Biomedical subjects

J Freney

Publications and source records attributed to J Freney.

At least 37 records · Page 2Linked to original sources

PubMed1999

Distribution of Staphylococcus sciuri subspecies among human clinical specimens, and profile of antibiotic resistance.

The distribution of three subspecies comprising Staphylococcus sciuri was determined for a collection of 30 clinical isolates originating from Morocco, the United Kingdom, and France. The sources of these isolates were principally wounds, skin, and soft tissue infections. At the species level, the isolates were identified according to biochemical characteristics and at the subspecies level by the ribotyping technique. PCR analysis performed with the 16S-23S ribosomal DNA intergenic spacer was less powerful for subspecies differentiation. S. sciuri subsp. sciuri was the most frequent subspecies (21 isolates) found in the collection, whereas S. sciuri subsp. rodentium (seven isolates) and S. sciuri subsp. carnaticus (two isolates) were less common. mecA or a mecA-related gene was detected by PCR and Southern blot in all 30 S. sciuri isolates, supporting the suggestion that S. sciuri species are the natural reservoir of the mecA gene. While the linA/linA' gene coding for lincomycin resistance was present in five isolates, an uncharacterized gene for this resistance was suspected in seventeen other isolates.

Bacterial Typing Techniques↗

PubMed1999

Legionella taurinensis sp. nov., a new species antigenically similar to Legionella spiritensis.

A group of 42 Legionella-like organisms reacting specifically with Legionella spiritensis serogroup 1 antisera were collected throughout Europe by the Centre National de Référence (French National Reference Centre) for Legionella. This group of isolates differed somewhat from L. spiritensis in terms of biochemical reactions, ubiquinone content and protein profile. The latter two analyses revealed that one of these L. spiritensis-like isolates, Turin I no. 1T, was highly related, but not identical to any of the red autofluorescent species of Legionella. In fact, this strain was the first of these particular isolates recognized to emit a red autofluorescence when exposed to UV light. Profile analysis of randomly amplified polymorphic DNA established that the red autofluorescent L. spiritensis-like isolates constituted a homogeneous group distinct from Legionella rubrilucens and Legionella erythra. DNA-DNA hybridization studies involving the use of S1 nuclease confirmed that the indicated group of isolates are a new species of Legionella, for which the name Legionella taurinensis is proposed with strain Turin I no. 1T (deposited as ATCC 700508T) as the type strain.

Antigens, Bacterial↗

PubMed1999

Recommended minimal standards for description of new staphylococcal species. Subcommittee on the taxonomy of staphylococci and streptococci of the International Committee on Systematic Bacteriology.

In accordance with Recommendation 30b of the International Code of Nomenclature of Bacteria, minimal standards are proposed for the genus Staphylococcus and the description of newly recognized species in this genus. Assignment of a strain to the genus Staphylococcus requires that it is a Gram-positive coccus that forms clusters, produces catalase, has an appropriate cell wall structure (including peptidoglycan type and teichoic acid presence) and G + C content of DNA in a range of 30-40 mol%. The recommended minimal standards for describing a new Staphylococcus species are based on the results of phenotypic and genomic studies of at least five independently isolated strains. They include colony morphology and the results of the following conventional tests: pigment production, growth requirements, fermentative and oxidative activity on carbohydrates, novobiocin susceptibility, enzymic activities (nitrate reductase, alkaline phosphatase, arginine dihydrolase, ornithine decarboxylase, urease, cytochrome oxidase, staphylocoagulase in rabbit plasma, heat-stable nuclease, amidases, oxidases, clumping factor, and haemolytic activity on sheep or bovine blood agar). DNA-DNA hybridization experiments may distinguish species when the difference between the binding in the homologous reaction and the binding in the heterologous reaction expressed as a percentage is less than 70%. In addition, rRNA signature sequence criteria, ribotyping characterization of the nomenclature type strain and other strains of the species, and reference strains of other species is recommended to describe the strains of the new species with sets of genetic attributes and reveal possible grouping errors. This proposal has been endorsed by the members of the Subcommittee on the taxonomy of staphylococci and streptococci of the international Committee on Systematic Bacteriology.

Animals↗

PubMed1998

Identification of Staphylococcus species by 16S-23S rDNA intergenic spacer PCR analysis.

