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R Ruimy

Publications and source records attributed to R Ruimy.

At least 19 recordsLinked to original sources
PubMed2003

Epidemiology of Pseudomonas aeruginosa and risk factors for carriage acquisition in an intensive care unit.

Because of a high prevalence of Pseudomonas aeruginosa infections, we conducted an epidemiological study to assess the need for systematic surveillance, as well as the value of applying barrier precautions toP. aeruginosa carriers. From July 1997 to February 1998, we conducted a prospective cohort study in an 18-bed medical intensive care unit (ICU), which is part of the infectious diseases department in a 1200-bed tertiary-care teaching hospital. Rectal and oropharyngeal swabs were obtained on admission and twice weekly. Acquired strains were genotypically characterized by pulsed-field gel electrophoresis (PFGE). A risk factor analysis for carriage, colonization and infection was performed. Among 269 eligible patients, 116 (43%) were P. aeruginosa carriers, with 46 (17%) detected on admission and 70 (26%) who acquired carriage during their stay in ICU. Among these 70 patients, 29 became colonized (N=13) or developed infection (N=16). Conversely, in the 121 patients who remained free of carriage, no colonization or infection were detected. Genotyping analysis using PFGE was performed for 81/85 (95%) acquired strains in 67 patients. The same genotype I was observed for 58/81 (70%) of these strains issued from 47 patients, and a distinct genotype II affected two other patients (three strains). The last 20 strains were not genetically related. In a multivariate model, mechanical ventilation was associated with the acquisition of P. aeruginosa carriage. Antibiotics ineffective against P. aeruginosa significantly increased the risk of colonization or infection in ICU. Although several recent studies concluded that endogenous sources account for the majority of P. aeruginosa colonizations or infections, we conclude that epidemiology may vary according to the ICU, and that cross-colonization (i.e., exogenous source) may occur and warrant reinforced barrier precautions.

Actuarial Analysis↗
PubMed2002

The changing clinical aspects of infective endocarditis: descriptive review of 90 episodes in a French teaching hospital and risk factors for death.

OBJECTIVE: We wanted to describe the epidemiological aspects of infective endocarditis (IE) in a French hospital and identify the prognostic factors. METHODS: We reviewed the clinical, echocardiographic and microbiological features, and the outcome of 89 patients (90 episodes, median age 60 years) with IE over 18 months. Logistic regression analysis was used to identify prognostic factors for death. RESULTS: A native valve was involved in 68 cases (75.5%); in 7 of these the patient was an intravenous drug user. A prosthetic valve was involved in 22 cases (24.5%); 5 of these were of early onset. Diagnosis was definite in 87% of cases. Median time to diagnosis was 3 days. Twenty-five patients (28%) were immunocompromised. A portal of entry, usually cutaneous, was identified in 65% of cases. Sixty-two percent of patients had an underlying heart disorder, usually degenerative. The infection involved the left heart in more than 75% of cases. One or more vegetations were detected in 75% of cases. The median size of vegetation was 15 mm. Isolated agents were mainly staphylococci (n=40 (44%), including 12 coagulase-negative isolates), and streptococci (n=23 (25%), including 7 enterococci). In 11 cases (12%), cultures remained negative. Nineteen episodes were nosocomial and Staphylococcus aureus was implicated in 11 of them. Fifty percent of patients had at least one complication: heart failure (n=42), kidney failure (n=44), embolism (n=35), septic shock (n=19). Surgery was performed in 49 cases (54%) due to heart failure (n=19), cerebral embolism (n=12), and/or severe valve lesions (n=27). Eighteen patients died, 10 of whom were infected with S. aureus. Nosocomial IE (P=0.0008), heart failure (P=0.004) and prosthetic valve (P=0.01), but not S. aureus were independently associated with death. CONCLUSIONS: S. aureus was the main microorganism isolated in our patients. However, it was not independently predictive of fatal outcome.

Adult↗
PubMed2001

Genetic diversity of Pseudomonas aeruginosa strains isolated from ventilated patients with nosocomial pneumonia, cancer patients with bacteremia, and environmental water.

