111 research outputs found
Comparison of Interpretation between Pyrosequencing and Xpert MTB/RIF Assay in Multidrug-Resistant Tuberculosis
No full textIndonesia is one of the countries with the highest multidrug-resistant tuberculosis cases in the world. Rapid molecular test using the Xpert MTB/RIF assay is one of the detection methods for MDR-TB. Early detection of MDR-TB is crucial for early initiation of treatment. However, Xpert MTB/RIF assay only detects the rpoB gene mutations associated with Rifampicin resistance. Recently, WHO recommends the use of Pyrosequencing, a DNA sequencing method that can detect not only the rpoB gene but also katG and/or inhA gene mutations associated with Isoniazid resistance. The aims of this study were to compare the interpretation between the two methods and to determine the differences in codon mutation position detection of the rpoB gene and mutation detection of the katG and/or inhA gene. This was a cross-sectional comparative observational study on patients ≥18 years old interpreted as RR-TB patients based on Xpert MTB/RIF assay results who had not received MDR-TB drugs at Dr. Hasan Sadikin General Hospital, Bandung, Indonesia. Results showed there were 40 Rifampicin-resistant TB subjects interpreted by Xpert MTB/RIF assay while Pyrosequencing interpreted 30 MDR-TB, 9 RR-TB and one Isoniazid-resistant TB subjects in January - February 2020. The detection of rpoB gene codon mutation position between Xpert MTB/RIF assay and Pyrosequencing methods was not significantly different (p=0.389). Pyrosequencing had detected 27 katG gene mutations, 3 inhA gene mutations, one katG and inhA gene mutation. To conclude, Pyrosequencing can be used for accurate detection of Rifampicin and Isoniazid resistance in MDR-TB. Perbandingan Hasil Interpretasi antara Pyrosequencing dengan Xpert MTB/RIF Assay pada Multidrug-Resistant TuberculosisIndonesia merupakan salah satu negara dengan kasus multidrug-resistant tuberculosis terbanyak. Penegakan diagnosis MDR-TB saat ini menggunakan tes cepat molekular Xpert MTB/RIF assay sehingga pasien segera mendapatkan pengobatan. Namun Xpert MTB/RIF assay hanya mendeteksi mutasi gen rpoB penyandi resistansi Rifampisin. World Health Organization merekomendasikan Pyrosequencing, metode sequencing nukleotida yang dapat mendeteksi mutasi gen rpoB, gen katG dan/atau inhA penyandi resistansi Isoniazid. Tujuan penelitian ini adalah menentukan apakah kedua alat ini memberikan hasil interpretasi yang sama, apakah ada perbedaan deteksi posisi mutasi kodon gen rpoB dan apakah ditemukan mutasi gen katG dan/atau inhA. Penelitian ini merupakan studi observasional komparatif dengan rancangan cross-sectional. Subjek penelitian adalah pasien usia ≥18 tahun yang diinterpretasi RR-TB berdasarkan Xpert MTB/RIF assay di RSUP Dr. Hasan Sadikin Bandung dan belum mendapat pengobatan. Xpert MTB/RIF assay menginterpretasi 40 subjek Rifampicin-resistant TB sedangkan Pyrosequencing menginterpretasi 30 subjek MDR-TB, 9 subjek RR-TB dan satu subjek Isoniazid-resistant TB pada bulan Januari-Februari 2020. Deteksi posisi mutasi kodon gen rpoB antara Xpert MTB/RIF assay dan Pyrosequencing tidak berbeda bermakna (p=0,389). Pyrosequencing mendeteksi 27 mutasi gen katG, 3 mutasi gen inhA, satu mutasi gen katG dan inhA. Kesimpulan, Pyrosequencing dapat digunakan untuk deteksi resistansi Rifampisin dan Isoniazid pada MDR-TB secara lebih akurat
Identification of Significant Pathogenic Nontuberculous Mycobacteria Species from Presumptive TB Patients Using Partial hsp65 Gene Sequencing
No full textDyshelly Nurkartika Pascapurnama,1 Nabilla Ghina Zavitri,1 Raspati Cundarani Koesoemadinata,1 Adi Imam Cahyadi,2 Lidya Chaidir2,3 1Research Center for Care and Control of Infectious Diseases, Universitas Padjadjaran, Bandung, West Java, Indonesia; 2Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Sumedang, West Java, Indonesia; 3Center for Translational Biomarker Research, Universitas Padjadjaran, Bandung, West Java, IndonesiaCorrespondence: Lidya Chaidir, Faculty of Medicine, Universitas Padjadjaran, Jln. Ir. Soekarno Km. 21 Jatinangor, Sumedang, 45363, West Java, Indonesia, Tel +62-22-8428812, Email [email protected]: To date, the diagnosis of nontuberculous mycobacteria (NTM) disease primarily relies on clinical symptoms and radiological features. Our