scholarly journals Development of Amplified 16S Ribosomal DNA Restriction Analysis for Identification of Actinomyces Species and Comparison with Pyrolysis-Mass Spectrometry and Conventional Biochemical Tests

1999 ◽  
Vol 37 (7) ◽  
pp. 2255-2261 ◽  
Author(s):  
Val Hall ◽  
G. L. O’Neill ◽  
J. T. Magee ◽  
B. I. Duerden
Keyword(s):  
Mass Spectrometry ◽  
Restriction Analysis ◽  
Species Level ◽  
Clinical Isolates ◽  
Pyrolysis Mass Spectrometry ◽  
Biochemical Tests ◽  
16S Ribosomal Dna ◽  
Routine Identification ◽  
Dna Restriction ◽  
Reference Strains

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 ofHaeIII 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 ofActinomyces spp. of clinical origin.

Photosynthetic Bradyrhizobia from Aeschynomene spp. Are Specific to Stem-Nodulated Species and Form a Separate 16S Ribosomal DNA Restriction Fragment Length Polymorphism Group

1999 ◽  
Vol 65 (7) ◽  
pp. 3084-3094 ◽  
Author(s):  
Flore Molouba ◽  
Jean Lorquin ◽  
Anne Willems ◽  
Bart Hoste ◽  
Eric Giraud ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Rhodobacter Capsulatus ◽  
Restriction Analysis ◽  
Dna Amplification ◽  
Rrna Gene ◽  
Gene Probe ◽  
16S Ribosomal Dna ◽  
Photosynthetic Genes ◽  
Dna Restriction ◽  
Layer Chromatography

ABSTRACT We obtained nine bacterial isolates from root or collar nodules of the non-stem-nodulated Aeschynomene species A. elaphroxylon, A. uniflora, or A. schimperi and 69 root or stem nodule isolates from the stem-nodulated Aeschynomene species A. afraspera, A. ciliata, A. indica,A. nilotica, A. sensitiva, and A. tambacoundensis from various places in Senegal. These isolates, together with 45 previous isolates from variousAeschynomene species, were studied for host-specific nodulation within the genus Aeschynomene, also revisiting cross-inoculation groups described previously by D. Alazard (Appl. Environ. Microbiol. 50:732–734, 1985). The whole collection ofAeschynomene nodule isolates was screened for synthesis of photosynthetic pigments by spectrometry, high-pressure liquid chromatography, and thin-layer chromatography analyses. The presence ofpuf genes in photosyntheticAeschynomene isolates was evidenced both by Southern hybridization with a Rhodobacter capsulatus photosynthetic gene probe and by DNA amplification with primers defined from photosynthetic genes. In addition, amplified 16S ribosomal DNA restriction analysis was performed on 45 Aeschynomeneisolates, including strain BTAi1, and 19 reference strains fromBradyrhizobium japonicum, Bradyrhizobium elkanii, and other Bradyrhizobium sp. strains of uncertain taxonomic positions. The 16S rRNA gene sequence of the photosynthetic strain ORS278 (LMG 12187) was determined and compared to sequences from databases. Our main conclusion is that photosynthetic Aeschynomene nodule isolates share the ability to nodulate particular stem-nodulated species and form a separate subbranch on the Bradyrhizobium rRNA lineage, distinct from B. japonicum and B. elkanii.

scholarly journals Identification of NDM-1 in a Putatively Novel Acinetobacter Species (“NB14”) Closely Related to Acinetobacter pittii

2015 ◽  
Vol 59 (10) ◽  
pp. 6657-6660 ◽  
Author(s):  
Paula Espinal ◽  
Noraida Mosqueda ◽  
Murat Telli ◽  
Tanny van der Reijden ◽  
Dora Rolo ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Restriction Analysis ◽  
Conjugative Plasmid ◽  
Acinetobacter Species ◽  
Content Type ◽  
16S Ribosomal Dna ◽  
Acinetobacter Pittii ◽  
Dna Restriction ◽  
Molecular Sequencing

ABSTRACTIn this study, we describe the molecular characterization of a plasmid-locatedblaNDM-1harbored by anAcinetobacterclinical isolate recovered from a patient in Turkey that putatively constitutes a novelAcinetobacterspecies, as shown by its distinct ARDRA (amplified 16S ribosomal DNA restriction analysis) profile and molecular sequencing techniques.blaNDM-1was carried by a conjugative plasmid widespread among non-baumannii Acinetobacterisolates, suggesting its potential for dissemination before reaching more clinically relevantAcinetobacterspecies.

scholarly journals Identification of Aspergillus Species Using Internal Transcribed Spacer Regions 1 and 2

2000 ◽  
Vol 38 (4) ◽  
pp. 1510-1515 ◽  
Author(s):  
Travis Henry ◽  
Peter C. Iwen ◽  
Steven H. Hinrichs
Keyword(s):  
Internal Transcribed Spacer ◽  
Its Region ◽  
Diagnostic Value ◽  
Species Level ◽  
Clinical Isolates ◽  
Rrna Genes ◽  
28S Rrna ◽  
Accurate Identification ◽  
Invasive Mold Infections ◽  
Reference Strains

