A Simple Method for Selective Isolation of Stenotrophomonas maltophilia from Environmental Samples

Stenotrophomonas maltophilia is a commonly found environmental bacterium that is associated with the plant rhizosphere. It shows increasing prevalence in immunocompromised patients. We report a simple method for selective isolation of S. maltophilia from soils which makes use of both its resistance to imipenem and its requirement for methionine.

Corynebacterium hansenii sp. nov., an alpha-glucosidase-negative bacterium related to Corynebacterium xerosis

A novel strain, C-138(T), belonging to the genus Corynebacterium was isolated from a severe thigh liposarcoma infection and its differentiation from Corynebacterium xerosis and Corynebacterium freneyi is described. Analysis of 16S rRNA gene sequences, rpoB sequences and the PCR profile of the 16S-23S spacer regions was not conclusive enough to differentiate strain C-138(T) from C. xerosis and C. freneyi. However, according to DNA-DNA hybridization data, strain C-138(T) constitutes a member of a distinct novel species. It can be differentiated from strains of C. xerosis and C. freneyi by colony morphology, the absence of alpha-glucosidase and some biochemical characteristics such as glucose fermentation at 42 degrees C and carbon assimilation substrates. The name Corynebacterium hansenii sp. nov. is proposed for this novel species; the type strain is C-138(T) (=CIP 108444(T)=CCUG 53252(T)).

Identification of an OprD Homologue inAcinetobacterbaumannii

With the increased number of resistant Acinetobacter baumannii strains, it is urgently required to decipher the molecular bases of outer membrane permeability. The analyses of the outer membrane from different A. baumannii strains indicated a modification in the expression of two proteins of 29 and 43 kDa, respectively. By electrophoresis and MALDI-MS analyses, the 43 kDa OMP was identified as a protein belonging to the OprD family, a basic amino acid and imipenem porin.

Successive emergence of Enterobacter aerogenes strains resistant to imipenem and colistin in a patient

Enterobacter aerogenes is an agent of hospital-acquired infection that exhibits a remarkable resistance to beta-lactam antibiotics during therapy. Five successive isolates of E. aerogenes infecting a patient and exhibiting a multiresistance phenotype to beta-lactam antibiotics and fluoroquinolones were investigated. Among these clinical strains, four presented resistant phenotypes during successive imipenem and colistin treatments. The involved resistance mechanisms exhibited by the successive isolates were associated with alterations of the outer membrane that caused a porin decrease and lipopolysaccharide modifications.

Aeromonas popoffii urinary tract infection

Aeromonas popoffii is a recently described species isolated mainly from freshwater. An isolate of Aeromonas popoffii was found to be responsible for a urinary tract infection in a 13-year-old boy suffering from spina bifida with enterocystoplasty. This is the first reported case of human infection attributed to this species.

RamA is an alternate activator of the multidrug resistance cascade in Enterobacter aerogenes

Multidrug resistance (MDR) in Enterobacter aerogenes can be mediated by induction of MarA, which is triggered by certain antibiotics and phenolic compounds. In this study, we identified the gene encoding RamA, a 113-amino-acid regulatory protein belonging to the AraC-XylS transcriptional activator family, in the Enterobacter aerogenes ATCC 13048 type strain and in a clinical multiresistant isolate. Overexpression of RamA induced an MDR phenotype in drug-susceptible Escherichia coli JM109 and E. aerogenes ATCC 13048, as demonstrated by 2- to 16-fold-increased resistance to beta-lactams, tetracycline, chloramphenicol, and quinolones, a decrease in porin production, and increased production of AcrA, a component of the AcrAB-TolC drug efflux pump. We show that RamA enhances the transcription of the marRAB operon but is also able to induce an MDR phenotype in a mar-deleted strain. We demonstrate here that RamA is a transcriptional activator of the Mar regulon and is also a self-governing activator of the MDR cascade.

Omp35, a new Enterobacter aerogenes porin involved in selective susceptibility to cephalosporins

In Enterobacter aerogenes, beta-lactam resistance often involves a decrease in outer membrane permeability induced by modifications of porin synthesis. In ATCC 15038 strain, we observed a different pattern of porin production associated with a variable antibiotic susceptibility. We purified Omp35, which is expressed under conditions of low osmolality and analyzed its pore-forming properties in artificial membranes. This porin was found to be an OmpF-like protein with high conductance values. It showed a noticeably higher conductance compared to Omp36 and a specific location of WNYT residues in the L3 loop. The importance of the constriction region in the porin function suggests that this organization is involved in the level of susceptibility to negative large cephalosporins such as ceftriaxone by bacteria producing the Omp35 porin subfamily.

Resistance to imipenem, cefepime, and cefpirome associated with mutation in Omp36 osmoporin of Enterobacter aerogenes

Enterobacter aerogenes develops increased multidrug resistance via a functional alteration of outer-membrane permeability associated with a decrease in porin function. We have sequenced the gene coding the major porin of Enterobacter aerogenes, omp36. The sequence shows a high similarity with the Klebsiella pneumoniae ompK36 gene and is closely related to the enterobacterial OmpC family. Sequence analysis of several Omp36 issued from clinical strains indicated variability in putative cell-surface exposed domains. Interestingly, substitution Gly112Asp was observed in the conserved eyelet L3 region of the porin produced by two strains, C and 3. This substitution is associated with a high general beta-lactam resistance observed in these isolates and with alteration of pore properties previously described in strain 3 porin [Mol. Microbiol. 41 (2001) 189]. This is the first genetic identification of impermeability-mediated resistance to beta-lactams in various clinical E. aerogenes strains.