To investigate whether 16S-23S rDNA (rDNA) spacer region length polymorphisms are suitable for the identification of Staphylococcus strains, the 16S-23S rDNA intergenic spacer region lengths of 221 strains belonging to 31 species were studied by using a PCR-based method. Each species presented a specific 16S-23S pattern made of 1-8 fragments ranging from 104-771 bp, with the exception of the species Staphylococcus warnei, Staphylococcus caprae and Staphylococcus piscifermentans, which presented larger or smaller fragments. Very few species showed more than one pattern, Staphylococcus saprophyticus subsp. saprophyticus and Staphylococcus aureus being the most heterogeneous species (five different patterns for eight strains). Five clinical strains that could not be identified at the species level by phenotypical tests were finally identified using this method. Discrimination between some species that showed close patterns (Staphylococcus aureus/Staphylococcus chromogenes/Staphylococcus equorum, Staphylococcus aureus/staphylococcus intermedius, Staphylococcus delphini/Staphylococcus felis, Staphylococcus gallinarum, Staphylococcus delphini/Staphylococcus felis, Staphylococcus vitulus/Staphylococcus auricularis) was further achieved after Dral digestion of the PCR products. Although it does not allow discrimination of subspecies, the use of 16S-23S spacer region length data determined by PCR-mediated amplification is suitable for the identification of the 31 Staphylococcus species tested in this study. The method is rapid, easy and may be a useful tool for the identification of Staphylococcus species in the clinical microbiology laboratory.

DNA, Ribosomal↗

PubMed1998

Differentiation of Corynebacterium amycolatum, C. minutissimum, and C. striatum by carbon substrate assimilation tests.

We tested the carbon substrate assimilation patterns of 40 Corynebacterium amycolatum strains, 19 C. minutissimum strains, 50 C. striatum strains, and 1 C. xerosis strain with the Biotype 100 system (bioMérieux, Marcy-l'Etoile, France). Twelve carbon substrates of 99 allowed discrimination among the species tested. Additionally, assimilation of 3 of these 12 carbon substrates (maltose, N-acetyl-D-glucosamine, and phenylacetate) was tested with the API 20 NE identification system (bioMérieux). Since concordant results were observed with the two systems for these three carbon substrates, either identification system can be used as a supplementary tool to achieve phenotypic differential identification of C. amycolatum, C. minutissimum, and C. striatum in the clinical microbiology laboratory.

Carbon↗

PubMed1998

Evaluation of the VITEK 2 system for rapid identification of medically relevant gram-negative rods.

The new VITEK 2 system (bioMérieux) was evaluated at two independent sites with the identification card for gram-negative bacilli (ID-GNB card). Of the 845 strains tested, which represented 70 different taxa belonging to either the family Enterobacteriaceae or the nonenteric bacilli, 716 (84.7%) were correctly identified at the species level. Thirty-two (3.8%) additional strains were identified to the species level after the performance of simple, rapid manual tests (oxidase, hemolysis, indole reaction, motility, and pigmentation). For 80 (9.5%) strains, these additional tests did not lead to an identification at the species level but the correct species identification was given among the organisms listed. Only 7 (0.8%) strains were misidentified, and 10 (1.2%) were not identified. Mistakes were randomly distributed over different taxa. Due to the new, more sensitive fluorescence-based technology of the VITEK 2 system, final results were available after 3 h. Since our evaluation was mainly a stress test, it is predicted that the VITEK 2 system in conjunction with the ID-GNB card would perform well under conditions of a routine clinical laboratory in identifying members of the family Enterobacteriaceae and selected species of nonenteric bacteria. This system is a promising, highly automated new tool for the rapid identification of gram-negative bacilli from human clinical specimens.

Bacteriological Techniques↗

PubMed1997

[Biological diagnosis of whooping cough: contribution of gene amplification].

An upsurge in pertussis infections, despite mandatory vaccination in France since 1966, has occurred again in developed countries due to progressive loss of vaccinal immunity and wider circulation of the causal bacterium, Bordetella pertussis. Unfortunately, the classical culture method is insufficiently sensitive and serology can only confirm diagnosis retrospectively. New techniques are needed for rapid diagnosis, and subsequent treatment and preventive measures. One new method, gene amplification using polymerase chain reaction (PCR), has been particularly useful in detecting Bordetella pertussis. PCR is highly specific and more sensitive than culture. It is thus quite useful in case of atypical clinical presentations and in previously treated or vaccinated patients. Less restrictions on sample transportation and preservation make PCR a technique which general practitioners can use for rapid easy diagnosis of pertussis.

Bordetella pertussis↗

PubMed1997

Identification of atypical strains of Staphylococcus epidermidis by use of molecular tools.

Four atypical coagulase-negative staphylococcal (CNS) isolates from clinical sources were compared with Staphylococcus epidermidis strains by ribotyping. The ribotypes of the four strains shared close rDNA restriction profiles with those of the S. epidermidis strains used. The DNA sequence encoding 16S rRNA demonstrated 99.9% homology with S. epidermidis. S1 nuclease experiments showed that these atypical strains formed a homogeneous genomic group. DNA-DNA homologies between the S. epidermidis type strain CCM 2124 and the four CNS isolates ranged from 70 to 89%. The guanine-plus-cytosine content of the deoxyribonucleic acid of the four strains ranged from 31 to 32 mol%.

