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Mario Vaneechoutte - One of the best experts on this subject based on the ideXlab platform.
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evaluation of amplified ribosomal DNA Restriction analysis for identification of acinetobacter genomic species
Systematic and Applied Microbiology, 1998Co-Authors: Lenie Dijkshoorn, Barbara Van Harsselaar, Ingela Tjernberg, Philippe Bouvet, Mario VaneechoutteAbstract:Summary Further to a previous study, the usefulness of amplified ribosomal DNA Restriction analysis (ARDRA) for identification of Acinetobacter genomic species (DNA groups) was tested. A set of 202 Acinetobacter strains of 18 described genomic species and 17 unclassified strains were used. Restriction patterns obtained with a standard panel of Restriction enzymes CfoI, AluI, MboI, RsaI and MspI allowed for separation of 11 DNA groups. With the additional use of Restriction enzymes BfaI and BsmAI, five other (genomic) species could be differentiated, leaving only A. haemolyticus and DNA group 13BJ/14TU unseparated. With the standard panel of enzymes, ten new ARDRA profiles were noted in 14 unclassified strains. Two other unclassified strains had a profile in common with DNA group 15BJ, but were differentiated from this DNA group by Restriction with BfaI. One remaining unclassified strain could not be differentiated from DNA group 17 by the standard panel of enzymes or by the enzymes BfaI and BsmAI. Results demonstrate the utility of ARDRA for identification of most genomic species of Acinetobacter. Furthermore, new ARDRA profiles that were shared by several unclassified strains may indicate so far undescribed genomic species in the genus.
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identification of acinetobacter genomic species by amplified ribosomal DNA Restriction analysis
Journal of Clinical Microbiology, 1995Co-Authors: Mario Vaneechoutte, Lenie Dijkshoorn, Ingela Tjernberg, A Elaichouni, P De Vos, G Claeys, Gerda VerschraegenAbstract:A total of 53 field and reference strains, including the type strains of the seven named species (nomenspecies) and belonging to the 18 described genomic species (DNA groups) of the genus Acinetobacter, were studied by amplified ribosomal DNA Restriction analysis (ARDRA). Restriction analysis with the enzymes AluI, CfoI, MboI, RsaI, and MspI of the enzymatically amplified 16S rRNA genes allowed us to identify all species except the genomic species 4 (Acinetobacter haemolyticus) and 7 (A. johnsonii), 5 (A. junii) and 17, and 10 and 11, which clustered pairwise in three respective groups. Further analysis with the enzyme HaeIII, HinfI, NciI, ScrFI, or TaqI did not allow us to differentiate the species within these three clusters. However, use of a few additional simple phenotypic tests (hemolysis, growth at 37 degrees C, production of acid from glucose, and gelatin hydrolysis) can be used to differentiate between the species within these clusters. ARDRA proved to be a rapid and reliable method for the identification of most of the Acinetobacter genomic species, including the closely related DNA groups 1 (A. calcoaceticus), 2 (A. baumannii), 3, and 13. The results of this study suggest that ARDRA can be used for the identification of Acinetobacter species and as such may help to elucidate the ecology and clinical significance of the different species of this genus. Since ARDRA uses universal 16S rRNA gene primers, it is expected to be applicable to the identification of most bacterial species. Furthermore, ARDRA is less prone to contamination problems than PCR for detection, since the use of cultured organisms results in a large initial quantity of target DNA.
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rapid identification of bacteria of the comamonadaceae with amplified ribosomal DNA Restriction analysis ardra
Fems Microbiology Letters, 1992Co-Authors: Mario Vaneechoutte, Monique Gillis, P De Vos, G Claeys, Rudi Rossau, Danielle Janssens, Noella Paepe, Ann De Rouck, Tom Fiers, Karel KerstersAbstract:Ribosomal rRNA gene fragments (rDNA) encompassing the 16S rDNA, the 16S–23S rDNA spacer region and part of the 23S rDNA of 95 strains belonging to 13 well-described taxa of the eubacterial family comamonadaceae (β subclass of the Proteobacteria or rRNA superfamily III) were enzymatically amplified using conserved primers. The fragments of approximately 2400 base pairs were subjected to Restriction analysis. Restriction fragment length patterns obtained with Hin fI enabled us to distinguish 9 of the 13 taxa studied. Restriction with Cfo I was necessary to differentiate Acidovorax delafieldii from A. temperans and Hydrogenophaga flava from H. pseudoflava . The results indicate that amplified rDNA Restriction analysis is a simple and reliable tool for the identification of bacterial species.