Molecular characterization of amoxicillin-clavulanate resistance in a clinical isolate of Escherichia coli

The resistance phenotype of the clinical isolate of Escherichia coli 1941 was characterized by high-level resistance to penicillins and to combinations amoxicillin-ticarcillin/clavulanate and ampicillin/sulbactam. This resistance was carried by the conjugative plasmid pEC1941 that encoded a beta-lactamase activity. The purified enzyme focused at pI 5.4 and was strongly inhibited in vitro by clavulanic acid (IC50 = 0.09 microM). Nucleotide sequence analysis revealed identity between the plasmid borne blaTEM gene of E. coli 1941 and the blaTEM-1B gene, except for a single C-to-T substitution at position 32 in the promoter region leading to the overlapping promoters Pa and Pb. No alterations in the expression of outer membrane porins OmpC and OmpF have been detected. These findings show that the resistance of E. coli 1941 to the combinations of beta-lactams with beta-lactamase inhibitors is related to high-level production of TEM-1 enzyme expressed from the strong promoters Pa and Pb.

Corynebacterium freneyi bacteremia

Corynebacterium freneyi is a recently described alpha-glucosidase-positive species of the genus CORYNEBACTERIUM: To our knowledge, there is no description of human infection due to this species. We report on a case of bacteremia due to C. freneyi following vascular surgery.

Eubacterium callanderi bacteremia: report of the first case

Eubacterium callanderi is an environmental anaerobic rod-shaped bacterium first isolated in 1998 from an industrial anaerobic digester. We report on the first clinical isolate of E. callanderi, which was recovered from the blood of a patient with a bladder carcinoma. Identification of the organism was made by cell fatty acid chromatographic analysis and 16S rRNA gene sequencing.

A multiple-antibiotic resistance-independent active chloramphenicol efflux in an Escherichia coli clinical isolate

The clinical isolate, Escherichia coli 1941, exhibits high resistance to chloramphenicol and tetracycline (minimum inhibitory concentrations of 512 micrograms/ml). Neither resistance is linked to the large conjugative plasmid present in the strain. The intracellular accumulation of radiolabeled chloramphenicol increased about 9-fold after the addition of the energy uncoupler carbonyl cyanide m-chlorophenol-hydrazone to an E. coli 1941 culture, indicating the presence of an active efflux mechanism. Sequence analysis and expression study suggested that the multiple-antibiotic resistance marRAB locus and the AcrAB drug-efflux pump were not involved in this active efflux of chloramphenicol.

Imipenem and expression of multidrug efflux pump in Enterobacter aerogenes

Imipenem is often used to treat intensive care unit patients infected by Enterobacter aerogenes, but it is leading to an increasing number of antibiotic resistant strains. Clinical isolates and imipenem resistant variants presented a high level of resistance to beta-lactam antibiotic group and to chemically unrelated drugs. We report here that imipenem selects strains which contain active efflux pumps ejecting various unrelated antibiotics including quinolones, tetracycline, and chloramphenicol. An increase of AcrA, an efflux pump component, was observed in the imipenem resistant variants. The overexpression of marA, involved in the genetic control of membrane permeability via porin and efflux pump expression, indicated the activation of the resistance genetic cascade in imipenem resistant variants.

prbA, a gene coding for an esterase hydrolyzing parabens in enterobacter cloacae and Enterobacter gergoviae strains

The new gene prbA encodes an esterase responsible for the hydrolysis of the ester bond of parabens in Enterobacter cloacae strain EM. This gene is located on the chromosome of strain EM and was cloned by several PCR approaches. The prbA gene codes for an immature protein of 533 amino acids, the first 31 of which represent a proposed signal peptide yielding a mature protein of a putative molecular mass of 54.6 kDa. This enzyme presents analogies with other type B carboxylesterases, mainly of eukaryotic origin. The cloning and expression of the prbA gene in a strain of Escherichia coli previously unable to hydrolyze parabens resulted in the acquisition of a hydrolytic capacity comparable to the original activity of strain EM, along with an increased resistance of the transformed strain to methyl paraben. The presence of homologues of prbA was tested in additional ubiquitous bacteria, which may be causative factors in opportunistic infections, including Enterobacter gergoviae, Enterobacter aerogenes, Pseudomonas agglomerans, E. coli, Pseudomonas aeruginosa, and Burkholderia cepacia. Among the 41 total strains tested, 2 strains of E. gergoviae and 1 strain of Burkholderia cepacia were able to degrade almost completely 800 mg of methyl paraben liter(-1). Two strains of E. gergoviae, named G1 and G12, contained a gene that showed high homology to the prbA gene of E. cloacae and demonstrated comparable paraben esterase activities. The significant geographical distance between the locations of the isolated E. cloacae and E. gergoviae strains suggests the possibility of an efficient transfer mechanism of the prbA gene, conferring additional resistance to parabens in ubiquitous bacteria that represent a common source of opportunistic infections.

mar Operon involved in multidrug resistance of Enterobacter aerogenes

We determined the sequence of the entire marRAB operon in Enterobacter aerogenes. It is functionally and structurally analogous to the Escherichia coli operon. The overexpression of E. aerogenes MarA induces a multidrug resistance phenotype in a susceptible strain, demonstrated by a noticeable resistance to various antibiotics, a decrease in immunodetected porins, and active efflux of norfloxacin.