Aspergillus species are the most frequent cause of invasive mold infections in immunocompromised patients. Although over 180 species are found within the genus, 3 species, Aspergillus flavus, A. fumigatus, and A. terreus, account for most cases of invasive aspergillosis (IA), with A. nidulans, A. niger, and A. ustus being rare causes of IA. The ability to distinguish between the various clinically relevant Aspergillus species may have diagnostic value, as certain species are associated with higher mortality and increased virulence and vary in their resistance to antifungal therapy. A method to identify Aspergillus at the species level and differentiate it from other true pathogenic and opportunistic molds was developed using the 18S and 28S rRNA genes for primer binding sites. The contiguous internal transcribed spacer (ITS) region, ITS 1–5.8S–ITS 2, from referenced strains and clinical isolates of aspergilli and other fungi were amplified, sequenced, and compared with non-reference strain sequences in GenBank. ITS amplicons fromAspergillus species ranged in size from 565 to 613 bp. Comparison of reference strains and GenBank sequences demonstrated that both ITS 1 and ITS 2 regions were needed for accurate identification ofAspergillus at the species level. Intraspecies variation among clinical isolates and reference strains was minimal. Sixteen other pathogenic molds demonstrated less than 89% similarity withAspergillus ITS 1 and 2 sequences. A blind study of 11 clinical isolates was performed, and each was correctly identified. Clinical application of this approach may allow for earlier diagnosis and selection of effective antifungal agents for patients with IA.

scholarly journals Classification of oral pigmented anaerobic bacilli by pyrolysis mass spectrometry and biochemical tests

1992 ◽  
Vol 37 (1) ◽  
pp. 56-61 ◽  
Author(s):  
J. T. Magee ◽  
J. M. Hindmarch ◽  
B. I. Duerden ◽  
L. Goodwin
Keyword(s):  
Mass Spectrometry ◽  
Pyrolysis Mass Spectrometry ◽  
Biochemical Tests

scholarly journals Mass Spectrometry–Based Escherichia coli H Antigen/Flagella Typing: Validation and Comparison with Traditional Serotyping

2016 ◽  
Vol 62 (6) ◽  
pp. 839-847 ◽  
Author(s):  
Keding Cheng ◽  
Yi-Min She ◽  
Huixia Chui ◽  
Larissa Domish ◽  
Angela Sloan ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Close Correlation ◽  
Clinical Isolates ◽  
Whole Genome ◽  
Sequence Coverage ◽  
E Coli ◽  
Reference Strains

Abstract BACKGROUND Escherichia coli H antigen typing with antisera, a useful method for flagella clinical identification and classification, is a time-consuming process because of the need to induce flagella growth and the occurrence of undetermined strains. We developed an alternative rapid and analytically sensitive mass spectrometry (MS) method, termed MS-based H antigen typing (MS-H), and applied it at the protein sequence level for H antigen typing. We also performed a comparison with traditional serotyping on reference strains and clinical isolates. METHODS On the basis of international guidelines, the analytical selectivity and sensitivity, imprecision, correlation, repeatability, and reproducibility of the MS-H platform was evaluated using reference strains. Comparison of MS-H typing and serotyping was performed using 302 clinical isolates from 5 Canadian provinces, and discrepant results between the 2 platforms were resolved through whole genome sequencing. RESULTS Repeated tests on reference strain EDL933 demonstrated a lower limit of the measuring interval at the subsingle colony (16.97 μg or 1.465 × 107 cells) level and close correlation (r2 > 0.99) between cell culture biomass and sequence coverage. The CV was <10.0% among multiple repeats with 4 reference strains. Intra- and interlaboratory tests demonstrated that the MS-H method was robust and reproducible under various sample preparation and instrumentation conditions. Using discrepancy analysis via whole genome sequencing, performed on isolates with discrepant results, MS-H accurately identified 12.3% more isolates than conventional serotyping. CONCLUSIONS MS-H typing of E. coli is useful for fast and accurate flagella typing and could be very useful during E. coli outbreaks.

scholarly journals Genetic diversity of Rhizobium spp. isolated from soil samples of Bangladesh

2019 ◽  
Vol 36 (1) ◽  
pp. 7-10
Author(s):  
Md Tauhidul Islam Tanim ◽  
Md Miraj Kobad Chowdhury ◽  
Latiful Bari ◽  
Md Mizanur Rahaman ◽  
Sabita Rezwana Rahman ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Restriction Analysis ◽  
Morphological Characteristics ◽  
Temperature Tolerance ◽  
Biochemical Tests ◽  
Banding Patterns ◽  
Response Characteristics ◽  
Dna Restriction ◽  
Rhizobium Spp ◽  
Group 1

Rhizobia are Gram-negative soil-inhabiting bacteria commonly found in nodules of leguminous plants. These bacteria exclusively fix atmospheric nitrogen into ammonia, which is convertible to urea to serve natural fertilizer to the plants. However, rhizobial microbiota of Bangladesh have been studied poorly. Here, twenty isolates were identified as Rhizobium through observation of cultural characteristics, morphological characteristics and different biochemical tests. Isolates differed from one another in terms of their stress response characteristics like salt-stress tolerance,temperature tolerance, antibiotic susceptibility, and pH. Most of the isolates were resistant to ampicillin and erythromycin and streptomycin; and were sensitive to kanamycin and ciprofloxacin. Isolates were clustered into three genotypic groups according to the banding patterns of Amplified Ribosomal DNA Restriction Analysis (ARDRA). All the strains in ARDRA group 1 were Rhizobium azibense, and the others were Rhizobium bangladeshense and Rhizobium qilianshanense. Future studies would validate their capacity of nitrogen fixation and the scope of improvement of these strains to increase their efficiency of nitrogen fixation. Bangladesh J Microbiol, Volume 36 Number 1 June 2019, pp 07-10

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