Brian I Duerden - One of the best experts on this subject based on the ideXlab platform.
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identification of clinical isolates of actinomyces species by amplified 16s ribosomal DNA Restriction analysis
Journal of Clinical Microbiology, 2001Co-Authors: Val Hall, Paul R Talbot, Simon L J Stubbs, Brian I DuerdenAbstract:Amplified 16S ribosomal DNA (rDNA) Restriction analysis (ARDRA), using enzymes HaeIII and HpaII, was applied to 176 fresh and 299 stored clinical isolates of putative Actinomyces spp. referred to the Anaerobe Reference Unit of the Public Health Laboratory Service for confirmation of identity. Results were compared with ARDRA results obtained previously for reference strains and with conventional phenotypic reactions. Identities of some strains were confirmed by analysis of partial 16S rDNA sequences. Of the 475 isolates, 331 (70%) were clearly assigned to recognized Actinomyces species, including 94 isolates assigned to six recently described species. A further 52 isolates in 12 ARDRA profiles were designated as apparently resembling recognized species, and 44 isolates, in 18 novel profiles, were confirmed as members of genera other than Actinomyces. The identities of 48 isolates in nine profiles remain uncertain, and they may represent novel species of Actinomyces. For the majority of species, phenotypic results, published reactions for the species, and ARDRA profiles concurred. However, of 113 stored isolates originally identified as A. meyeri or resembling A. meyeri by phenotypic tests, only 21 were confirmed as A. meyeri by ARDRA; 63 were reassigned as A. turicensis, 7 as other recognized species, and 22 as unidentified actinomycetes. Analyses of incidence and clinical associations of Actinomyces spp. add to the currently sparse knowledge of some recently described species.
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development of amplified 16s ribosomal DNA Restriction analysis for identification of actinomyces species and comparison with pyrolysis mass spectrometry and conventional biochemical tests
Journal of Clinical Microbiology, 1999Co-Authors: Val Hall, G L Oneill, J T Magee, Brian I DuerdenAbstract:Identification of Actinomyces spp. by conventional phenotypic methods is notoriously difficult and unreliable. Recently, the application of chemotaxonomic and molecular methods has clarified the taxonomy of the group and has led to the recognition of several new species. A practical and discriminatory identification method is now needed for routine identification of clinical isolates. Amplified 16S ribosomal DNA Restriction analysis (ARDRA) was applied to reference strains (n = 27) and clinical isolates (n = 36) of Actinomyces spp. and other gram-positive rods. Clinical strains were identified initially to the species level by conventional biochemical tests. However, given the low degree of confidence in conventional methods, the findings obtained by ARDRA were also compared with those obtained by pyrolysis-mass spectrometry. The ARDRA profiles generated by the combination of HaeIII and HpaII endonuclease digestion differentiated all reference strains to the species or subspecies level. The profiles correlated well with the findings obtained by pyrolysis-mass spectrometry and by conventional tests and enabled the identification of 31 of 36 clinical isolates to the species level. ARDRA was shown to be a simple, rapid, cost-effective, and highly discriminatory method for routine identification of Actinomyces spp. of clinical origin.
Karel Kersters - One of the best experts on this subject based on the ideXlab platform.