Corynebacterium freneyi sp. nov., alpha-glucosidase-positive strains related to Corynebacterium xerosis

Three coryneform strains from clinical specimens were studied. They belonged to the genus Corynebacterium, since they had type IV cell walls containing corynemycolic acids. They had phenotypic characteristics that included alpha-glucosidase, pyrazinamidase and alkaline phosphatase activities and fermentation of glucose, ribose, maltose and sucrose. These are the characteristics of Corynebacterium xerosis. Since this species is very rare in human pathology, the strains were studied in more detail by comparing the 16S-23S intergenic spacers, rDNA sequences and levels of DNA similarity of these three strains and those of the reference strains C. xerosis ATCC 373T and Corynebacterium amycolatum CIP 103452T. According to DNA-DNA hybridization data, the three novel strains are members of the same species (level of DNA similarity >72%). Phylogenetic analysis revealed that these strains are closely related to C. xerosis and C. amycolatum, but DNA-relatedness experiments showed clearly that they constitute a distinct new species, with levels of DNA relatedness of less than 23% to C. xerosis ATCC 373T and less than 5% to C. amycolatum CIP 103452T. Two other alpha-glucosidase-positive strains presenting the same biochemical characteristics were included in the study and proved to be C. amycolatum. This new species can be differentiated from C. xerosis and C. amycolatum strains by carbon source utilization, intergenic spacer region length profiles and some biochemical characteristics such as glucose fermentation at 42 degrees C and growth at 20 degrees C. The name Corynebacterium freneyi sp. nov. is proposed with the type strain ISPB 6695110T (= CIP 106767T = DSM 44506T).

Samsonia erythrinae gen. nov., sp. nov., isolated from bark necrotic lesions of Erythrina sp., and discrimination of plant-pathogenic Enterobacteriaceae by phenotypic features

Bacterial strains isolated from diseased erythrina (Erythrina sp.) trees in Martinique (French West Indies) were studied using phenotypic tests, 16S rDNA sequence analysis and DNA-DNA hybridization. Numerical analysis of phenotypic characteristics showed that these strains formed an homogeneous phenon among plant-pathogenic Enterobacteriaceae, and gave useful and updated information for the identification of these bacteria. Results of DNA-DNA hybridization indicated that strains from erythrina belonged to a discrete genomospecies (89-100% hybridization) and had low levels of DNA relatedness (2-33% hybridization) with reference strains of phytopathogenic Erwinia, Brenneria, Pectobacterium, Pantoea and Enterobacter species. 16S rDNA sequence analysis using three different methods revealed that the position of strain CFBP 5236T isolated from erythrina was variable in the different trees, so that strains from erythrina could not be assigned to any recognized genus. It is proposed that these strains are included in a new genus, Samsonia. The name Samsonia erythrinae is proposed for the new species. The G+C content of the DNA of the type strain, CFBP 5236T (= ICMP 13937T), is 57.0 mol%.

Phylogenetic analyses of Klebsiella species delineate Klebsiella and Raoultella gen. nov., with description of Raoultella ornithinolytica comb. nov., Raoultella terrigena comb. nov. and Raoultella planticola comb. nov

The phylogenetic relationships of the type strains of 9 Klebsiella species and 20 species from 11 genera of the family Enterobacteriaceae were investigated by performing a comparative analysis of the sequences of the 16S rRNA and rpoB genes. The sequence data were phylogenetically analysed by the neighbourjoining and parsimony methods. The phylogenetic inference of the sequence comparison confirmed that the genus Klebsiella is heterogeneous and composed of species which form three clusters that also included members of other genera, including Enterobacter aerogenes, Erwinia clusters I and II and Tatumella. Cluster I contained the type strains of Klebsiella pneumoniae subsp. pneumoniae, Klebsiella pneumoniae subsp. rhinoscleromatis and Klebsiella pneumoniae subsp. ozaenae. Cluster II contained Klebsiella ornithinolytica, Klebsiella planticola, Klebsiella trevisanii and Klebsiella terrigena, organisms characterized by growth at 10 degrees C and utilization of L-sorbose as carbon source. Cluster III contained Klebsiella oxytoca. The data from the sequence analyses along with previously reported biochemical and DNA-DNA hybridization data support the division of the genus Klebsiella into two genera and one genogroup. The name Raoultella is proposed as a genus name for species of cluster II and emended definitions of Klebsiella species are proposed.

Enumeration and characterization of cellulolytic bacteria from refuse of a landfill

Enumeration and phenotypic characterization of aerobic cellulolytic bacteria were performed on fresh, 1 year old and 5 years old refuse samples of a French landfill site. Numbers of cellulolytic bacteria ranged from 1.1x10(6) to 2.3x10(8) c.f.u. (g dry wt.)(-1) and were lower in 5 years old refuse samples. A numerical analysis of phenotypic data based on 80 biochemical tests and performed on 321 Gram-positive isolates from refuse, revealed a high phenotypic diversity of cellulolytic bacteria which were distributed into 21 clusters. Based on the phenotypic analysis and the sequencing of 16S rDNA of five representative strains of major clusters, the predominant cellulolytic groups could be assigned to the family of Bacillaceae and to the genera Cellulomonas, Microbacterium and Lactobacillus. Furthermore, chemical parameters such as pH, carbohydrates and volatile solid contents influenced the composition of the cellulolytic bacterial groups which were reduced essentially to the family of Bacillaceae in the oldest refuse samples.