objective was to apply a sequence-based analysis method by using partial gene sequencing of heat shock protein 65 (hsp65) to identify NTM species.Patients and Methods: A total of 32 stored isolates obtained from individuals suspected of having pulmonary NTM infection were subjected to solid Ogawa culture. Genomic DNA from each sample was extracted and used in a conventional polymerase chain reaction (PCR) targeting a specific region of hsp65 gene. Identified amplicons from the PCR were then subjected to targeted sequencing. Analysis of the obtained hsp65 sequence was performed using DNA Baser tool. The consensus sequences obtained were compared to references in the GenBank NCBI database to determine NTM species.Results: We identified several important NTM species which posses opportunistic characteristics. M. abscessus and M. chelonae are the most frequent NTM species identified in this study (40.63% and 18.75%, respectively). These two species have the potential to cause significant infections in human, ranging from opportunistic pulmonary infection to localized skin infection. Additionally, pathogenic NTM members of M. fortuitum group (MFG), M. avium, M. intracellulare, M. kansasii, and M. celatum were also found among all identified species.Conclusion: Sequence-based analysis is a promising method for identifying species of NTM. The hsp65 gene has a high discriminatory power to identify opportunistic pathogen NTM species in specimens in Indonesia. Consequently, hsp65 partial gene sequencing is considerable as an alternative and reliable approach for NTM speciation.Keywords: nontuberculous mycobacteria, species identification, hsp65 gene, sequence-based analysi
Reliability of RT-qPCR Pooling Method for COVID-19 Detection in Various Cycle Threshold Values
No full textBackground: Reverse Transcriptase Quantitative Real-time Polymerase Chain Reaction (RT-qPCR) is a standard method to detect SARS-CoV-2, the cause of COVID-19 disease, albeit expensive for some laboratory settings. The pooling test is widely used for large-scale screening to speed up the turn-around time and reduce the cost of the RT-qPCR. However, the pooling test involves mixing a certain number of specimens which theoretically increases the possibility of false-negative results. This study aimed to evaluate the accuracy of the pooling test compared with the non-pooling test in different Ct values as a surrogate for viral load.Methods: RT-qPCR was performed in three groups of samples: non-pooling (individual samples), pooling of 5 samples and 11 samples, with various ranges of Ct value in the respective group: x<25 (n=4); 25<x<30 (n=5), x<30 (n=16), and negative sample (n=5). Agreement and kappa values were calculated. Four of twenty-five individual samples resulted in false-negative after pooling.Results: By taking all samples without applying the cut-off value to the calculation, the agreement in pooling of 5 samples was 0.86 (Kappa 0.31) and of 11 samples was 0.64 (Kappa 0.96). When the cut-off value of Ct<37 was applied, percent agreement and kappa were 1.00, respectively, for both pooling methods.Conclusions: Pooling up to 11 samples shows high concordance with RT-qPCR with individual samples with Ct<37. Interpreting pooling results in a very low viral load (Ct≥37) must be considered due to the increased possibility of inconclusive results
Transcriptional Biomarkers for Treatment Monitoring of Pulmonary Drug-Resistant Tuberculosis: Protocol for a Prospective Observational Study in Indonesia
No full textMany blood-based gene expression biomarkers for monitoring tuberculosis (TB) treatment have been suggested so far, but promising biomarker results for drug-resistant TB treatment response have not been studied. This protocol presents a prospective observational study in Indonesia to profile the human blood transcriptome for predicting the response to drug-resistant TB treatment, focusing on pulmonary TB, and to adapt the specific RNA signature to the qRT-PCR platform. Longitudinal blood samples will be collected from 44 subjects with rifampicin resistant TB, confirmed by Xpert MTB/RIF, and 52 healthy controls. RNA-Seq will be performed to identify changes in the transcriptome following TB treatment. A discriminative RNA signature will be chosen and translated into a score for use in a quantitative PCR-based assay. This study will provide crucial information to guide the discovery and design of a clinically implementable tool to monitor the response of TB treatment
