scholarly journals Bacteriological and molecular study of Pseudomonas aeruginosa strains isolated from different clinical cases in Erbil and Kurkuk

2018 ◽  
Vol 41 (2) ◽  
pp. 124-130
Author(s):  
Asif Hasan Abdul Razzaq
Keyword(s):  
Molecular Weight ◽  
Polymerase Chain Reaction ◽  
Virulence Genes ◽  
Antibiotic Sensitivity ◽  
Molecular Study ◽  
Clinical Samples ◽  
Chain Reaction ◽  
Biochemical Tests ◽  
Antibiotic Sensitivity Test ◽  
Polymerase Chain

     This study included isolates of bacteria from 125 clinical samples in Erbil and Kirkuk Hospital including (burns, wounds, urine and sputum); 38 isolates were identified as P. aeruginosa after conducting microscopic and biochemical tests. The results of antibiotic sensitivity test showed that all isolates of P. aeruginosa  were different in resistance to Pipracillin, Erythromycin with rate of (100%) and to the Nalidixic acid (94.73%) while the lowest resistant antibiotics were to Co-trimoxazole, Ceftazidime and Ciprofloxacin, which amounted to (26.31%, 23.68 and 21.05%) respectively. For molecular diagnosis of P. aeruginosa some virulence genes the alg D and exo A were amplified through Polymerase Chain Reaction technique. The results showed that in 38 isolates cases only 22 (57.9%) were positive for algD gene by amplification of 520 bp band. While in urinary tract infection; 6 samples (60%) had alg D gene, and 8 (57.14%) isolates had alg D gene in wounds samples; also 7(70%) isolates from burns had that gene, while the sputum samples showed only one with alg D gene which was the lowest ratio; but in amplification of exo A, the results showed the presence of only one isolate from burns with molecular weight 396 bp with no appearance in others. 

scholarly journals Polymerase Chain Reaction: An Innovative Tool in Periodontal Diagnosis

2013 ◽  
Vol 4 (1) ◽  
pp. 60-66
Author(s):  
Suvarna H Patil ◽  
Kishore G Bhat ◽  
Paresh S Lotlekar ◽  
Laxmi V Hombal
Keyword(s):  
Polymerase Chain Reaction ◽  
Bacterial Species ◽  
Antibiotic Sensitivity ◽  
Periodontal Pathogen ◽  
Current Status ◽  
Clinical Samples ◽  
Chain Reaction ◽  
Biochemical Tests ◽  
Innovative Tool ◽  
Polymerase Chain

ABSTRACT Bacterial species colonizing the surfaces of the human oral cavity play an important role in oral health and disease and thus an accurate means of identification is crucial. Traditionally, identification has been based on microscopy, biochemical tests, immunofluorescence staining and antibiotic sensitivity. However, these tests are labor-intensive and costly, providing sometimes inconsistent results that make identification rather tentative. Recently, molecular DNA-based techniques have been used to identify bacteria directly from clinical samples. Development of a microbiological diagnostic kit using this technology therefore requires the ability to extract the bacterial DNA from the plaque sample and amplify the specific DNA sequence of the target periodontal pathogen. Polymerase chain reaction has emerged as the most powerful tool for the amplification of the genes and their RNA transcripts. The focus of this review is to describe the current status of the DNA-based method PCR which has become a standard diagnostic and research tool in dentistry. How to cite this article Patil SH, Bhat KG, Lotlekar PS, Hombal LV. Polymerase Chain Reaction: An Innovative Tool in Periodontal Diagnosis. World J Dent 2013;4(1):60-66.

scholarly journals Resistansi Antibiotik Secara Fenotip Dan Deteksi Gen TetA pada Sampel Hati Ayam di Pasar Dukuh Kupang Surabaya

2022 ◽  
Vol 11 (3) ◽  
pp. 284
Author(s):  
Reina Puspita Rahmaniar ◽  
Dyah Widhowati ◽  
Nurul Hidayah
Keyword(s):  
Escherichia Coli ◽  
Polymerase Chain Reaction ◽  
Antibiotic Resistance ◽  
Antibiotic Sensitivity ◽  
Chicken Liver ◽  
Methyl Red ◽  
Chain Reaction ◽  
Biochemical Tests ◽  
Tetracycline Antibiotics ◽  
Polymerase Chain