16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates

Some bacteria are difficult to identify with phenotypic identification schemes commonly used outside reference laboratories. 16S ribosomal DNA (rDNA)-based identification of bacteria potentially offers a useful alternative when phenotypic characterization methods fail. However, as yet, the usefulness of 16S rDNA sequence analysis in the identification of conventionally unidentifiable isolates has not been evaluated with a large collection of isolates. In this study, we evaluated the utility of 16S rDNA sequencing as a means to identify a collection of 177 such isolates obtained from environmental, veterinary, and clinical sources. For 159 isolates (89.8%) there was at least one sequence in GenBank that yielded a similarity score of > or =97%, and for 139 isolates (78.5%) there was at least one sequence in GenBank that yielded a similarity score of > or =99%. These similarity score values were used to defined identification at the genus and species levels, respectively. For isolates identified to the species level, conventional identification failed to produce accurate results because of inappropriate biochemical profile determination in 76 isolates (58.7%), Gram staining in 16 isolates (11.6%), oxidase and catalase activity determination in 5 isolates (3.6%) and growth requirement determination in 2 isolates (1.5%). Eighteen isolates (10.2%) remained unidentifiable by 16S rDNA sequence analysis but were probably prototype isolates of new species. These isolates originated mainly from environmental sources (P = 0.07). The 16S rDNA approach failed to identify Enterobacter and Pantoea isolates to the species level (P = 0.04; odds ratio = 0.32 [95% confidence interval, 0.10 to 1.14]). Elsewhere, the usefulness of 16S rDNA sequencing was compromised by the presence of 16S rDNA sequences with >1% undetermined positions in the databases. Unlike phenotypic identification, which can be modified by the variability of expression of characters, 16S rDNA sequencing provides unambiguous data even for rare isolates, which are reproducible in and between laboratories. The increase in accurate new 16S rDNA sequences and the development of alternative genes for molecular identification of certain taxa should further improve the usefulness of molecular identification of bacteria.

Characterization of plasmid-borne and chromosome-encoded traits of Agrobacterium biovar 1, 2, and 3 strains from France

We collected 111 Agrobacterium isolates from galls of various origins (most of them from France) and analyzed both their plasmid-borne and chromosome-encoded traits. Phenotypic analysis of these strains allowed their classification in three phena which exactly matched the delineation of biovars 1, 2, and 3. A fourth phenon was identified which comprises three atypical strains. The phenotypic analysis has also allowed us to identify 12 additional characteristics which could be used to identify the three biovars of Agrobacterium. Our results also suggest that biovar 1 and 2 represent distinct species. Analysis of plasmid-borne traits confirmed that tartrate utilization is a common feature of biovar 3 strains (now named Agrobacterium vitis) and of Agrobacterium grapevine strains in general. Among pathogenic strains of Agrobacterium, several exhibited unusual opine synthesis and degradation patterns, and one strain of biovar 3 induced tumors containing vitopine and a novel opine-like molecule derived from putrescine. We have named this compound ridéopine.

Imipenem resistance of enterobacter aerogenes mediated by outer membrane permeability

Multidrug-resistant Enterobacter aerogenes strains are increasingly isolated in Europe and especially in France. Treatment leads to imipenem resistance, because of a lack of porin. We studied the evolution of resistance in 29 strains isolated from four patients during their clinical course. These strains belonged to the prevalent epidemiological type observed in France in previous studies (C. Bosi, et al., J. Clin. Microbiol. 37:2165-2169, 1999; A. Davin-Regli et al., J. Clin. Microbiol. 34:1474-1480, 1996). They also harbored a TEM-24 extended-spectrum beta-lactamase-coding gene. Thirteen strains were susceptible to gentamicin and resistant to imipenem and cefepime. All of the patients showed E. aerogenes strains with this resistance after an imipenem treatment. One patient showed resistance to imipenem after a treatment with cefpirome. Twelve of these 13 strains showed a lack of porin. Cessation of treatment with imipenem for three patients was followed by reversion of susceptibility to this antibiotic and the reappearance of porins, except in one case. For one patient, we observed three times in the same day the coexistence of resistant strains lacking porin and susceptible strains possessing porin. The emergence of multidrug-resistant E. aerogenes strains is very disquieting. In our study, infection by E. aerogenes increased the severity of the patients' illnesses, causing a 100% fatality rate.

Molecular identification of a Nocardiopsis dassonvillei blood isolate

Nocardiopsis dassonvillei is an environmental aerobic actinomycete seldom isolated in cutaneous and pulmonary infections. We herein report the first N. dassonvillei blood isolate in a patient hospitalized for cholangitis. Although morphological characteristics and biochemical tests allowed a presumptive identification of this isolate, cell wall fatty acid chromatographic analysis confirmed identification at the genus level, and 16S rRNA gene sequencing achieved definite identification. This study illustrates the usefulness of 16S rRNA gene sequencing as a routine method for the identification of actinomycetes.

Most Enterobacter aerogenes strains in France belong to a prevalent clone

The aim of this study was to determine the distribution in France of the Enterobacter aerogenes prevalent clone isolated in the hospitals of the Marseille area (A. Davin-Regli, D. Monnet, P. Saux, C. Bosi, R. Charrel, A. Barthelemy, and C. Bollet, J. Clin. Microbiol. 34:1474-1480, 1996). A total of 123 E. aerogenes isolates were collected from 23 hospital laboratories and analyzed by random amplification of polymorphic DNA and enterobacterial repetitive intergenic consensus-PCR to determine their epidemiological relatedness. Molecular typing revealed that 21 of the 23 laboratories had isolated this prevalent clone harboring the plasmid encoding for extended-spectrum beta-lactamase of the TEM-24 type. Most isolates were susceptible only to imipenem and gentamicin. Their dissemination seems to be clonal and was probably the result of the general use of broad-spectrum cephalosporins and quinolones. Four isolates showed an alteration of their outer membrane proteins, causing decrease of susceptibility to third-generation cephalosporins and imipenem and leading to the critical situation of having no alternative therapeutic. The large dissemination of the E. aerogenes prevalent clone probably results from its good adaptation to the antibiotics administered in France and the hospital environment, particularly in intensive care units.

