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

2013 ◽  
Vol 24 (2) ◽  
pp. 85-88 ◽  
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.

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

1999 ◽  
Vol 122 (2) ◽  
pp. 323-328 ◽  
Author(s):  
M. T. E. P. ALLSOPP ◽  
C. M. HATTINGH ◽  
S. W. VOGEL ◽  
B. A. ALLSOPP
Keyword(s):  
16S Rrna ◽  
Ribosomal Rna ◽  
Pcr Amplification ◽  
16S Ribosomal Rna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Amblyomma Hebraeum ◽  
Ribosomal Rna Gene ◽  
Group Iii ◽  
16S Ribosomal Rna Gene

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.

Cultural and molecular characterization of photobionts of Peltigera Membranacea

1997 ◽  
Vol 29 (6) ◽  
pp. 571-586 ◽  
Author(s):  
V.P.W. Mioa ◽  
A. Rabenau ◽  
A. Lee
Keyword(s):  
16S Rdna ◽  
Ribosomal Rna ◽  
Molecular Study ◽  
16S Ribosomal Rna ◽  
Chain Reaction ◽  
Ribosomal Rna Gene ◽  
Pcr Product ◽  
16S Ribosomal Rna Gene ◽  
Polymerase Chain

AbstractA molecular study was undertaken to clarify the identity of the photobiont in colourmorphs of the lichen, Peltigera membranacea. Two strains of cyanobacteria, identified as Nosroc sp. by morphology, were cultivated from each of two lichen specimens. Prokaryotic (16S) ribosomal RNA gene fragments were amplified by the polymerase chain reaction (PCR) from DNA extracted from the isolated strains and the lichens, and sequenced directly. Sequences were 98 1% identical between lichen specimens, TDI#AR94 and TDI#AR95, and highly similar to sequences published, or generated in this study from a type culture, for Nostoc. The 16S ribosomal RNA gene sequences (‘ 16S rDNA’) of all four lichen-derived cyanobacteria appeared the same, even though the lichen specimens from which they originated had different sequences. The 16S rDXA from strains 9A and 9B were different from that of specimen TDI#AR94, the thallus from which they were isolated, and instead were the same as that of strains 10A and 10B, and their source, specimen TDI#AR95. When primers selective for the strain 9A sequence were used, however, a small amount of PCR product corresponding to the 16S rDNA of strain 9A was obtained from lichen TDI#AR94. The results confirm that the photobionts of P. membranacea belong to Nostoc, and suggest that genetic differences in the photobiont may be a factor in the occurrence of colourmorphs among cyanolichens.

scholarly journals Seleksi dan Identifikasi Secara Molekuler Bakteri Pendegradasi Insektisida Piretroid dari Tanah

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

scholarly journals Molecular Approaches to Studying Microbial Communities: Targeting the 16S Ribosomal RNA Gene

2016 ◽  
Vol 38 (3) ◽  
pp. 223-232 ◽  
Author(s):  
Kazumasa FUKUDA ◽  
Midori OGAWA ◽  
Hatsumi TANIGUCHI ◽  
Mitsumasa SAITO
Keyword(s):  
Microbial Communities ◽  
Ribosomal Rna ◽  
16S Ribosomal Rna ◽  
Approaches To Studying ◽  
Ribosomal Rna Gene ◽  
Molecular Approaches ◽  
16S Ribosomal Rna Gene
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