Evaluation of 16S, map1 and pCS20 probes for detection of 
Cowdria and Ehrlichia species

A panel of 16S ribosomal RNA gene probes has been developed for the study of the epidemiology of heartwater; five of these detect different cowdria genotypes, one detects five distinct genotypes; one detects any Group III Ehrlichia species other than Cowdria and one detects any Group II Ehrlichia species. These probes have been used on PCR-amplified rickettsial 16S rRNA genes from over 200 Amblyomma hebraeum ticks. Control ticks were laboratory-reared and either uninfected or fed on sheep experimentally infected with different cowdria isolates, field ticks were collected from animals in heartwater-endemic areas. All tick-derived DNA samples were also examined by PCR amplification and probing for two other cowdria genes (map1 and pCS20) which have previously been used for heartwater epidemiology. This paper describes the first direct comparison of all currently available DNA probes for heartwater-associated organisms.

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Heterogeneity between 16S ribosomal RNA gene copies borne by one Desulfitobacterium strain is caused by different 100-200 bp insertions in the 5´ region

Canadian Journal of Microbiology ◽

10.1139/w06-111 ◽

2007 ◽

Vol 53 (1) ◽

pp. 116-128 ◽

Cited By ~ 13

Author(s):

Richard Villemur ◽

Philippe Constant ◽

Annie Gauthier ◽

Martine Shareck ◽

Réjean Beaudet

Keyword(s):

In Situ Hybridization ◽

16S Rrna ◽

16S Rrna Gene ◽

Ribosomal Rna ◽

16S Ribosomal Rna ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Gene Copies

Strains of Desulfitobacterium hafniense, such as strains PCP-1, DP7, TCE1, and TCP-A, have unusual long 16S ribosomal RNA (rRNA) genes due to an insertion of approximately 100 bp in the 5' region. In this report, we analyzed the 16S rRNA genes of different Desulfitobacterium strains to determine if such an insertion is a common feature of desulfitobacteria. We amplified this region by polymerase chain reaction (PCR) from eight Desulfitobacterium strains (D. hafniense strains PCP-1, DP7, TCP-A, TCE1, and DCB-2; D. dehalogenans; D. chlororespirans; and Desulfitobacterium sp. PCE1) and resolved each PCR product by denaturing gradient gel electrophoresis (DGGE). All strains had from two to seven DGGE- migrating bands, suggesting heterogeneity in their 16S rRNA gene copies. For each strain, the 5' region of the 16S rRNA genes was amplified and a clone library was derived. Clones corresponding to most PCR–DGGE migration bands were isolated. Sequencing of representative clones revealed that the heterogeneity was generated by insertions of 100–200 bp. An insertion was found in at least one copy of the 16S rRNA gene in all examined strains. In total, we found eight different types of insertions (INS1–INS8) that varied from 123 to 193 nt in length. Two-dimensional structural analyses of transcribed sequences predicted that all insertions would form an energetically stable loop. Reverse transcriptase – PCR experiments revealed that most of the observed insertions in the Desulfitobacterium strains were excised from the mature 16S rRNA transcripts. Insertions were not commonly found in bacterial 16S rRNA genes, and having a different insertion in several 16S rRNA gene copies borne by a single bacterial species was rarely observed. The function of these insertions is not known, but their occurrence can have an important impact in deriving 16S rRNA oligonucleotidic fluorescence in situ hybridization probes, as these insertions can be excised from 16S rRNA transcripts.Key words: Desulfitobacterium, 16S ribosomal RNA genes, heterogeneity, gene insertions, fluorescence in situ hybridization.

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Influence of 16S Ribosomal RNA Gene Polymerase Chain Reaction and Sequencing on Antibiotic Management of Bone and Joint Infections

Canadian Journal of Infectious Diseases and Medical Microbiology ◽

10.1155/2013/747145 ◽

2013 ◽

Vol 24 (2) ◽

pp. 85-88 ◽

Cited By ~ 7

Author(s):

B Alraddadi ◽

S Al-Azri ◽

KR Forward

Keyword(s):