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applicability of combined amplified ribosomal DNA Restriction analysis ardra patterns in bacterial phylogeny and taxonomy
Journal of Microbiological Methods, 1996Co-Authors: Marc Heyndrickx, Luc Vauterin, Peter Vandamme, Karel KerstersAbstract:Abstract A standardized method for amplified ribosomal DNA Restriction analysis (ARDRA) is described. The first step involves selection of five tetracutter Restriction enzymes on the basis of theoretical digestions of known 16S rDNA (rRNA) sequences. In the second step, the experimentally obtained Restriction patterns are normalized and combined by means of the pattern recognition and analysis software GelCompar. Finally, numerical analysis allows the strains to be grouped according to the similarities in their combined ARDRA patterns. Results obtained with representatives of two phylogenetic lineages, the genera Alcaligenes and Bordetella and the genera Bacillus and Paenibacillus , are presented. In general, the clustering of the strains corresponded well with known species delineations and topology of phylogenetic groupings except for the discrepant position of the Bacillus lautus type strain, which can probably be explained by non-authenticity of this strain in one of the analyses. The effect of using less than five Restriction enzymes on the clustering was evaluated. The frequent occurrence of interoperon variability of the 16S rRNA gene in Bacillus and Paenibacillus was also demonstrated. Because ARDRA detects interspecies and interstrain as well as interoperon variability and enables a relatively fast multiple strain analysis per taxon, this technique is appropriate to obtain indicative phylogenetic and taxonomic information. This information can be used to select strains for further detailed taxonomic studies. ARDRA fingerprinting also allows the construction of a database for indentification purposes.
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rapid identification of bacteria of the comamonadaceae with amplified ribosomal DNA Restriction analysis ardra
Fems Microbiology Letters, 1992Co-Authors: Mario Vaneechoutte, Monique Gillis, P De Vos, G Claeys, Rudi Rossau, Danielle Janssens, Noella Paepe, Ann De Rouck, Tom Fiers, Karel KerstersAbstract:Ribosomal rRNA gene fragments (rDNA) encompassing the 16S rDNA, the 16S–23S rDNA spacer region and part of the 23S rDNA of 95 strains belonging to 13 well-described taxa of the eubacterial family comamonadaceae (β subclass of the Proteobacteria or rRNA superfamily III) were enzymatically amplified using conserved primers. The fragments of approximately 2400 base pairs were subjected to Restriction analysis. Restriction fragment length patterns obtained with Hin fI enabled us to distinguish 9 of the 13 taxa studied. Restriction with Cfo I was necessary to differentiate Acidovorax delafieldii from A. temperans and Hydrogenophaga flava from H. pseudoflava . The results indicate that amplified rDNA Restriction analysis is a simple and reliable tool for the identification of bacterial species.
Val Hall - One of the best experts on this subject based on the ideXlab platform.
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identification of clinical isolates of actinomyces species by amplified 16s ribosomal DNA Restriction analysis
Journal of Clinical Microbiology, 2001Co-Authors: Val Hall, Paul R Talbot, Simon L J Stubbs, Brian I DuerdenAbstract:Amplified 16S ribosomal DNA (rDNA) Restriction analysis (ARDRA), using enzymes HaeIII and HpaII, was applied to 176 fresh and 299 stored clinical isolates of putative Actinomyces spp. referred to the Anaerobe Reference Unit of the Public Health Laboratory Service for confirmation of identity. Results were compared with ARDRA results obtained previously for reference strains and with conventional phenotypic reactions. Identities of some strains were confirmed by analysis of partial 16S rDNA sequences. Of the 475 isolates, 331 (70%) were clearly assigned to recognized Actinomyces species, including 94 isolates assigned to six recently described species. A further 52 isolates in 12 ARDRA profiles were designated as apparently resembling recognized species, and 44 isolates, in 18 novel profiles, were confirmed as members of genera other than Actinomyces. The identities of 48 isolates in nine profiles remain uncertain, and they may represent novel species of Actinomyces. For the majority of species, phenotypic results, published reactions for the species, and ARDRA profiles concurred. However, of 113 stored isolates originally identified as A. meyeri or resembling A. meyeri by phenotypic tests, only 21 were confirmed as A. meyeri by ARDRA; 63 were reassigned as A. turicensis, 7 as other recognized species, and 22 as unidentified actinomycetes. Analyses of incidence and clinical associations of Actinomyces spp. add to the currently sparse knowledge of some recently described species.
