Abiotrophia defectiva
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA37353 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| DRR015936_1.fastq.gz | Fastqsanger.gz | |||
| DRR015936_2.fastq.gz | Fastqsanger.gz | |||
| SRR036015.fastq.gz | Fastqsanger.gz | |||
| SRR036015_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Whole genome sequencing of Abiotrophia defectiva, an opportunistic pathogen
| PRJDB2563 | ENA
Project description:The genus Abiotrophia represents a heterogeneous group of fastidious cocci that show a dependence on pyridoxal hydrochloride analogs for growth. The genetic heterogeneity in the genus Abiotrophia was examined by DNA-DNA hybridization, PCR assay of genomic DNA sequences, and restriction fragment length polymorphism and sequence homology analyses of the PCR-amplified 16S rRNA gene. Nine type or reference strains of Abiotrophia defectiva, Abiotrophia adiacens, and Abiotrophia elegans and 36 oral Abiotrophia isolates including the ones presumptively identified as Gemella morbillorum by the rapid ID32 STREP system were divided into four groups: A. defectiva (genotype 1), A. adiacens (genotype 2), A. elegans (genotype 4), and a fourth species (genotype 3) which we propose be named Abiotrophia para-adiacens sp. nov. A PCR assay specific for detection and identification of the novel Abiotrophia species was developed. A. para-adiacens generally produced beta-glucosidase but did not produce alpha- or beta-galactosidase or arginine dihydrolase, did not ferment, trehalose, pullulan, or tagatose, and was serotype IV, V, or VI. Thus, it was distinguished phenotypically from A. adiacens, A. elegans, and A. defectiva as well as, apparently, from the recently described species Abiotrophia balaenopterae sp. nov., which produces arginine dihydrolase and which ferments pullulan but not sucrose (P. A. Lawson et al., Int. J. Syst. Bacteriol. 49:503-506, 1999). Strain ATCC 27527, currently listed as G. morbillorum, was a member of the species A. para-adiacens.
| S-EPMC86132 | biostudies-literature
Project description:Abiotrophia adiacens and Abiotrophia defectiva, previously referred to as nutritionally variant streptococci, Streptococcus adjacens and Streptococcus defectivus, respectively, are causes of infective endocarditis. We describe a method of identifying these two species and also of distinguishing them from 15 other major etiological pathogens of infective endocarditis by means of 16S rRNA gene PCR amplification followed by restriction fragment length polymorphism analysis (PCR-RFLP). The 16S rRNA genes were successfully amplified with a set of universal primers from all 17 species of bacteria examined, including viridans group streptococci. The RFLP patterns of A. adiacens and A. defectiva obtained by HaeIII or MspI digestion were readily distinguished from each other and from those of other bacteria. When PCR analysis was performed with the supernatant of a suspension of a boiled colony, the 16S rRNA genes of 80 of 82 isolates (97%) of A. adiacens and all isolates (11 of 11) of A. defectiva were amplified. The HaeIII RFLP patterns of the isolates were the same as those of the corresponding type strains, although 28% of A. adiacens isolates revealed intraspecies polymorphism. The detection limit of this method was 0.1 pg of genomic DNA, as assessed by using the digoxigenin-labeling DNA detection system. Thus, the PCR-RFLP analysis that we developed is applicable for the routine detection of Abiotrophia from clinical specimens.
| S-EPMC229992 | biostudies-other
Project description:BackgroundAbiotrophia species have rarely been implicated in osteoarticular infections. We report one case of an A. defectiva knee prosthesis infection.Case presentationA 71-year-old man of Italian origin presented with pain and swelling of the knee four years after the implantation of a total knee replacement prosthesis. While standard culturing of the synovial fluid resulted in no isolation of microorganisms, the direct inoculation of the synovial fluid into a rich culture medium resulted in the identification of A. defectiva by polymerase chain reaction sequencing. Repeated attempts of culturing microorganisms from blood were negative, and echocardiograms and colonoscopies were unremarkable. High-dose amoxicillin for nine months and a two-stage replacement of the knee prosthesis led to full patient recovery by the time of the 12-month follow-up examination.ConclusionsBecause Abiotrophia spp. are fastidious microorganisms, it is likely that cases of Abiotrophia orthopedic infection are misdiagnosed as culture-negative infections. Direct inoculation of synovial fluids into rich broth medium and further polymerase chain reaction-based detection of culture-negative synovial fluids are key tests for accurate documentation and detection of these infections.