Random amplified polymorphic DNA typing was used to study the genetic diversity of Pseudomonas aeruginosa strains from (i) ventilated patients with nosocomial pneumonia who were hospitalized in intensive care units, (ii) cases of bacteremia in cancer patients with severe neutropenia, and (iii) rivers and swimming pools. Genetic diversity was determined by three phylogenetic methods and by statistical analysis of population genetics. The population studied undergoes epidemic clonality with a high rate of genetic recombination. P. aeruginosa bacteremia and pneumonia are not caused by specific clones within this species.

Bacteremia↗
PubMed2000

Prevalence of virulence genes and clonality in Escherichia coli strains that cause bacteremia in cancer patients.

Phenotypic analysis of Escherichia coli strains causing bacteremia in cancer patients suggests that they possess specific virulence properties. To investigate this hypothesis, we compared the frequency of the virulence-related genes cnf1, cnf2, papC, hlyC, and iut in 155 E. coli strains isolated from hospitalized cancer patients with epidemiologically unrelated cases of bacteremia to their frequency in 70 E. coli strains isolated from the feces of healthy unrelated volunteers. Of the blood isolates, 24, 37, and 26% were positive for cnf1, papC, and hlyC, respectively, versus only 6, 17, and 6% of the fecal isolates (P < 0.05 in all instances). By contrast, 47% of both isolates carried the iut gene. The patients' clinical characteristics did not significantly influence these frequencies. The presence on various pathogenicity islands (PAIs) of a combination of the cnf1, papC, and hlyC genes on the chromosome was strongly suggested by Southern blotting of pulsed-field gel electrophoresis (PFGE) patterns with specific DNA probes. The phylogenetic relatedness among 60 strains carrying three, two, one, or no virulence genes and 6 ECOR strains included as references was determined by neighbor joining, the unweighted pair-group method with arithmetic mean, and Wagner analysis of the randomly amplified polymorphic DNA (RAPD) patterns generated by 11 primers. Identification of a major cluster including 96.4% of the strains carrying the cnf1, papC, and hlyC genes and ECOR subgroup B2 strains suggested that the virulent E. coli strains causing bacteremia in cancer patients are closely related to ECOR B2 strains. The presence in the E. coli population surveyed of a strong linkage disequilibrium, and especially of a highly significant correlation between PFGE and RAPD genetic distances, confirms that clonal propagation has a major impact on the E. coli population structure. Nevertheless, low bootstrap values in the phylogenetic tree suggested that frequent genetic exchange inhibits the individualization of discrete genetic lineages, which are stable on an evolutionary scale.

Animals↗
PubMed1997

Alteromonas infernus sp. nov., a new polysaccharide-producing bacterium isolated from a deep-sea hydrothermal vent.

A deep-sea, aerobic, mesophilic and heterotrophic new bacterium was isolated from a sample of fluid collected among a dense population of Riftia pachyptila, in the vicinity of an active hydrothermal vent of the Southern depression of the Guaymas basin (Gulf of California). On the basis of phenotypic and phylogenetic analyses and DNA/DNA relatedness, the strain GY785 was recognized as a new species of the genus Alteromonas and the name of Alteromonas infernus is proposed. During the stationary phase in batch cultures in the presence of glucose, this bacterium secreted two unusual polysaccharides. The water-soluble exopolysaccharide-1 produced contained glucose, galactose, galacturonic and glucuronic acids as monosaccharides. The gel-forming exopolysaccharide-2 was separated from the bacterial cells by dialysis against distilled water and partially characterized.

Base Composition↗
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↗
PubMed1996

Species identities and antimicrobial susceptibilities of corynebacteria isolated from various clinical sources.

Over a 14-month period, 415 clinical isolates of coryneform gram-positive rods were recovered from various sources and identified to the species level according to recent identification schemes. Corynebacterium urealyticum, Corynebacterium striatum, Corynebacterium amycolatum, and Corynebacterium jeikeium predominated, accounting for 63% of all isolates. Corynebacterium accolens, Corynebacterium striatum, Corynebacterium argentoratense, Corynebacterium propinquum and Corynebacterium pseudodiphtheriticum were mostly recovered from the respiratory tract, whereas Corynebacterium afermentans, CDC group G, and Corynebacterium jeikeium were mainly isolated from blood. None of the isolates was identified as Corynebacterium diphtheriae or Corynebacterium xerosis. Ampicillin resistance was detected in Corynebacterium jeikeium (96%) and Corynebacterium urealyticum (99%) and varied among Corynebacterium amycolatum (56%) and CDC group G (26%). These data emphasize the need for an accurate identification of coryneform organisms at the species level and for antimicrobial susceptibility testing of these organisms.