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development of amplified 16s ribosomal DNA Restriction analysis for identification of actinomyces species and comparison with pyrolysis mass spectrometry and conventional biochemical tests
Journal of Clinical Microbiology, 1999Co-Authors: Val Hall, G L Oneill, J T Magee, Brian I DuerdenAbstract:Identification of Actinomyces spp. by conventional phenotypic methods is notoriously difficult and unreliable. Recently, the application of chemotaxonomic and molecular methods has clarified the taxonomy of the group and has led to the recognition of several new species. A practical and discriminatory identification method is now needed for routine identification of clinical isolates. Amplified 16S ribosomal DNA Restriction analysis (ARDRA) was applied to reference strains (n = 27) and clinical isolates (n = 36) of Actinomyces spp. and other gram-positive rods. Clinical strains were identified initially to the species level by conventional biochemical tests. However, given the low degree of confidence in conventional methods, the findings obtained by ARDRA were also compared with those obtained by pyrolysis-mass spectrometry. The ARDRA profiles generated by the combination of HaeIII and HpaII endonuclease digestion differentiated all reference strains to the species or subspecies level. The profiles correlated well with the findings obtained by pyrolysis-mass spectrometry and by conventional tests and enabled the identification of 31 of 36 clinical isolates to the species level. ARDRA was shown to be a simple, rapid, cost-effective, and highly discriminatory method for routine identification of Actinomyces spp. of clinical origin.
Lenie Dijkshoorn - One of the best experts on this subject based on the ideXlab platform.
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evaluation of amplified ribosomal DNA Restriction analysis for identification of acinetobacter genomic species
Systematic and Applied Microbiology, 1998Co-Authors: Lenie Dijkshoorn, Barbara Van Harsselaar, Ingela Tjernberg, Philippe Bouvet, Mario VaneechoutteAbstract:Summary Further to a previous study, the usefulness of amplified ribosomal DNA Restriction analysis (ARDRA) for identification of Acinetobacter genomic species (DNA groups) was tested. A set of 202 Acinetobacter strains of 18 described genomic species and 17 unclassified strains were used. Restriction patterns obtained with a standard panel of Restriction enzymes CfoI, AluI, MboI, RsaI and MspI allowed for separation of 11 DNA groups. With the additional use of Restriction enzymes BfaI and BsmAI, five other (genomic) species could be differentiated, leaving only A. haemolyticus and DNA group 13BJ/14TU unseparated. With the standard panel of enzymes, ten new ARDRA profiles were noted in 14 unclassified strains. Two other unclassified strains had a profile in common with DNA group 15BJ, but were differentiated from this DNA group by Restriction with BfaI. One remaining unclassified strain could not be differentiated from DNA group 17 by the standard panel of enzymes or by the enzymes BfaI and BsmAI. Results demonstrate the utility of ARDRA for identification of most genomic species of Acinetobacter. Furthermore, new ARDRA profiles that were shared by several unclassified strains may indicate so far undescribed genomic species in the genus.
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identification of acinetobacter genomic species by amplified ribosomal DNA Restriction analysis
Journal of Clinical Microbiology, 1995Co-Authors: Mario Vaneechoutte, Lenie Dijkshoorn, Ingela Tjernberg, A Elaichouni, P De Vos, G Claeys, Gerda VerschraegenAbstract:A total of 53 field and reference strains, including the type strains of the seven named species (nomenspecies) and belonging to the 18 described genomic species (DNA groups) of the genus Acinetobacter, were studied by amplified ribosomal DNA Restriction analysis (ARDRA). Restriction analysis with the enzymes AluI, CfoI, MboI, RsaI, and MspI of the enzymatically amplified 16S rRNA genes allowed us to identify all species except the genomic species 4 (Acinetobacter haemolyticus) and 7 (A. johnsonii), 5 (A. junii) and 17, and 10 and 11, which clustered pairwise in three respective groups. Further analysis with the enzyme HaeIII, HinfI, NciI, ScrFI, or TaqI did not allow us to differentiate the species within these three clusters. However, use of a few additional simple phenotypic tests (hemolysis, growth at 37 degrees C, production of acid from glucose, and gelatin hydrolysis) can be used to differentiate between the species within these clusters. ARDRA proved to be a rapid and reliable method for the identification of most of the Acinetobacter genomic species, including the closely related DNA groups 1 (A. calcoaceticus), 2 (A. baumannii), 3, and 13. The results of this study suggest that ARDRA can be used for the identification of Acinetobacter species and as such may help to elucidate the ecology and clinical significance of the different species of this genus. Since ARDRA uses universal 16S rRNA gene primers, it is expected to be applicable to the identification of most bacterial species. Furthermore, ARDRA is less prone to contamination problems than PCR for detection, since the use of cultured organisms results in a large initial quantity of target DNA.