Abstract The purpose of this study was to determine the resistance of several antibiotics phenotypically and genotypically to detect the tetA gene from broiler chicken liver samples at Dukuh Kupang market, Surabaya. A total of 30 samples were taken and then prepared aseptically and sterile. Isolation on Eosin Methylene Blue Agar (EMBA) media, then microscopic examination using gram staining and biochemical tests of Triple Sugar Iron Agar (TSIA), Sulfide Indole Motility (SIM), Methyl Red (MR), Voges Prouskauers (VP) and Simons Citrate Agar (SCA). The identified Escherichia coli colonies were tested for antibiotic sensitivity using the Kirby Bauer method, then isolates that were proven to be resistant to tetracycline antibiotics were followed by genetic testing using the Polymerase Chain Reaction (PCR) method. The results showed that 20 of the 30 samples were positive for Escherichia coli. Escherichia coli isolates from chicken liver samples showed resistance to 30 µg tetracycline antibiotics by 85% (17 of 20 samples) Researchers also compared with other antibiotics, the highest resistance to ampicillin 10 µg was 90% (18 out of 20 samples), gentamicin resistance was 10 µg by 50% (10 of 20 samples) and 30 µg chloramphenicol antibiotic resistance by 30% (6 of 20 samples). The isolates that were resistant to tetracycline were confirmed by Polymerase Chain Reaction to detect the tetA gene with the final product in the form of a band with a length of 210 bp. Bacterial isolates resistant to Tetracycline antibiotics did not always show TetA gene expression in the PCR test. Keywords: Antibiotic Resistance; Escherichia coli; Market; TetA gene   Abstrak Tujuan dari penelitian ini yaitu untuk mengetahui resistansi beberapa antibiotik secara fenotip dan secara genotip mendeteksi gen tetA dari sampel hati ayam broiler di pasar Dukuh Kupang Surabaya. Sebanyak 30 sampel diambil kemudian dipreparasi secara aseptis dan steril. Isolasi pada media Eosin Methilen Blue Agar (EMBA), selanjutnya dilakukan pemeriksaan mikroskopis menggunakan pewarnaan gram dan uji biokimiawi Triple Sugar Iron Agar (TSIA), Sulfide Indol Motility (SIM), Methyl Red (MR), Voges Prouskauers (VP), dan Simons Citrat Agar (SCA). Koloni Escherichia coli yang teridentifikasi dilakukan uji sensitifitas antibiotik dengan metode Kirby bauer, selanjutnya isolat yang terbukti resistan terhadap antibiotik tetrasiklin dilanjutkan pemeriksaan genetik dengan metode Polymerase Chain Reaction (PCR).  Hasil penelitian menunjukkan bahwa 20 dari 30 sampel positif Escherichia coli. Isolat Escherichia coli asal sampel hati ayam menunjukkan resistansi terhadap antibiotik Tetrasiklin 30 µg sebesar 85 % (17 dari 20 sampel) Peneliti juga melakukan perbandingan dengan antibiotik lainnya, resistensi tertinggi pada antibiotik ampisilin 10 µg sebesar 90 % (18 dari 20 sampel), resistensi gentamisin 10 µg sebesar 50 % (10 dari 20 sampel) dan resistensi antibiotik kloramfenikol 30 µg sebesar 30 % (6 dari 20 sampel). Isolat yang resisten terhadap tetrasiklin dikonfirmasi dengan Polymerase Chain Reaction untuk mendeteksi gen tetA dengan produk akhir berupa band dengan panjang 210 bp. Isolat bakteri yang resistan terhadap antibiotik Tetrasiklin tidak selalu menunjukkan ekspresi gen tetA pada uji PCR. Kata kunci: Escherichia coli; Gen TetA; Pasar; Resistansi Antibiotik.