Porin alteration and active efflux: two in vivo drug resistance strategies used by Enterobacter aerogenes

Enterobacter aerogenes is among the five most frequently isolated nosocomial pathogens in France, and this bacterium also shows increasing multidrug resistance. In this study, various E. aerogenes strains isolated from hospital units were characterized for their outer-membrane proteins, antibiotic susceptibilities (inhibition diameters and MICs) and resistance mechanisms associated with modification of envelope permeability (porin alteration and active efflux). Diminished outer-membrane permeability due to porin alterations was found in conjunction with the expression of an enzymic barrier in resistant isolates. Interestingly, changes in the functional expression of porins appeared to play a special role in susceptibility to cefepime. An active efflux to quinolones was also identified. Simultaneous changes in envelope permeability, i.e. a porin deficiency (in) and an efflux mechanism (out), were clearly evident in two clinical strains.

A cluster of cases of infections due to Aeromonas hydrophila revealed by combined RAPD and ERIC-PCR

Two polymerase chain reaction (PCR)-based methods were used for epidemiological typing of Aeromonas hydrophila. Random amplification of polymorphic DNA (RAPD) and enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) were applied to an outbreak involving seven patients. The epidemiological situation appeared complex; with the exception of two clinical isolates, all gave unique patterns with both techniques. These methods demonstrated nosocomial transmission in one unit and permitted the study to exclude a common environmental source in the hospital. The coincidental clustering of patients infected with A. hydrophila probably resulted from an increased prevalence of aeromonads in waters during summer, although no single RAPD or ERIC-PCR pattern was found among both clinical and environmental samples. RAPD and ERIC-PCR proved to be effective for the epidemiological study of A. hydrophila strains.

Taxonomy of Pseudomonas strains isolated from tomato pith necrosis: emended description of Pseudomonas corrugata and proposal of three unnamed fluorescent Pseudomonas genomospecies

Thirty-three fluorescent Pseudomonas strains isolated from tomato pith necrosis (FPTPN strains) and 89 Pseudomonas corrugata strains were studied by numerical taxonomy. In the dendrogram of distances, the P. corrugata strains constituted a single phenon (phenon 1), whereas 17 of the 33 FPTPN strains clustered in a separate phenon (phenon 2). The other 16 FPTPN strains were included in phena consisting of well-characterized fluorescent Pseudomonas species or were isolated phenotypes. Phena 1 and 2 were distinguished by fluorescence on King B medium, accumulation of poly-beta-hydroxybutyrate, production of levan, and assimilation of sorbitol. DNA-DNA hybridization showed that P. corrugata is a true genomic species (66 to 100% DNA relatedness) and that the FPTPN strains of phenon 2 were divided into three genomic groups. Genomic groups 1 and 2 were not distinct from each other phenotypically, and genomic group 3 could be distinguished from genomic groups 1 and 2 only on the basis of assimilation of citraconate and laevulinate. Genomic groups 1 and 2 are related to P. corrugata (40 to 55% DNA relatedness), whereas genomic group 3 is less closely related to P. corrugata (20 to 23% DNA relatedness). The lipopolysaccharide patterns on electrophoresis gels and fatty acid profiles of strains belonging to genomic group 1 through 3 are different from each other and from the lipopolysaccharide patterns and fatty acid profiles of P. corrugata. However, cross-reactions were observed between P. corrugata and the FPTPN strain genomic groups, indicating that there are common epitopes of the lipopolysaccharides. The three FPTPN strain genomic groups were not named as species but were designated Pseudomonas genomospecies FP1, FP2, and FP3.

A nosocomial outbreak due to Enterobacter cloacae strains with the E. hormaechei genotype in patients treated with fluoroquinolones

During a 7-month period, we isolated 21 highly fluoroquinolone-resistant Enterobacter cloaecae strains in units from two hospitals in Marseille, France. Random amplification of polymorphic DNA showed clonal identity between isolates which, furthermore, presented the Enterobacter hormaechei genotype on DNA-DNA hybridization. The emergence of this clone was observed only in patients treated with fluoroquinolones.

Stenotrophomonas africana sp. nov., an opportunistic human pathogen in Africa

A gram-negative bacterium was isolated from a cerebrospinal fluid sample from an HIV-seropositive Rwandan refugee with primary meningoencephalitis. This Marseille-Goma sample B isolate, strain MGBT (T = type strain), was found to exhibit evolutionary homology with Stenotrophomonas maltophilia, as determined by a 16S rRNA gene sequence analysis, and this finding was reflected by similar phenotypic traits. MGBT could, however, be distinguished from the S. maltophilia type strain by using a number of biochemical and physiological tests, and a genotypic analysis of the two strains in which DNA homology was used revealed only 35% homology between them. Furthermore, the antibiotic susceptibility of MGBT was restricted to netilmicin, ciprofloxacin, trimethoprim-sulfamethoxazole, and colimycin. On the basis of these results we propose that MGBT is a representative of a new species in the genus Stenotrophomonas, Stenotrophomonas africana.

