Helicobacter cinaedi
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA37539 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| DRR090193_1.fastq.gz | Fastqsanger.gz | |||
| DRR090193_2.fastq.gz | Fastqsanger.gz | |||
| DRR118821.fastq.gz | Fastqsanger.gz | |||
| DRR118821_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Whole-cell protein electrophoresis and biochemical examination by means of a panel of 64 tests were used to identify 14 putative helicobacters to the species level. The results were confirmed by means of DNA-DNA hybridization experiments and were used to discuss misidentification of helicobacters based on 16S rRNA gene sequence data. The data indicated that comparison of near-complete 16S ribosomal DNA sequences does not always provide conclusive evidence for species level identification and may prove highly misleading. The data also indicated that "Helicobacter westmeadii" is a junior synonym of Helicobacter cinaedi and that Helicobacter sp. strain Mainz belongs to the same species. H. cinaedi occurs in various animal reservoirs, including hamsters, dogs, cats, rats, and foxes. Appropriate growth conditions and identification strategies will be required to establish the genuine significance of this widely distributed Helicobacter species.
| S-EPMC86777 | biostudies-literature
Project description:Helicobacter cinaedi is an enterohepatic Helicobacter that causes bacteremia and other diseases in humans. While H. cinaedi-like strains are isolated from animals, including dog isolates belonging to a recently proposed H. canicola, little is known about the genetic differences between H. cinaedi and these animal isolates. Here, we sequenced 43 H. cinaedi- or H. canicola-like strains isolated from humans, hamsters, rats and dogs and collected 81 genome sequences of H. cinaedi, H. canicola and other enterohepatic Helicobacter strains from public databases. Genomic comparison of these strains identified four distinct clades (clades I-IV) in H. cinaedi/canicola/'magderbugensis' (HCCM) complex. Among these, clade I corresponds to H. cinaedi sensu stricto and represents a human-adapted lineage in the complex. We identified several genomic features unique to clade I. They include the accumulation of antimicrobial resistance-related mutations that reflects the human association of clade I and the larger genome size and the presence of a CRISPR-Cas system and multiple toxin-antitoxin and restriction-modification systems, both of which indicate the contribution of horizontal gene transfer to the evolution of clade I. In addition, nearly all clade I strains but only a few strains belonging to one minor clade contained a highly variable genomic region encoding a type VI secretion system (T6SS), which could play important roles in gut colonization by killing competitors or inhibiting their growth. We also developed a method to systematically search for H. cinaedi sequences in large metagenome data sets based on the results of genome comparison. Using this method, we successfully identified multiple HCCM complex-containing human faecal metagenome samples and obtained the sequence information covering almost the entire genome of each strain. Importantly, all were clade I strains, supporting our conclusion that H. cinaedi sensu stricto is a human-adapted lineage in the HCCM complex.