Corynebacterium↗
PubMed1996

Nocardia pseudobrasiliensis sp. nov., a new species of Nocardia which groups bacterial strains previously identified as Nocardia brasiliensis and associated with invasive diseases.

We studied five strains of a new Nocardia taxon recently identified among Nocardia brasiliensis strains associated with invasive diseases (R. J. Wallace, Jr., B. A. Brown, Z. Blacklock, R. Ulrich, K. Jost, J. M. Brown, M. M. McNeil, G. Onyi, V. A. Steingrube, and J. Gibson, J. Clin. Microbiol. 33:1528-1533, 1995) to determine their taxonomic status. Several characteristics of these organisms, including the presence of chemotype IV cell walls, nocardomycolic acids, a predominant menaquinone similar to that of Nocardia asteroides ATCC 19247T (T = type strain), and G+C contents ranging from 67 to 68 mol%, are characteristics of the genus Nocardia. Phylogenies based on small-subunit ribosomal DNA sequences clearly confirmed that all five strains belong to the genus Nocardia and occur on a single branch that is clearly distinct from N. brasiliensis. This branch forms a clade with Nocardia vaccinii, Nocardia nova, Nocardia otitidiscaviarum, and Nocardia seriolae. The five new strains exhibited high levels of DNA relatedness with each other, as determined by DNA-DNA hybridization experiments (S1 nuclease procedure), but not with N. brasiliensis strains or with strains of the four phylogenetically related Nocardia species mentioned above. The five new strains differ from N. brasiliensis in the following characteristics: mycolic acid pattern, decomposition of adenine, nitrate reduction, and antimicrobial agent susceptibilities. Therefore, we propose that these strains belong to a new species, Nocardia pseudobrasiliensis. The type strain is strain ATCC 51512, which was isolated from a leg abscess on a patient suffering from ulcerative colitis.

DNA, Bacterial↗
PubMed1996

Bacterial diversity in a deep-subsurface clay environment.

The presence of bacteria in a deep clay sediment was analyzed in a 20-m-long core horizontally drilled from a mine gallery at a depth of 224 m in the Boom clay formation (Mol, Belgium). This clay deposit is the result of a marine sedimentary process that occurred 35 million years ago. Bacterial activities were estimated by measuring respiration on [14C]glucose. Using the same samples, universal primers for the genes coding for eubacterial 16S rRNA were used to amplify extracted DNA. PCR products were then cloned, sequenced, and analyzed by molecular phylogeny. Our data showed a decrease in bacterial densities as a function of distance from the gallery, with few bacteria detectable by culture at more than 80 cm from the gallery wall. PCR experiments showed the presence of bacteria in all samples, and phylogenetic analyses were then used to tentatively identify these organisms. Because of low bacterial densities in deep clay samples, direct counts and enumeration of viable bacteria on diverse culture media remained negative. All experiments, both cultures and PCR, demonstrated the difficulty of analyzing samples that contain only a few poorly active bacteria as it is difficult to avoid a small contamination by active bacteria during sampling. Since the porosity of the Boom clay formation is less than the expected size of bacteria, it is possible that some of the bacteria present in this 35-million-year-old deep clay deposit derive from cells initially trapped during the sedimentation process.

Bacteria↗
PubMed1996

A recent fixation of cfiA genes in a monophyletic cluster of Bacteroides fragilis is correlated with the presence of multiple insertion elements.