Epidemiological investigation of Pseudomonas aeruginosa nosocomial bacteraemia isolates by PCR-based DNA fingerprinting analysis

Between July 1994 and March 1995, 64 isolates of Pseudomonas aeruginosa were implicated in bacteraemia in 25 cancer patients in five wards of two hospitals. These, together with 24 environmental isolates and one isolate from a bacteraemia in a non-cancer patient were examined by three PCR-based DNA fingerprinting methods: random amplified polymorphic DNA (RAPD), enterobacterial-repetitive intergenic consensus (ERIC)-PCR, and 16S-23S spacer region-based RAPD. These methods were reproducible, discriminatory and showed close agreement; all indicated that 47 isolates that had caused bacteraemia in 19 cancer patients were indistinguishable. Seventeen other isolates that had caused bacteraemia in 10 cancer patients were discriminated into eight further groups, and the 24 environmental and non-cancer patient isolates into further distinct groups. No environmental source of the epidemic strain was found, but it was suspected that the outbreak was related to infusion implants.

A blind study of the polymerase chain reaction for the detection of Mycobacterium tuberculosis DNA. Azay Mycobacteria Study Group

SETTING

Nine French laboratories routinely involved in mycobacterial work.

OBJECTIVE

To assess the detection of Mycobacterium tuberculosis in experimental samples by polymerase chain reaction (PCR) using the insertion sequence IS6110 as a target for deoxyribonucleic acid (DNA) amplification.

DESIGN

Nine laboratories participated in a blind study of the detection of M. tuberculosis by PCR in 20 coded samples containing either a definite number of M. tuberculosis complex (positive samples) or environmental mycobacteria (four samples) or no mycobacteria (five samples).

RESULTS

Five laboratories reported false-positive PCR results, with an average rate of 7%. All laboratories except one reported positive PCR results for samples containing 10(5) cfu/ml or more. M. tuberculosis DNA was detected in two thirds of samples containing 10(4) and 10(3) cfu/ml, and in one third of the samples containing 10(2) cfu/ml.

CONCLUSION

The results of the study suggest that PCR using IS6110 as a target for DNA amplication is neither very sensitive nor really specific for the detection of M. tuberculosis.

Serratia marcescens nosocomial outbreak due to contamination of hexetidine solution

During a 10-week period, 16 patients in a neurosurgery intensive care unit were involved in an outbreak of Serratia marcescens. The epidemic strain was found in several flasks of 1:4 diluted hexetidine solution, an antiseptic used for patient mouth washing. Testing of the bactericidal activity of the diluted antiseptic revealed that all the epidemic strains were able to grow in the diluted antiseptic solution. Strains isolated from clinical samples and from the antiseptic solution were compared by random amplification of polymorphic DNA. Epidemiologic typing data implicated the diluted antiseptic solution as the single source of this S. marcescens outbreak.

Investigation of outbreaks of Enterobacter aerogenes colonisation and infection in intensive care units by random amplification of polymorphic DNA

During a 4-month period, 41 isolates of Enterobactor aerogenes were cultured from different specimens from a 14-bed intensive care unit (ICU1). These were obtained from 12 patients out of a total of 187 patients admitted to the ICU. Sixteen E. aerogenes isolates were cultured from another ICU (ICU2) 6 months later. Six non-outbreaks associated strains were included as controls and all the isolates were compared by random amplification of polymorphic DNA (RAPD), with three different 10-mer oligonucleotide primers. RAPD fingerprinting with primer AP12h was as discriminatory as the combined results from all three primers and defined 22 different patterns for the 41 isolates from the ICU1. In nine instances, isolates with indistinguishable RAPD patterns were detected in two-to-five patients over a 3-15-day period, suggesting patient-to-patient transmission. During their stay in ICU1, patients harboured one-to-12 distinguishable isolates. Isolates from ICU2 were indistinguishable by RAPD analysis with the three different primers. These findings suggest that the cluster of colonisations and infections in ICU1 was a 'false outbreak', consisting of successive patient-to-patient transmission of different E. aerogenes strains. In contrast, the outbreak on ICU2 probably involved the extensive spread of a single strain.

Use of random amplified polymorphic DNA for epidemiological typing of Stenotrophomonas maltophilia

We used the technique of random amplification of polymorphic DNA (RAPD) to type 130 isolates of Stenotrophomonas (Xanthomonas) maltophilia, using four arbitrary short primers. Of the 130 isolates, 51 were from the hospital environment, 48 from clinical specimens and 31 were geographically diverse environmental isolates. DNA amplification with the four sets of primers generated 112 RAPD patterns that differed by two or more bands in one of the four primers. Sixteen pairs of isolates were of the same RAPD pattern and some of these pairs represented clinical strains obtained from patients hospitalized at the same time in the same ward. In three patients, two to three strains of S. maltophilia which gave different RAPD fingerprints were isolated on the same day from different specimens. RAPD fingerprinting demonstrated great genomic diversity within the species S. maltophilia and provided an effective method for the study of the epidemiology of both clinical and environmental strains.