Amino Acids↗

PubMed1997

Corynebacterium singulare sp. nov., a new species for urease-positive strains related to Corynebacterium minutissimum.

We studied two coryneform strains from clinical specimens. These strains had type IV and corynemycolic acids in their cell walls and also had phenotypic characteristics, such as urease activity and fermentation of glucose and sucrose but not trehalose, which did not permit assignment to any previously recognized taxon. According to DNA-DNA hybridization data, these two strains are members of the same species (level of DNA similarity, 86%). Phylogenetic analysis based on comparisons of almost complete small-subunit ribosomal DNA sequences revealed that these strains are closely related to Corynebacterium minutissimum, but DNA relatedness experiments clearly showed that they constitute a distinct new species with a level of DNA relatedness to the C. minutissimum type strain of less than 40%. This new species can be differentiated from C. minutissimum strains by its enzymatic activities and carbon source utilization, and the name Corynebacterium singulare is proposed for it. The type strain is strain IBS B52218 (= CCUG 37330), which was isolated from a semen specimen.

Base Composition↗

PubMed1997

Multicenter evaluation of the updated and extended API (RAPID) Coryne database 2.0.

In a multicenter study, 407 strains of coryneform bacteria were tested with the updated and extended API (RAPID) Coryne system with database 2.0 (bioMérieux, La-Balme-les-Grottes, France) in order to evaluate the system's capability of identifying these bacteria. The design of the system was exactly the same as for the previous API (RAPID) Coryne strip with database 1.0, i.e., the 20 biochemical reactions covered were identical, but database 2.0 included both more taxa and additional differential tests. Three hundred ninety strains tested belonged to the 49 taxa covered by database 2.0, and 17 strains belonged to taxa not covered. Overall, the system correctly identified 90.5% of the strains belonging to taxa included, with additional tests needed for correct identification for 55.1% of all strains tested. Only 5.6% of all strains were not identified, and 3.8% were misidentified. Identification problems were observed in particular for Corynebacterium coyleae, Propionibacterium acnes, and Aureobacterium spp. The numerical profiles and corresponding identification results for the taxa not covered by the new database 2.0 were also given. In comparison to the results from published previous evaluations of the API (RAPID) Coryne database 1.0, more additional tests had to be performed with version 2.0 in order to completely identify the strains. This was the result of current changes in taxonomy and to provide for organisms described since the appearance of version 1.0. We conclude that the new API (RAPID) Coryne system 2.0 is a useful tool for identifying the diverse group of coryneform bacteria encountered in the routine clinical laboratory.

Actinomycetales↗

PubMed1997

Kinetics of chlorhexidine on intact skin following a single application.

Residual chlorhexidine concentrations were measured after application of a single dose on the skin of 22 healthy volunteers. Dosage by high-pressure liquid chromatography in the skin cleansers revealed that the residual concentrations were higher than chlorhexidine MICs for most organisms of the resident skin flora and some responsible for hand-borne infections, even 24 h after application.

Anti-Infective Agents, Local↗

PubMed1996

Rapid identification of Staphylococcus aureus in bronchoalveolar lavage fluid using a DNA probe (Accuprobe).

OBJECTIVE: Staphylococcus aureus is one of the prominent causative agents of ventilator-associated pneumonia (VAP). Gram staining of bronchoalveolar lavage (BAL) fluid is not always reliable. A nonisotopid probe (Accuprobe) has been developed by Gen-Probe for the specific identification of S. aureus isolated from cultures. This study was undertaken to assess the reliability of this probe for the early diagnosis of S. aureus VAP. DESIGN: A prospective study in 120 consecutive patients. SETTING: Department of intensive care medicine at a university hospital. PATIENTS: 120 ventilated patients (70 males and 50 females; mean age 52 +/- 12 years; mean simplified acute physiologic score = 13 +/- 4) were studied. INTERVENTIONS: 164 bronchoalveolar lavages were performed (none of the patients received prior antibiotic therapy). MEASUREMENTS AND RESULTS: S. aureus was identified 29 times at significant concentrations (> or = 10(4) cfu/ml) and 7 times at < 10(4) cfu/ml. The sensitivity and specificity of the Accuprobe system were 100 and 96%, respectively. We found agreement between quantitative cultures and probes in 96.3% of cases. CONCLUSIONS: We conclude that this probe provides a rapid (< or = 7 h) and accurate diagnosis of S. aureus pulmonary infection.