Molecular Analysis of Uropathogenic E.coli Isolates from Urinary Tract Infections

2019 ◽  
Vol 19 (3) ◽  
pp. 322-326 ◽  
Author(s):  
Hassan Valadbeigi ◽  
Elham Esmaeeli ◽  
Sobhan Ghafourian ◽  
Abbas Maleki ◽  
Nourkhoda Sadeghifard
Keyword(s):  
Escherichia Coli ◽  
Polymerase Chain Reaction ◽  
Urinary Tract ◽  
Urinary Tract Infections ◽  
Multiplex Polymerase Chain Reaction ◽  
Virulence Genes ◽  
Uropathogenic Escherichia Coli ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Tract Infections

Introduction: The aim of the current study was to investigate the prevalence of virulence genes in uropathogenic Escherichia coli (UPEC) isolates in Ilam. Materials and Methods: For this purpose, a total of 80 UPEC isolates were collected for patients with UTIs during a 6 months period. The multiplex polymerase chain reaction (multiplex PCR) was used to detect the papEF, fimH, iucD, hlyA, fyuA, and ompT genes. Results: The prevalence of fimH, papEF, iucD, fyuA, hlyA, hlyA, and ompT genes were 87.5%, 47.5%, 60%, 67.5%, 27.5%, 47.5% and 71.2%, respectively. Among all of the isolates, 27 profiles were obtained. Conclusion: Our findings demonstrated that the most prevalence was found for fimH, and different distribution of virulence genes suggested different ability of pathogenicity.

Using a Polymerase Chain Reaction as a Complementary Test to Improve the Detection of Dermatophyte Fungus in Nails

2014 ◽  
Vol 104 (3) ◽  
pp. 233-237 ◽  
Author(s):  
María José Iglesias Sánchez ◽  
Ana María Pérez Pico ◽  
Félix Marcos Tejedor ◽  
María Jesús Iglesias Sánchez ◽  
Raquel Mayordomo Acevedo
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequences ◽  
Classical Method ◽  
Clinical Manifestations ◽  
Culture Method ◽  
Clinical Samples ◽  
Chain Reaction ◽  
Nested Polymerase Chain Reaction ◽  
Traditional Procedure ◽  
Polymerase Chain

Background Dermatomycoses are a group of pathologic abnormalities frequently seen in clinical practice, and their prevalence has increased in recent decades. Diagnostic confirmation of mycotic infection in nails is essential because there are several pathologic conditions with similar clinical manifestations. The classical method for confirming the presence of fungus in nail is microbiological culture and the identification of morphological structures by microscopy. Methods We devised a nested polymerase chain reaction (PCR) that amplifies specific DNA sequences of dermatophyte fungus that is notably faster than the 3 to 4 weeks that the traditional procedure takes. We compared this new technique and the conventional plate culture method in 225 nail samples. The results were subjected to statistical analysis. Results We found concordance in 78.2% of the samples analyzed by the two methods and increased sensitivity when simultaneously using the two methods to analyze clinical samples. Now we can confirm the presence of dermatophyte fungus in most of the positive samples in just 24 hours, and we have to wait for the result of culture only in negative PCR cases. Conclusions Although this PCR cannot, at present, substitute for the traditional culture method in the detection of dermatophyte infection of the nails, it can be used as a complementary technique because its main advantage lies in the significant reduction of time used for diagnosis, in addition to higher sensitivity.

scholarly journals Analysis and validation of a highly sensitive one-step nested quantitative real-time polymerase chain reaction assay for specific detection of severe acute respiratory syndrome coronavirus 2

2020 ◽  
Vol 17 (1) ◽  
Author(s):  
Yang Zhang ◽  
Chunyang Dai ◽  
Huiyan Wang ◽  
Yong Gao ◽  
Tuantuan Li ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Quantitative Polymerase Chain Reaction ◽  
Clinical Samples ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Qrt Pcr ◽  
Highly Sensitive ◽  
One Step ◽  
Polymerase Chain