Bronchoscopic or blind sampling techniques for the diagnosis of ventilator-associated pneumonia

The purpose of this prospective postmortem study was to assess the diagnostic accuracy of bronchoscopic techniques (bronchoalveolar lavage [BAL] and protected specimen brush [PSB]) and nonbronchoscopic techniques (blind bronchial sampling [BBS] and mini-BAL) in the diagnosis of ventilator-associated pneumonia (VAP). The results of each technique were compared with histology and culture of lung tissue specimens obtained by surgical pneumonectomies in 38 patients who died after at least 72 h of mechanical ventilation. Histology was positive for VAP in 18 patients and negative in 20 patients. There were 12 definite VAP (positive histology and positive lung cultures) and 6 histologic VAP (positive histology and negative cultures). Clinical pulmonary infection score (CPIS) at a threshold of 6 achieved a sensitivity of 72% and a specificity of 85%. When the CPIS was combined with the logarithmic concentration of the predominant microorganism obtained from the BBS sample culture, specificity was increased to 95%, for a threshold of 10. Using 10(3) cfu/ml as the threshold of positivity for cultures obtained with PSB and mini-BAL samples and 10(4) cfu/ml for cultures obtained with BBS and BAL, the respective sensitivities of these techniques for definite VAP were 42, 67, 83, and 58%. The sensitivity of BBS was significantly higher than that of PSB (p < 0.05). The area under the receiver operator characteristic curve was significantly greater for BBS than PSB (p < 0.05). Given that it is more sensitive and noninvasive, BBS is preferable to PSB for the diagnosis of VAP.

Variations in DNA concentrations significantly affect the reproducibility of RAPD fingerprint patterns

The influence of the DNA concentration was tested using two different primers and nine DNA samples. Major modifications in the DNA banding pattern were apparent between successive dilutions. Such differences could be explained by concomitant changes in three different molecular conditions: the presence of perfect priming sites, the amplification of rare sites and the existence of mismatch annealing events. At low DNA concentrations (less than 1 pg/microliter), molecular events occurred at random and had a direct consequence on the reproducibility of RAPD profiles. At the appropriate DNA concentration (between 100 ng/microliters and 10 pg/microliters), reproducibility was adequate at a given concentration, but RAPD profiles differed from one dilution to another. These observations demonstrate the usefulness of the bis-benzimide method for quantification of DNA extracts.

Demonstration of Mycobacterium kansasii species heterogeneity by the amplification of the 16S-23S spacer region

Amplification of the region separating the genes coding for the two rRNA species 16S and 23S was performed with 56 strains of several mycobacterial species, including 21 clinical isolates of Mycobacterium kansasii and the M. kansasii type strain ATCC 12478. On the basis of PCR product profiles, the previously suggested heterogeneity of M. kansasii species was confirmed. Three subgroups were identified; members of the first subgroup showed the same PCR profile as the reference strain. Different profiles were obtained for the two other subgroups. Amplification of the 16S-23S spacer is rapid and simple and, consequently, may be a helpful tool for identification and characterisation of M. kansasii isolates in epidemiological analysis.

Identification and strain differentiation of Mycobacterium species on the basis of DNA 16S-23S spacer region polymorphism

Amplification of the region separating the genes coding for the two rRNA species 16S and 23S was performed to identify 56 mycobacterial strains, belonging to eleven species: Mycobacterium tuberculosis, M. avium, M. kansasii, M. gordonae, M. abscessus, M. fortuitum, M. xenopi, M. bovis, M. bovis/BCG, M. africanum and M. intracellulare. Reproducible amplification patterns were obtained with most species with the exception of M. kansasii which showed heterogeneity, confirming the existence of a genetically distinct subspecies within this species. In addition, we used the amplified products as target DNA for restriction endonuclease digestion and RAPD (randomly amplified polymorphic DNA) analysis to compare strains of M. abscessus, M. tuberculosis and M. avium. The discriminatory power of these two typing methods was higher than when whole genomic DNA is used as target. Our results demonstrate that the two-step approach to identification and typing on the basis of the hypervariability of 16S-23S spacer region is reliable, rapid and simple, and consequently could be an epidemiological tool in clinical laboratories.

Efficient discrimination of Mycobacterium tuberculosis strains by 16S-23S spacer region-based random amplified polymorphic DNA analysis

Amplification of the region separating the genes coding for 16S and 23S rRNA was performed with 15 Mycobacterium tuberculosis isolates and the type strain, ATCC 27294. Reproducible amplification patterns were obtained. PCR products were then used as target DNA for random amplified polymorphic DNA (RAPD) analysis. The discriminatory power was higher than when whole genomic DNA was used as a RAPD template. 16S-23S spacer region-based RAPD analysis was a simple and efficient method of differentiation. Consequently, it may be a useful tool for epidemiologic studies of tuberculosis.

[Evaluation of the extra- and intracellular activity of clarithromycin against Mycobacterium chelonae]

The in vitro activity of clarithromycin alone and in combination with amikacin, ethambutol and rifabutin was tested against twelve strains of M. chelonae abscessus and eight strains of M. chelonae chelonae isolated from patients. Extracellular activity of clarithromycin was assessed by determining MICs using the 1 p. cent proportion method in Middlebrook 7H11 agar media compared to the radiometric methodology in 7H12 broth at two pHs 6.8 and 7.4. The MICs obtained at pH 7.4 were 2 to 4 more dilutions lower than those obtained at pH 6.8. By both methods, clarithromycin appeared more active against isolates of M. chelonae chelonae than against isolates of M. chelonae abscessus. Clarithromycin- amikacin combination demonstrated the most important additive effect. The use of three drugs in association resulted in syngergistic effect. Studies of intracellular bacteria showed that the most effective bactericidal combination was clarithromycin amikacin and ethambutol together.