Small-subunit ribosomal DNA sequences of 16 strains of Bacteroides fragilis were determined and compared with previously published sequences. Three phylogenetic methods (the neighbor-joining, maximum-likelihood, and maximum-parsimony methods) as well as a bootstrap analysis were used to assess the robustness of each topology. All phylogenetic analyses demonstrated that the B. fragilis strains were clearly divided into two robust monophyletic units which corresponded to the cfiA-negative and cfiA-positive groups. Strains of two previously identified DNA homology groups separated similarly into the two monophyletic units. According to the intensity of the hybridization signal with a cfiA probe, the cfiA-positive cluster could be further divided into two groups. This difference might reflect the existence of two, probably closely related cfiA-type genes. In the strongly hybridizing cfiA-positive strains, the gene is capable of conferring high-level resistance to the carbapenems and to most beta-lactamase inhibitors as well, while in the weakly hybridizing cfiA-positive strains, only the latter type of resistance is known to occur. The presence of the cfiA-type genes within a monophyletic cluster of B. fragilis that apparently represents only a minority of the species B. fragilis is suggestive of a recent acquisition. The fact that this cluster is also the predominant pool of all known B. fragilis insertion elements, which have been found to play an important role in the expression of carbapenem resistance, raises the possibility that both genetic determinants, i.e., the resistance gene(s) and insertion elements, may have coevolved.

Bacterial Proteins↗
PubMed1996

Genetic identification of cryptic genospecies of Haemophilus causing urogenital and neonatal infections by PCR using specific primers targeting genes coding for 16S rRNA.

Previous genetic analysis of Haemophilus influenzae strains isolated from genital and neonatal infections identified a group of biotype IV that constitutes a cryptic genospecies only distantly related to H. influenzae and H. Haemolyticus. Small-subunit rRNA genes of two representative strains of this genital Haemophilus genospecies (strains 16N and 2406) were sequenced. The analysis indicated that these strains form a monophyletic unit with H. haemolyticus and H. influenzae biogroups Influenzae and Aegyptius and are more closely related to H. haemolyticus than to H. influenzae biogroups Influenzae and Aegyptius. 16S rRNA gene sequences were used to formulate primers for PCR-based identification of cryptic genital Haemophilus organisms. A 242-bp fragment was amplified from strains belonging to the genital Haemophilus genospecies but not from strains of 12 other Haemophilus species, including strains of H. influenzae biotype IV sensu stricto.

Base Sequence↗
PubMed1996

Bacteremia due to Gordona sputi in an immunocompromised patient.

We report a case of bacteremia due to a strain identified as Gordona sputi in a patient with metastatic melanoma. The origin of infection remains unknown, but extensive cutaneous lesions due to interleukin-2 treatment may have been the portal of entry. The isolate was related to G. sputi on the basis of its biochemical and genomic properties but exhibited some differences from the type strain.

Actinomycetales Infections↗
PubMed1995

Taxonomy of Corynebacterium diphtheriae and related taxa, with recognition of Corynebacterium ulcerans sp. nov. nom. rev.

Levels of genomic DNA relatedness were determined using a S1 nuclease procedure for reference bacteria identified as biotypes of Corynebacterium diphtheriae, biovars of Corynebacterium pseudotuberculosis, and 'Corynebacterium ulcerans'. These results showed that the three species are separate taxa at the genomospecies level whereas biotypes and biovars are closely related genomically within each species. Phylogenetic analyses of small-subunit rDNA sequences revealed that 'Corynebacterium ulcerans' forms a tight cluster with Corynebacterium pseudotuberculosis within the robust branch that groups all Corynebacterium sequenced to date. Therefore, we propose that the species incertae sedis 'C. ulcerans' should be conclusively recognized as a distinct species within the genus Corynebacterium with strain CCUG 2708 = NCTC 7910 as type strain. This species is characterized by urease production and fermentation of glycogen.

Base Composition↗
PubMed1995

Genomic diversity and phylogenetic relationships among lipid-requiring diphtheroids from humans and characterization of Corynebacterium macginleyi sp. nov.

DNA relatedness experiments were performed with 38 clinical isolates and 13 reference strains of coryneform taxa exhibiting a lipid requirement for optimal growth. Forty-five of these strains split into five genomic groups at the species level, whereas six other strains remained unclustered. Genomospecies II fits Corynebacterium accolens, but the other genomospecies were not genetically related to any of the defined Corynebacterium species. Phylogenetic analyses of genes coding for small-subunit rRNA sequences revealed that two genomospecies (I and III) and C. accolens form a tight cluster within the robust branch that groups all Corynebacterium species presently sequenced. Reference strains of biotypes C-1, C-2, and C-3 of "Corynebacterium pseudogenitalium" were found to fall into genomospecies I, as well as "Corynebacterium tuberculostearicum," Centers for Disease Control and Prevention (CDC) coryneform group G-1, and CDC coryneform group G-2 reference strains. Biochemical tests allowed differentiation between genomospecies except between genomospecies IV and V and between six unclustered strains and genomospecies I. We propose a new classification for these lipid-requiring diphtheroids within the genus Corynebacterium with the delineation of some CDC coryneform group G-1 strains (genomospecies III) as a new species for which the name Corynebacterium macginleyi is proposed. The type strain is strain JCL-2 (CIP 104099), isolated from a human corneal ulcer.