| S-EPMC3177934 | biostudies-literature
Project description:Abiotrophia and Granulicatella species have been associated with various infections. Antimicrobial susceptibility data for these nutritionally variant streptococcus-like organisms, especially for pediatric isolates, are very limited. Little is known about the genetic bases of their resistance mechanisms. We report the results of identification to bacterial species level, antimicrobial susceptibility testing, macrolide resistance testing, and detection of genes encoding that resistance for a collection of 15 pediatric clinical isolates from normally sterile sites. Our results indicate that the prevalence of beta-lactam and macrolide resistance is high and that both erm and mef are found in these isolates.
| S-EPMC516320 | biostudies-literature
Project description:A 41-year-old African male presented with worsening dyspnea and cachexia concerning for congestive heart failure. Transesophageal echocardiogram revealed a large mass attached to the aortic valve leaflet, mass attached to the flail anterior mitral valve leaflet, severe pulmonary hypertension and dilatation of the aortic root along with fistula between the right coronary aortic cusp and the right ventricular (RV) outflow tract. Blood cultures grew Abiotrophia Defectiva (AD) sensitive to vancomycin. Patient underwent emergent surgical closure of aorto RV fistula and aortic root replacement along with pulmonary and mitral valve replacement. Endocarditis caused by AD has been reported to result in heart failure, septic embolization and destruction of the valve despite use of appropriate antibiotics. To our knowledge, this is the only case of AD endocarditis without any identified entrance route; requiring replacement of pulmonary, mitral and aortic valve due to extensive valvular damage and large vegetations.
| S-EPMC5495012 | biostudies-literature
Project description:BackgroundAbiotrophia defectiva, although infrequently occurring, is a notable cause of culture-negative infective endocarditis with limited research on its virulence. Associated with oral infections such as dental caries, exploring its secretome may provide insights into virulence mechanisms. Our study aimed to analyze and characterize the secretome of A. defectiva strain CCUG 27639.MethodsSecretome of A. defectiva was prepared from broth cultures and subjected to mass spectrometry and proteomics for protein identification. Inflammatory potential of the secretome was assessed by ELISA.ResultsEighty-four proteins were identified, with diverse subcellular localizations predicted by PSORTb. Notably, 20 were cytoplasmic, 12 cytoplasmic membrane, 5 extracellular, and 9 cell wall-anchored proteins. Bioinformatics tools revealed 54 proteins secreted via the 'Sec' pathway and 8 via a non-classical pathway. Moonlighting functions were found in 23 proteins, with over 20 exhibiting potential virulence properties, including peroxiredoxin and oligopeptide ABC transporter substrate-binding protein. Gene Ontology and KEGG analyses categorized protein sequences in various pathways. STRING analysis revealed functional protein association networks. Cytokine profiling demonstrated significant proinflammatory cytokine release (IL-8, IL-1β, and CCL5) from human PBMCs.ConclusionsOur study provides a comprehensive understanding of A. defectiva's secretome, laying the foundation for insights into its pathogenicity.
| S-EPMC10863525 | biostudies-literature
Project description:BackgroundAbiotrophia and Granulicatella species, previously referred to as nutritionally variant streptococci (NVS), are significant causative agents of endocarditis and bacteraemia. In this study, we reviewed the clinical manifestations of infections due to A. defectiva and Granulicatella species that occurred at our institution between 1998 and 2004.MethodsThe analysis included all strains of NVS that were isolated from blood cultures or vascular graft specimens. All strains were identified by 16S rRNA sequence analysis. Patients' medical charts were reviewed for each case of infection.ResultsEleven strains of NVS were isolated during the 6-year period. Identification of the strains by 16S rRNA showed 2 genogroups: Abiotrophia defectiva (3) and Granulicatella adiacens (6) or "para-adiacens" (2). The three A. defectiva strains were isolated from immunocompetent patients with endovascular infections, whereas 7 of 8 Granulicatella spp. strains were isolated from immunosuppressed patients, mainly febrile neutropenic patients. We report the first case of "G. para-adiacens" bacteraemia in the setting of febrile neutropenia.ConclusionWe propose that Granulicatella spp. be considered as a possible agent of bacteraemia in neutropenic patients.
| S-EPMC1360077 | biostudies-literature
Project description:Abiotrophia defectiva E11004 Genome sequencing and assembly
| PRJNA1080312 | ENA