In-vitro evaluation of clarithromycin, temafloxacin, and ethambutol in combination against Mycobacterium avium complex

The in-vitro activity of clarithromycin, temafloxacin, and ethambutol were assessed by MIC, FIC and intra-macrophage killing determinations alone and in various combinations against ten pigmented and ten non-pigmented strains of Mycobacterium avium complex bacteria. Alone, either clarithromycin or temafloxacin were found to be active against M. avium, but the best results were obtained from combinations of drugs. Clarithromycin and temafloxacin together were found to have an additive effect against two of ten pigmented variants and one of ten non-pigmented variants. Clarithromycin and ethambutol demonstrated a synergistic effect against two pigmented and one non-pigmented strain, and an additive effect against five and three pigmented and non-pigmented strains, respectively. For temafloxacin and ethambutol, additive effects were observed in four and two pigmented and non-pigmented strains, respectively. In cultures of macrophages both clarithromycin and temafloxacin alone reduced the numbers of bacteria growing intracellularly after six days, but the most effective bactericidal combination was clarithromycin, temafloxacin, and ethambutol together.

Pseudomonas aeruginosa and cystic fibrosis: intrastrain variability in relation to intensity of immune response and clinical outcome

Over periods exceeding two years, 63 Pseudomonas aeruginosa strains isolated from three children with cystic fibrosis were characterized using a 154 character auxanogram. Numerical analysis was carried out to establish intrastrain variability in relation to intensity of immune response and clinical outcome. For two patients, strains segregated in two distinct phenons. For the last patient, strains did not cluster. The degree of intrastrain variability during the infection was correlated with an increasing number of precipitins and with an unfavorable clinical outcome. This would suggest that strains which have a singular potential for antigenic variability are more likely to promote a host-bacteria conflict.

A rapid DNA extraction method from culture and clinical samples. Suitable for the detection of human cytomegalovirus by the polymerase chain reaction

We propose an one-step DNA extraction method suitable for the polymerase chain reaction. This procedure utilizes Chelex 100, a chelating in exchange resin. This technique was compared with a traditional technique (proteinase K lysis, phenol-chloroform extraction and ethanol precipitation) for isolation of human cytomegalovirus DNA from clinical samples. The procedure using Chelex 100 appeared to be a simple and fast extraction method for human cytomegalovirus DNA.

Fatal pneumonia due to Serratia proteamaculans subsp. quinovora

Serratia proteamaculans subsp. quinovora was isolated from several samples (blood cultures, tracheal aspirates, pleural effusion) from a patient with pneumonia. This is the first clinical isolate and the first documented human infection caused by this organism.

Detection and identification of Mycobacterium tuberculosis, M. bovis/BCG, and M. avium by two-step polymerase chain reaction. Comparison with ELISA using A60 antigen

We propose a rapid two-step PCR to amplify a 767-bp sequence present in the gene coding for the 65-kD antigen of mycobacteria. The high G+C content (80%) permitted annealing to occur at 70 degrees C, enhancing the specificity. The amplified fragment contains a restriction site for differentiation between M. tuberculosis, M. bovis/BCG, and M. avium. Complete diagnosis can be achieved in less than four hours without labelled probe or nucleic acid transfer.

A one-step microbial DNA extraction method using "Chelex 100" suitable for gene amplification

"Chelex 100" chelating resin has been previously proposed for the rapid extraction of human DNA for polymerase chain reaction. Protocols are given for the rapid extraction of bacterial and viral DNA from cultures or clinical samples. The DNA samples obtained were suitable for use in polymerase chain reaction.

Serological response of tuberculosis patients to antigen 60 of BCG

Two ELISA tests (IgG and IgM) for the serodiagnosis of tuberculosis, both based on antigen 60 (A60) of M. bovis BCG, were applied to 1,644 controls and patients to analyse the immune response in different forms of this infectious disease. Out of 200 healthy individuals, 148 being tuberculin--positive BCG-vaccinated adults, only 10 contacts--nurses of the pneumology department and laboratory technicians of the mycobacterial laboratory--were found positive for anti-A60 IgG. One quarter of hospitalized patients affected by non-tuberculous pneumopathies (194 in total) were found weakly positive for anti-A60 IgG. We suppose that these positive cases have suffered from inapperant infections and are in a "persistent state". Out of 344 cases of primary pulmonary tuberculosis, 88% were positive for anti-A60 IgG and 75% for the corresponding IgM. Among 97 cases of primary extra-pulmonary tuberculosis, 94% were found IgG positive and 33% IgM positive. The difference between active and inactive post-primary (chronic) tuberculosis was striking: about 100% of both pulmonary and extra-pulmonary cases (367 altogether) had high titers of anti-A60 IgG but IgM positivity was observed in only 15% of the cases, whereas in inactive and quiescent noncavitary tuberculosis (442 cases), 57% of the patients were weakly positive for anti-A60 IgG and none were positive for IgM. Kinetics of synthesis of anti-A60 IgG and IgM were analysed in primary and post-primary (chronic) active tuberculosis. The IgM tracing immune response to A60 was shorter and lower during primary tuberculosis as compared to post-primary tuberculosis. Our findings point to the high prognostic value of the A60- ELISA test for tuberculosis. Anti-A60 IgM mark initial stages of the disease or reactivation processes whereas anti-A60 IgG last longer than IgM and provide an evaluation of the intensity of the infectious process. Repeated serological tests allow monitoring of the course of the infection and the efficacy of therapy. The test is negative in healthy BCG-vaccinated persons (tuberculin-positive) and healed tuberculous infection cases. The combined use of both IgG and IgM tests helps in the correct diagnosis of "false positive" cases.