Abstract Background Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, is posing a serious threat to global public health. Reverse transcriptase real-time quantitative polymerase chain reaction (qRT-PCR) is widely used as the gold standard for clinical detection of SARS-CoV-2. Due to technical limitations, the reported positive rates of qRT-PCR assay of throat swab samples vary from 30 to 60%. Therefore, the evaluation of alternative strategies to overcome the limitations of qRT-PCR is required. A previous study reported that one-step nested (OSN)-qRT-PCR revealed better suitability for detecting SARS-CoV-2. However, information on the analytical performance of OSN-qRT-PCR is insufficient. Method In this study, we aimed to analyze OSN-qRT-PCR by comparing it with droplet digital PCR (ddPCR) and qRT-PCR by using a dilution series of SARS-CoV-2 pseudoviral RNA and a quality assessment panel. The clinical performance of OSN-qRT-PCR was also validated and compared with ddPCR and qRT-PCR using specimens from COVID-19 patients. Result The limit of detection (copies/ml) of qRT-PCR, ddPCR, and OSN-qRT-PCR were 520.1 (95% CI: 363.23–1145.69) for ORF1ab and 528.1 (95% CI: 347.7–1248.7) for N, 401.8 (95% CI: 284.8–938.3) for ORF1ab and 336.8 (95% CI: 244.6–792.5) for N, and 194.74 (95% CI: 139.7–430.9) for ORF1ab and 189.1 (95% CI: 130.9–433.9) for N, respectively. Of the 34 clinical samples from COVID-19 patients, the positive rates of OSN-qRT-PCR, ddPCR, and qRT-PCR were 82.35% (28/34), 67.65% (23/34), and 58.82% (20/34), respectively. Conclusion In conclusion, the highly sensitive and specific OSN-qRT-PCR assay is superior to ddPCR and qRT-PCR assays, showing great potential as a technique for detection of SARS-CoV-2 in patients with low viral loads.

scholarly journals UTILITY OF ANTIGEN DETECTION TEST AND POLYMERASE CHAIN REACTION IN THE DIFFERENTIATION OF TUBERCULOUS AND NON-TUBERCULOUS MYCOBACTERIA

2017 ◽  
Vol 10 (6) ◽  
pp. 289
Author(s):  
Yogita Singh ◽  
Raji Vasanth ◽  
Shrikala Baliga ◽  
Dhanashree B
Keyword(s):  
Polymerase Chain Reaction ◽  
False Negative ◽  
Diagnostic Methods ◽  
Clinical Samples ◽  
Chain Reaction ◽  
College Hospital ◽  
Medical College ◽  
Negative Results ◽  
Polymerase Chain ◽  
Mycobacterium Spp

Objectives: Cultivation and identification of mycobacteria to species level remains difficult and time-consuming. Hence, easy and rapid diagnostic methods are necessary for the differentiation of Mycobacterium tuberculosis (MTB) from non-tuberculous mycobacteria (NTM). The present study aims to detect and differentiate MTB from NTM isolated from clinical samples by immunochromatographic test (ICT) and polymerase chain reaction (PCR). Methods: Over a period of 1 year, clinical samples (n=496) received from suspected cases of TB, at the Department of Microbiology, Kasturba Medical College Hospital, Mangalore were cultured to isolate Mycobacterium spp. Identification of all the isolates was done by conventional biochemical technique, ICT, and PCR. Results: Among the 496 samples processed, 49 (9.87%) were acid-fast bacilli smear positive and 59 (11.89%) samples showed the growth of Mycobacterium spp. Among these, 10 were rapid growers, 49 were slow-growing mycobacteria, out of which 30 were MTB as identified by conventional biochemical reaction. Out of 59 Mycobacterial isolates subjected to ICT for the detection of MPT 64 antigen, only 28 were identified as MTB. However, all the 30 isolates were correctly identified as MTB by PCR. Conclusion: Hence, PCR is essential for rapid differentiation of non-tuberculous Mycobacterium from MTB. False negative results seen with immunochromatographic MPT 64 antigen assay could be due to mutations within the mpt64 gene. Further studies are necessary to characterize these PCR-positive and immunochromatographic assay negative MTB isolates.

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