Microbiological Testing of Gastric Aspirate Improves the Diagnosis of Pulmonary Tuberculosis in Unconscious Adults with TB Meningitis
No full textConventional sputum collection for TB diagnosis is difficult in TB meningitis patients since most of them are admitted with decreased consciousness. It is assumed that unconscious patients swallow their sputum; therefore, gastric aspiration can replace sputum collection in unconscious patients. A prospective study was conducted to see whether examining gastric aspirate could increase the diagnosis certainty of pulmonary TB in such subjects. The inclusion criteria were age 18–60 years, decreased level of consciousness, and use of a nasogastric tube. Subjects who had taken antituberculosis drugs for more than 3 days were excluded. Gastric lavage was performed in the morning after an overnight fast. Specimens were examined for direct smear, culture, and rapid molecular testing. Demographic, clinical, chest X-ray, and laboratory data were also recorded. During the study period, 31 subjects were available. The positivity rates for microbiological tests were 19.3%, 41.9%, and 48.4% for smear, culture, and rapid molecular testing, respectively. All positive smears were confirmed by either culture or rapid molecular testing. Gastric lavage can be considered a tool for improving extraneural TB diagnosis in unconscious patients
Pengembangan Prekultur Oxgall sebagai Sampel Klinis untuk Deteksi Salmonella typhi dengan Metode Real-time PCR
No full textDemam tifoid merupakan beban kesehatan masyarakat yang signifikan di negara berpenghasilan rendah yang disebabkan oleh Salmonella enterica serotype typhi (S.typhi). Manifestasi klinis demam tifoid bervariasi dan tidak spesifik, sehingga membuat diagnosis menjadi sulit. Dengan menggunakan oxgall untuk pra-inkubasi sebagai media kultur selektif sebelum amplifikasi Real-time PCR (RT-PCR) pada wholeblood menghasilkan diagnostic yang cepat dan sensitif. Tujuan dari penelitian ini adalah untuk mengetahui kinerja oxgall sebelum amplifikasi RT-PCR untuk deteksi Salmonella sp . Sebelum proses pengambilan sampel, dilakukan optimasi spike sampel untuk mengetahui bahwa reagen yang digunakan baik untuk spesimen klinis. Dalam proses sampel, sampel wholeblood diambil dari 30 pasien dengan positif Widal tes. Sampel darah vena dari pasien demam tifoid diambil pada hari diagnosis; 5 ml untuk kultur darah, dan 5 ml untuk RT-PCR. Bakteri ditanam di oxgall 10% (standar mikrobiologi laboratorium klinik) dan diinkubasi selama 6 jam (37 ° C) sebelum DNA bakteri diisolasi untuk deteksi RT-PCR. Hasil penelitian menunjukkan bahwa reagen RT-PCR baik digunakan untuk sampel klinis dan kultur darah lebih baik daripada RT-PCR dengan menggunakan oxgall (hasil kultur darah positif lebih dari 24 jam). Hal ini menunjukkan bahwa harus ada penelitian lebih lanjut mengenai durasi inkubasi dan konsentrasi oxgall pada RT-PCR dan pemilihan sampel klinis
SISTEM INFORMASI DATA KREDIT BERBASIS WEB PADA PT SUMMIT OTO FINANCE KOTA PALEMBANG 02
No full textCredit Information System Web-Based Data at PT Summit Oto Finance
Palembang 02
This report discusses information systems web-based credit data at PT Summit Oto Finance Palembang 02. During the study authors found that the unavailability of a credit information system process is not efficient motors for consumers who do not have much time to look at the data of credit, the company also not mempunnyai credit data information system that can be viewed on the website, Based on these problems, the authors establish a credit information System web-Based Data on pt Summit Oto Finance Palembang 02 by using the programming language PHP (PHP Hypertext Preprocessor). As a result, consumers can easily view the data using the web and consumer credit painstakingly no longer come to the company to see the motorcycle and employee credit data is not hard anymore to display customer data for customers in credit data has appeared on the web. Therefore. The author suggested that PT Summit Oto Finance should consider the application of the Credit Information System Web-Based Data that has been created by the author