Aged↗

PubMed1996

Identification and ribotyping of Staphylococcus xylosus and Staphylococcus equorum strains isolated from goat milk and cheese.

Twenty-five strains of staphylococci isolated from goat milk and cheese were identified as belonging to the Staphylococcus xylosus/equorum group using the ID 32 Staph system (bioMérieux, Marcy-L'Etoile, France). This system, however, was not able to discriminate between these two species for 19 of the strains tested. Ribotyping was performed on these 25 strains, as well as on three reference strains of each of these two species. Hybridization membranes were scanned and analyzed using the Taxotron software package (Taxolab, Institut Pasteur, Paris, France). A dendrogram representation showed that ribotypes were distributed in two clear-cut clusters corresponding to S. equorum (21 strains) and S. xylosus (four strains).

Animals↗

PubMed1996

Staphylococcus saprophyticus subsp. bovis subsp. nov., isolated from bovine nostrils.

A new coagulase-negative subspecies, Staphylococcus saprophyticus subsp. bovis, is described on the basis of a study of five strains isolated from the anterior nares of cows. This subspecies is differentiated from the other novobiocin-resistant staphylococci by its phenotypic properties, cell wall composition, and levels of genetic relatedness. The type strain of the new subspecies is KV 12 (=CCM 4410).

Animals↗

PubMed1996

Identification of Turicella otitidis isolated from a patient with otorrhea associated with surgery: differentiation from Corynebacterium afermentans and Corynebacterium auris.

Turicella otitidis is a newly described coryneform bacterium isolated from middle ear fluids. We report here on the diagnosis of a strain isolated from otorrhea. The API Coryne system (bioMérieux, Marcy I'Etoile, France) used alone failed to differentiate T. otitidis, Corynebacterium afermentans, and Corynebacterium auris (ANF group). Biochemical tests such as DNase, enzymatic reactions (API ZYM; bioMérieux), and carbon substrate assimilation tests (Biotype 100; bioMérieux) allow presumptive identification. However, only chemotaxonomy and molecular biology can achieve unequivocal differentiation among these three species.

Cerebrospinal Fluid Otorrhea↗

PubMed1996

Ribotyping: a tool for taxonomy and identification of the Nocardia asteroides complex species.

Ribotyping has been evaluated as a taxonomic tool for studying bacteria belonging to the Nocardia asteroides complex. The probe used was obtained by PCR from DNA extracted from the type strain Nocardia asteroides ATCC 19247, a sequence that codes partly for 16S rRNA. Interpretation of hybridization after EcoRI restriction of total DNA of 21 strains of the N. asteroides complex allowed for the identification of only four different ribotypes: two related to N. asteroides sensu stricto, one related to N. farcinica and one related to N. nova. These results confirm the classification established by Tsukamura in 1982 (M. Tsukamura, Microbiol. Immunol. 26:1101-1119, 1982) as well as the heterogeneity of N. asteroides sensu stricto species. Ribotyping may also provide a major identification technique for the species belonging to the N. asteroides complex.

Bacterial Typing Techniques↗

PubMed1996

Comparison of the new API Candida system to the ID 32C system for identification of clinically important yeast species.

API Candida was evaluated in comparison with the ID 32C system for the identification of 619 yeast isolates. The sensitivity of API Candida for the identification of the 15 species it claims to identify with and without additional tests was 97.4% (593 of 609) and 75.2% (458 of 609), respectively. The API Candida system is easy to use and rapid (result in 18 to 24 h).

Candida↗

PubMed1995

Rapid diagnosis of Mycobacterium tuberculosis infections by an ELISA-like detection of polymerase chain reaction products.

A polymerase chain reaction (PCR) assay was developed for the detection in clinical samples of mycobacteria belonging to the Mycobacterium tuberculosis complex. PCR products were detected with a simple and rapid colormetric method. With this method, 50 fg of M. tuberculosis DNA were detectable with the repetitive DNA-sequence-derived primers, corresponding to 10 genome equivalents. Detection of M. tuberculosis in 258 clinical samples by PCR was compared with detection by culture. PCR was positive for 56 of 57 culture-positive and Ziehl-Neelsen-staining-positive (ZN) samples, 11 of 18 culture-positive and ZN-negative samples. The presence of groEL DNA sequences was also investigated by PCR for all the specimens with the same revelation protocol. Three of the eight false-negative samples with the repetitive element-derived primers were found to contain groEL DNA sequences specific for the Mycobacterium genus. Among the 183 culture-negative samples, 30 were positive by PCR. When clinical data were known, the diagnosis of tuberculosis was established for the patients from whom those samples had been obtained. The results show that the rapid and simplified PCR assay described here is slightly more sensitive than culture and can be used in routine clinical practice.

Bacteriological Techniques↗