Cinaedi presenting with thyroid storm
    BMC Infectious Diseases, 2019
    Co-Authors: Tomohiro Takehara, Yoshihito Otsuka, Tetsuo Tani, Ken Yajima, Mako Watanabe, Hidefumi Koh
    Abstract:

    Background Helicobacter Cinaedi is a microaerobic Gram-negative spiral-shaped bacterium that causes enteritis, cellulitis, and bacteremia in both immunocompromised and immunocompetent patients. While there have been increasing numbers of reported H. Cinaedi infections recently, there has been no thyroid abscess case caused by H. Cinaedi presenting with thyroid storm.

  • First case report of thyroid abscess caused by Helicobacter Cinaedi presenting with thyroid storm
    BMC, 2019
    Co-Authors: Tomohiro Takehara, Yoshihito Otsuka, Tetsuo Tani, Ken Yajima, Mako Watanabe, Hidefumi Koh
    Abstract:

    Abstract Background Helicobacter Cinaedi is a microaerobic Gram-negative spiral-shaped bacterium that causes enteritis, cellulitis, and bacteremia in both immunocompromised and immunocompetent patients. While there have been increasing numbers of reported H. Cinaedi infections recently, there has been no thyroid abscess case caused by H. Cinaedi presenting with thyroid storm. Case presentation A 50-year-old Japanese man presented with a 9-day history of high fever associated with palpitations, dry cough, and chronic diarrhea. The patient had a history of Basedow’s disease that had been treated with thiamazole in the past. During the current episode, the patient was diagnosed with thyroid storm and treated accordingly. The blood culture taken on admission was positive for H. Cinaedi. This finding was confirmed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOFMS). A systemic computed tomography (CT) scan revealed a thyroid abscess as the site of infection and cause of the bacteremia. The 16S rRNA gene sequencing identified the pathogen of thyroid abscess as H. Cinaedi. Clinical symptoms and laboratory data normalized on admission day 7 after treatment with both effective antibiotics and antithyroid drugs. Conclusions The case study described a patient with a history of Basedow’s disease that presented with a thyroid abscess caused by H. Cinaedi with symptoms similar to those of thyroid storm. While this bacterium has been implicated in other infections, we believe this is the first time the bacteria has been documented to have caused a thyroid abscess