16S Rrna ◽

Ribosomal Rna ◽

16S Ribosomal Rna ◽

Pcr Assay ◽

Ribosomal Rna Gene ◽

Joint Infections ◽

Bone And Joint Infections ◽

Antibiotic Management ◽

16S Ribosomal Rna Gene ◽

Polymerase Chain

INTRODUCTION: Amplification of the 16S ribosomal RNA gene by polymerase chain reaction (PCR) followed by analysis of generated sequences can be an important adjunct to conventional cultures.OBJECTIVE: To determine how the results of this approach influence physicians’ decisions regarding the management of bone and joint infections.METHOD: Clinical and laboratory findings of patients seen at the Queen Elizabeth II Health Sciences Centre (Halifax, Nova Scotia) between December 2005 and September 2009 were reviewed. Patients who had negative cultures but likely or possible bone and joint infections were further evaluated using 16S rRNA PCR. The impact of the 16S rRNA PCR result on antibiotic management was evaluated and it was assessed whether untreated patients with negative 16S rRNA PCR subsequently presented with infections, suggesting a false-negative result.RESULT: A total of 36 patients (mean age 62 years) were reviewed. Thirty-two patients were evaluated by infectious disease consultants; of these, 20 were considered likely to have infections. Seventeen patients were admitted with suspected prosthetic joint infections. Twenty-nine patients received antimicrobial treatment before the sample for the 16S rRNA PCR assay was obtained. Of the 36 patients, 26 (72.2%) were treated appropriately with modifications to their antibiotic regimen in response to the 16S rRNA PCR assay results. Antimicrobials were discontinued for 19 patients based on negative PCR assay and, in seven patients, antibiotics were changed based on a positive result. There were no relapses among patients with negative PCR assay in whom antibiotics were discontinued.CONCLUSION: 16S ribosomal RNA gene PCR and sequencing is a valuable tool in the guidance of antimicrobial therapy for bone and joint infections.

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Seleksi dan Identifikasi Secara Molekuler Bakteri Pendegradasi Insektisida Piretroid dari Tanah

Indonesia Journal of Halal ◽

10.14710/halal.v1i1.3110 ◽

2018 ◽

Vol 1 (1) ◽

pp. 8

Author(s):

Salindri Prawitasari ◽

Siti Nur Jannah ◽

Alina Akhdiya

Keyword(s):

16S Rrna ◽

Ribosomal Rna ◽

Soil Bacteria ◽

Negative Impact ◽

16S Ribosomal Rna ◽

Partial Sequence ◽

Rrna Sequence ◽

16S Rrna Sequence ◽

Ribosomal Rna Gene ◽

16S Ribosomal Rna Gene

ABSTRAKAkumulasi residu insektisida pada lahan pertanian berdampak negatif bagi lingkungan dan organisme di sekitarnya. Salah satu teknologi alternatif untuk merehabilitasi lahan pertanian yang tercemar adalah dengan teknologi bioremediasi. Bioremediasi adalah teknologi untuk memecah atau menguraikan zat pencemar menjadi bahan yang kurang beracun atau tidak beracun (karbondioksida dan air) dengan memanfaatkan organisme atau produk organisme. Penelitian ini bertujuan untuk menyeleksi dan mengidentifikasi secara molekuler bakteri pendegradasi insektisida piretroid sintetik asal sampel tanah Pangalengan. Seleksi terhadap sembilan isolat bakteri tanah asal Pangalengan menggunakan medium NMS cair yang mengandung 100 ppm piretroid menghasilkan dua isolat bakteri yang memiliki kemampuan terbaik dalam mendegradasi piretroid. Isolat S-9 merupakan isolat bakteri yang memiliki kemampuan mendegradasi residu piretroid paling tinggi dibandingkan dengan 8 isolat lainnya, yaitu sebesar 87,38%. Hasil degradasi insektisida tersebut dimanfaatkan oleh bakteri sebagai sumber C, N, dan P untuk mendukung pertumbuhannya. Berdasarkan sekuens gen 16S rRNA, isolat S-9 menunjukkan kemiripan dengan Bosea eneae 16S ribosomal RNA gene (partial sequence) dengan similaritas 89%.Kata kunci: bakteri, bioremediasi, degradasi insektisida, piretroid ABSTRACTThe accumulation of insecticide residue in farmfield caused negative impact to the environment and organisms which surround it. One of the lastest technology to rehabilitate polluted farmfield is bioremediation technology. Bioremediation is technology for degradating pollute to be unpollute (carbondioxide and water) using microorganisms or its product. The purpose of this research was to selecting and molecular identifying pyrethroid insecticide-degradating bacteria from Pangalengan soil sample. Nine isolates of soil bacteria from Pangalengan was selected by liquid NMS contains 100 ppm pyrethroid, only 2 isolates that indicated best ability to degrade pyrethroid. The best ability to degrade pyrethroid was S-9 isolate, with highest value 87,38%. Degradation pyrethroid’s product utilized by the bacteria as C, N, and P source to support their growth. Based on 16S rRNA sequence gene, S-9 isolate represented its similarity with Bosea eneae 16S ribosomal RNA gene (partial sequence) with 89% similarity value.Keywords: bacteria, bioremediation, insecticide degradation, pyrethroid

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