KETERLIBATAN PEREMPUAN DALAM MUSRENBANG TINGKAT DESA KOTA BANDA ACEH
No full textThe Development Planning Conference is a means for government at all levels to gather development aspirations in all areas of community life. However, unfortunately, so far Musrenbang activities at all levels still face low participation from women's groups, in fact their participation tends to be considered only symbolic. As a consequence, many planned programs are gender biased, where discussions are dominated by infrastructure and economic development plans. Based on this, the author is interested in comparing the level of women's participation in the Village Development Planning Conference (Musrenbangdes) in Gampong Beurawe and Gampong Jawa which have quite different levels of development to see the level of women's participation in Musrenbangdes in the two gampongs. Apart from that, we will see what factors influence high or low participation in the two gampongs. This research uses a comparative analysis method with a qualitative approach and data collection techniques in the form of observation, interviews and documentation obtained from the two variables studied. The results of this research show that the level of women's participation in Gampong Beurawe is better than the level of women's participation in Gampong Jawa in the Musrenbangdes in both gampongs. The factors that influence high and low levels of participation are educational, cultural and political factors
Menyibak Penerapan PSAK 102 Atas Prosedur Akad Murabahah
No full textThis study aims to determine how the procedure or implementation of the murabahah financing contract at KSPPS BMT ARMA is it in accordance with PSAK 102 concerning murabahah or not. This research explains how the murabahah financing contract in KSPPS BMT ARMA. This study also discusses PSAK 102 regarding murabahah. The method used in this research is descriptive qualitative. This research was conducted at KSPPS BMT ARMA Magelang. In collecting data, the author uses several methods including observation is a method of direct observation carried out by researchers and interview methods. The results of the study can be seen that the accounting treatment of murabahah financing carried out at BMT ARMA is in accordance with accounting principles, namely PSAK 102
Application of Replicate Organism Detection and Counting Method (RODAC) in Measuring Mycobacterium Tuberculosis Contamination in High Burden Laboratories
No full textBackground: Technicians working in high burden tuberculosis (TB) laboratories pose a higher risk of being infected by Mycobacterium tuberculosis from clinical samples. Contamination control is mandatory to detect the release of bacteria into the working environment and to minimize the risk of exposure to the workers. The contamination measurement is rarely performed due to the lack of standard methodology. This study optimized and applied a unique culture-based method named Replicate Organism Detection and Counting (RODAC) plates to assess the presence of M. tuberculosis contaminant in the laboratory with high burden of clinical samples. Methods: RODAC was applied on twenty working surfaces in the Mycobacteriology Laboratory of Universitas Padjadjaran. The results of RODAC were compared with DNA-based detection from the same working surfaces using in-house IS6110 real-time PCR (IS6110-qPCR). The detection limit of the RODAC plate was 19.6 CFU mL-1.Results: From all working surfaces tested, two distinct colonies were found on RODAC plate stamped on the Ziehl-Neelsen staining basin. Those colonies were identified as M. tuberculosis and non-tuberculous mycobacteria (NTM), as confirmed by the MPT64 antigen test and the presence of acid-fast bacilli. IS6110-qPCR detected the presence of M. tuberculosis DNA in ten sampling points, including the ZN staining basin, incubators, and microscopy areas. IS6110-qPCR detected more working surface contamination versus RODAC. However, it was noted that RODAC, which was a culture-based method, detected live bacteria, while PCR could not distinguish between live and dead bacteria.Conclusion: The application of the RODAC plate is more suitable for monitoring the contamination of live bacteria in the working environment and to inform a proper corrective action
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