| S-EPMC9465070 | biostudies-literature
Project description:Genome sequencing of Helicobacter cinaedi
| PRJDB12330 | ENA
Project description:Whole genome sequencing of Helicobacter cinaedi, which caused recurrent infection
| PRJDB7134 | ENA
Project description:TPA_asm:Genomic analysis of Helicobacter cinaedi
| PRJDB7074 | ENA
Project description:BackgroundUp to 20% of all infective endocarditis are blood culture-negative and therefore a diagnostic challenge. Here we present the case of an infective endocarditis due to Helicobacter cinaedi finally diagnosed using different molecular methods. This highly fastidious gram-negative spiral rod is increasingly recognized as a human pathogen, above all in immunocompromised patients. So far H. cinaedi has been associated with bacteremia, cellulitis, arthritis and meningitis.Case presentationA 71-year-old man presented with fever and progressive dyspnea for weeks. He was immunocompromised by long-term steroid therapy. As one major and two minor Duke's criteria (vegetation, fever and aortic valve stenosis as predisposition) were present, an infective endocarditis was suspected and an empiric therapy with amoxicillin/clavulanic acid and gentamicin was established. The persistent severe aortic regurgitation resulted in a valve replacement. Histological evaluation of the aortic valve showed a polypous-ulcerative endocarditis. Gram stain and culture remained negative. Broad-range bacterial PCR targeting the 16S rRNA gene on the biopsy of the aortic valve identified H. cinaedi as the causative agent. The antibiotic therapy was simplified accordingly to ceftriaxone and gentamicin with a recommended duration of 6 weeks. Ten days after valve replacement the patient was discharged. To complete our molecular finding, we sequenced nearly the complete 16S rRNA gene (accession number KF914917) resulting in 99.9% identity with H. cinaedi reference sequences. Based on this result, 2 species-specific PCR tests amplifying part of the ctd gene were established and applied to the valve specimen. The 2 PCRs confirmed H. cinaedi. In addition, we analyzed stool, urine and saliva from the patient using H. cinaedi PCR. The fecal and urine specimen showed a positive signal, saliva was PCR-negative.ConclusionWe identified H. cinaedi as causative agent of a culture-negative endocarditis in an immunocompromised patient using broad-range and specific PCR. In addition to 2 cases from Japan presented on international meetings in 2010 and 2013, our case report shows that H. cinaedi should be recognized as additional causative organism of infective endocarditis. The use of molecular diagnostic techniques proved to be a powerful complement for the detection of blood culture-negative infective endocarditis.
| S-EPMC4243372 | biostudies-literature
Project description: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.
| S-EPMC5640232 | biostudies-literature
Project description:Helicobacter cinaedi is an emerging bacterial pathogen of immunosuppressed individuals. The species is traditionally thought to require an H2-enhanced microaerobic atmosphere for growth, although it can proliferate under aerobic conditions when co-cultured with epithelial monolayers or supplemented with certain metabolites (notably, L-lactate). The goal of this experiment was to assess the global transcription changes that occur in the H. cinaedi type strain (ATCC BAA-847) under various media and atmospheric conditions. These include bacterial monoculture, as well as co-culture with Caco-2 intestinal epithelial cells. In total, Illumina mRNA-seq (stranded, paired-end) was performed on H. cinaedi grown under 9 in vitro culture conditions (4-5 biologic replicates per condition).
2016-09-19 | E-MTAB-5062 | biostudies-arrayexpress
Project description:Helicobacter cinaedi infection is now recognized as an increasingly important emerging disease. Its pathogenesis and epidemiological features are not fully understood, however. Here, we investigated the antigenic protein of H. cinaedi and the immunological response to it in H. cinaedi-infected patients. We constructed a genomic library of H. cinaedi from an H. cinaedi clinical isolate, and various H. cinaedi recombinant proteins were expressed. We identified the 30-kDa protein, encoded in an 822-bp H. cinaedi genome, as a major antigen, which was specifically recognized by serum from an H. cinaedi-immunized rabbit and H. cinaedi-infected patients. The gene encoding this 30-kDa antigen had high sequence similarity with genes encoding putative membrane proteins of bacteria. To evaluate whether the 30-kDa protein can be applied in serological testing for H. cinaedi infections, the recombinant protein was expressed in Escherichia coli as a His-tagged fusion protein and purified by Ni(2+) affinity chromatography. Western blot analysis revealed strong immunoreactivity of the 31-kDa fusion protein with serum antibody from patients infected with H. cinaedi, but such an immunoreaction was absent or was very weak with uninfected control serum. An enzyme-linked immunosorbent assay using this H. cinaedi major antigen showed significantly high antibody titers for H. cinaedi-infected subjects compared with those of various control groups. We therefore conclude that the 30-kDa putative membrane protein is a major antigen of H. cinaedi and is useful for immunological and serological testing for clinical diagnosis and for further epidemiological study of H. cinaedi infection in humans.
| S-EPMC2268252 | biostudies-literature