Search results for "Molecular sequence"
showing 10 items of 1972 documents
Bronchial microbiome of severe COPD patients colonised by Pseudomonas aeruginosa
2014
The bronchial microbiome in severe COPD during stability and exacerbation in patients chronically colonised by Pseudomonas aeruginosa (PA), has not been defined. Our objective was to determine the characteristics of the bronchial microbiome of severe COPD patients colonised and not colonised by P. aeruginosa and its changes during exacerbation. COPD patients with severe disease and frequent exacerbations were categorised according to chronic colonisation by P. aeruginosa. Sputum samples were obtained in stability and exacerbation, cultured, and analysed by 16S rRNA gene amplification and pyrosequencing. Sixteen patients were included, 5 of them showing chronic colonisation by P. aeruginosa.…
Characterization of a Catalase-Negative Methicillin-Resistant Staphylococcus aureus Strain
2007
ABSTRACT We describe an unusual clinical strain of catalase-negative methicillin-resistant Staphylococcus aureus sensu stricto. Sequence analysis of its catalase gene showed 99.60% identities to the catalase genes of the reference strains. A 5-base deletion, however, led to a shift of the nucleotide reading frame and a loss of the enzymatic activity.
Borrelia miyamotoi is widespread in Ixodes ricinus ticks in southern Norway.
2015
From April to October 2007, host-seeking Ixodes ricinus ticks were collected from four locations in southern Norway; Farsund, Mandal, Sogne and Tromoy, respectively. Larvae (n=210), nymphs (n=1130) and adults (n=449) were investigated for infection with Borrelia miyamotoi by real-time polymerase chain reaction (PCR) amplification of part of the 16S rRNA gene. Results were verified by direct sequencing of the PCR amplicon generated from the rrs (16S)-rrl (23S) intergenetic spacer. B. miyamotoi was detected at all sites and throughout the period of questing activity, with infection prevalence (≤1.26%) similar to what has been seen in other European countries. Detection of the relapsing fever …
PCR testing for Treponema pallidum in paraffin-embedded skin biopsy specimens: test design and impact on the diagnosis of syphilis
2007
Background: Syphilis, a chronic infection caused by Treponema pallidum (T. pallidum), is a disease which is increasing in incidence, and thus more and more becoming a differential diagnosis in routine pathology. Aim: Since histological changes are not specific, we sought to develop a polymerase chain reaction (PCR)-based molecular assay for the detection of T. pallidum in formalin-fixed, paraffin-embedded tissues, and evaluate its diagnostic power, especially in comparison with other ancillary methods, i.e. immunohistochemistry and Dieterle staining. Methods: 36 skin biopsies with the clinical and /or serological diagnosis of syphilis were evaluated by morphology, immunohistochemistry and s…
pilF polymorphism-based PCR to distinguish Vibrio vulnificus strains potentially dangerous to public health
2010
ABSTRACT Vibrio vulnificus is a heterogeneous species that comprises strains virulent and avirulent for humans and fish, and it is grouped into three biotypes. In this report, we describe a PCR-based methodology that allows both the species identification and discrimination of those isolates that could be considered dangerous to public health. Discrimination is based on the amplification of a variable region located within the gene pilF , which seems to be associated with potential human pathogenicity, regardless of the biotype of the strain.
Cloning and characterization of the genes encoding the malolactic enzyme and the malate permease of Leuconostoc oenos
1996
Using degenerated primers from conserved regions of the protein sequences of malic enzymes, we amplified a 324-bp DNA fragment by PCR from Leuconostoc oenos and used this fragment as a probe for screening a Leuconostoc oenos genomic bank. Of the 2,990 clones in the genomic bank examined, 7 with overlapping fragments were isolated by performing colony hybridization experiments. Sequencing 3,453 bp from overlapping fragments revealed two open reading frames that were 1,623 and 942 nucleotides long and were followed by a putative terminator structure. The first deduced protein (molecular weight, 59,118) is very similar (level of similarity, 66%) to the malolactic enzyme of Lactococcus lactis; …
Marinomonas aquamarina sp. nov., isolated from oysters and seawater.
2005
Abstract The characterization of three bacterial strains isolated from cultured oysters and seawater at the Spanish Mediterranean coast has been performed. Strains were phenotypically and genetically characterized and the results led us to identify them as members of the genus Marinomonas . A phylogenetic analysis based on the almost complete 16S rDNA sequences clustered all three strains together (with sequence similarities around 99.8%) in the vicinity of M. communis and M. vaga sequences and distantly related to the other four species of the genus. The most closely related species was M. communis that shared 97.4–97.6% with the Mediterranean strains. DNA–DNA hybridizations were performed…
Quantification of a novel group of nitrate-reducing bacteria in the environment by real-time PCR
2004
Abstract Nitrate reduction is performed by phylogenetically diverse bacteria. Analysis of narG (alpha subunit of the membrane bound nitrate reductase) trees constructed using environmental sequences revealed a new cluster that is not related to narG gene from known nitrate-reducing bacteria. In this study, primers targeting this as yet uncultivated nitrate-reducing group were designed and used to develop a real-time SYBR® Green PCR assay. The assay was tested with clones from distinct nitrate-reducing groups and applied to various environmental samples. narG copy number was high ranging between 5.08×108 and 1.12×1011 copies per gram of dry weight of environmental sample. Environmental real-…
Identification of a clone of Escherichia coli O103:H2 as a potential agent of hemolytic-uremic syndrome in France
1993
In a French multicenter study, six verocytotoxin-producing Escherichia coli strains were isolated from the stools of 6 of 69 children suffering from hemolytic-uremic syndrome. All strains belonged to serotype O103:H2, a serotype commonly associated with diarrhea in weaned rabbits in France. To determine whether the strains from humans and rabbits were genetically related, they were compared by analyzing their esterase electropherotypes and the restriction fragment length polymorphisms of the ribosomal DNA regions. A common clonal origin of these pathogenic strains was suggested by their identical esterase electropherotypes and their identical ribotypes, in addition to their identical seroty…
DNA Amplification Fingerprinting for Subtyping Neisseria gonorrhoeae Strains
1995
Background and Objectives DNA amplification fingerprinting is used in most epidemiologic studies as a substitute for conventional typing methods. DNA amplification fingerprinting and conventional typing methods were compared in this epidemiologic study of Neisseria gonorrhoeae. Goal of This Study To differentiate 70 Neisseria gonorrhoeae isolates from untreated patients with urogenital gonococcal infection. Study Design Gonococcal strains were characterized by auxo-typing, serotyping, plasmid profile, antibiotic sensitivity, and DNA amplification fingerprinting. The method of unweighted pair-group average linkage was used for cluster analysis. Discriminatory power was calculated applying Si…