Base Sequence↗
PubMed1995

Small-subunit rRNA sequences and whole DNA relatedness concur for the reassignment of Pasteurella piscicida (Snieszko et al.) Janssen and Surgalla to the genus Photobacterium as Photobacterium damsela subsp. piscicida comb. nov.

The taxonomic status of Pasteurella piscicida (strain NCIMB 2058T [T = type strain] and a strain isolated from the environment) was investigated by performing phylogenetic analyses of small-subunit rRNA sequences, DNA-DNA hybridization analyses, and biochemical characterization analyses. The results of the phylogenetic analyses and the levels of DNA-DNA complementarity demonstrated conclusively that Pasteurella piscicida is extremely closely related to Photobacterium damsela ATCC 33539T. Since the two taxa exhibited a level of DNA-DNA relatedness of 80%, they are members of the same species. The high level of DNA relatedness and the presence of specific morphological and biochemical characteristics support the hypothesis that two subspecies should be recognized. On the basis of its phylogenetic position, we concluded that Pasteurella piscicida should be renamed Photobacterium damsela subsp. piscicida comb. nov.

Base Sequence↗
PubMed1995

Roseobacter algicola sp. nov., a new marine bacterium isolated from the phycosphere of the toxin-producing dinoflagellate Prorocentrum lima.

We describe a new species on the basis of phenotypic characteristics and the results of an analysis of small-subunit rRNA sequences. Three strains of this organism were isolated from a culture of the toxin-producing dinoflagellate Prorocentrum lima. These bacteria are gram-negative, strictly aerobic, ovoid organisms that are motile by means of one or two subpolar flagella. They grow at temperatures ranging from 10 to 37 degrees C and in the presence of NaCl concentrations ranging from 0.1 to 2 M and have an absolute requirement for sodium ions. They are strictly aerobic with a nonfermentative type of metabolism and are not able to grow anaerobically in presence or absence of nitrate. They do not denitrify. They exhibit oxidase, catalase, gelatinase, esculinase, beta-galactosidase, and (to a lesser extent) amylase activities. The three strains which we examined require thiamine and biotin for growth. They grow only when glucose, trehalose, saccharose, fructose, maltose, pyruvate, malate, citrate, esculin, 2-ketoglutarate, 5-ketogluconate, glutamate, or shikimate is present as a sole carbon source. The three strains have identical small-subunit rRNA sequences. A phylogenetic analysis of these sequences revealed that these bacteria belong to the alpha subdivision of the Proteobacteria and that they form a distinct and robust monophyletic group with Roseobacter denitrificans and Roseobacter litoralis. This result and the general phenotypic characteristics of the organisms place them in the genus Roseobacter, although they do not produce bacteriochlorophyll a, in contrast to previously described Roseobacter species.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1995

Corynebacterium argentoratense sp. nov., from the human throat.

A new Corynebacterium species, Corynebacterium argentoratense was isolated from the throats of four human patients. It is characterized by the presence of chemotype IV, a cell wall, corynomycolic acids, and a G+C content ranging from 60 to 61 mol%. Strains belonging to this species exhibit high levels of DNA relatedness as determined by DNA-DNA hybridization experiments (S1 nuclease procedure) but no close DNA relatedness with related Corynebacterium species. Phylogenies based on comparative analyses of nearly complete small-subunit rDNA sequences confirmed the inclusion of this new species within the genus Corynebacterium and grouped it in a cluster with C. diphtheriae, C. ulcerans, C. pseudotuberculosis, and C. kutscheri. PCR experiments revealed an absence of the gene coding for diphtheria toxin. This new species can be identified by its mycolic acid pattern, fermentation of sugars, and enzymatic activities. Strain IBS B10697 (CIP 104296) is the type strain of C. argentoratense.

Amidohydrolases↗