129 research outputs found
Comparison of Interpretation between Pyrosequencing and Xpert MTB/RIF Assay in Multidrug-Resistant Tuberculosis
Get PDFIndonesia 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
Get PDFBackground: 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
STRATEGIPEEREDUCATOR DALAMPENINGKATAN KESADARANPEKERJASEKSPEREMPUAN TERHADAPKESEHATANREPRODUKSI (StudiProgramPencegahanHIV/AIDSuntukpekerjaseks perempuanolehPerkumpulanKeluargaBerencanaIndonesia SumateraBarat)
Get PDFABSTRAK
LIDYA FEBRINA, 1510812020. Jurusan Sosiologi, Fakultas Ilmu Sosial dan Ilmu Politik Universitas Andalas Padang. Judul Skripsi: Strategi Peer Educator Dalam Peningkatan Kesadaran Pekerja Seks Perempuan Terhadap Kesehatan Reproduksi (Studi dalam Program “Pencegahan HIV/AIDS untuk Pekerja Seks Perempuan” oleh Perkumpulan Keluarga Berencana Indonesia Sumatra Barat). Pembimbing I, Dr. Jendrius, M.Si dan Pembimbing II, Drs. Yulkardi, M.Si
Skripsi ini membahas tentang Strategi peer educator dalam peningkatan kesadaran pekerja seks perempuan terhadap kesehatan reproduksi. Tujuan dari penelitian ini adalah 1) Mendeskripsikan bentuk-bentuk strategi yang digunakan peer educator dalam memberikan edukasi mengenai kesehatan reproduksi pekerja seks perempuan 2) Mengidentifikasi hambatan peer educator dalam memberikan edukasi mengenai kesehatan reproduksi kepada pekerja seks perempuan.
Teori yang digunakan dalam penelitian ini adalah Teori Pertukaran Sosial dari George C, Homans. Sementara pendekatan yang digunakan adalah pendekatan kualitatif dengan tipe penelitian deskriptif. Informan dalam penelitian ini ditentukan dengan menggunakan teknik purposive sampling dan snowball sampling. Untuk mendapatkan data, penulis menggunakan teknik wawancara mendalam dan observasi.
Hasil penelitian menunjukkan bahwa peer educator yang telah menjalankan perannya sesuai dengan tugas pokok dan fungsi yang ditetapkan mampu meningkatkan kesadaran pekerja seks perempuan akan kesehatan reproduksinya, baik itu kesadaran untuk melakukan tes VCT, penggunaan kondom saat berhubungan seks, maupun memiliki kendali penuh akan kesehatan alat reproduksinya sehingga ia bisa meyakinkan pelanggannya untuk mau menggunakan kondom saat melakukan hubungan seks. Peningkatan kesadaran ini terjadi berhubungan dengan strategi dan hambatan peer educator dalam memberikan edukasi mengenai kesehatan reproduksi tersebut. Strategi peer educator dalam memberikan edukasi mengenai kesehatan reproduksi yaitu 1) melalui paksaan, 2) melalui nasihat, 3) melalui persuasi, Sementara hambatan yang ditemukan peer educator dalam memberikan edukasi mengenai kesehatan reproduksi yaitu: 1)kurangnya ketersediaan waktu yang dimiliki peer educator dalam memberikan edukasi kepas pekerja seks perempuan, 2) kesulitan berkomunikasi, (3) razia dadakan yang dilakukan Satpol PP, 4) ketidakpercayaaan pekerja seks perempuan terhadap peer educator.
Kata Kunci: Strategi, Peer Educator, Pekerja Seks Perempuan, Kesehatan Reproduksi, HIV/AIDS
ABSTRACT
LIDYA FEBRINA, 1510812020. Department of Sociology, Faculty of Social and Political Sciences University Andalas Padang.These title: Peer Educator strategies in incrase awareness of women sex workers about reproductive health (study in the Program "Prevention of HIV/AIDS for female sex workers" by Perkumpulan Keluarga Berencana Indonesia of West Sumatra). Supervisor I, Dr. Jendrius, M.Si and Supervisor II, Drs. Yulkardi, M.Si
This these discusses peer educator strategies in raising awareness of female sex workers against reproductive health. The purposes of this research were 1) identifying the strategy used by peer educator to educate the reproductive health of female sex workers 2) identify a peer educator barrier in providing education on Reproductive health to female sex workers.
The theory used in the study was the social that exchange theory of George C, Homans. While the approach used is a qualitative approach to the type of descriptive research. The informant in this study was determined using purposive sampling technique. To get data, the author uses deep interview techniques and observations that use self disclousure.
The results showed that the peer educator that had performed its role in accordance with the basic tasks and established functions were able to raise the awareness of female sex workers to the health of the reproductions, be it awareness to do the VCT test , the use of condoms during sex, or to have full control of the health of its production equipment so that it can convince its customers to want to use condoms when having sex. This increased awareness occurred in relation to the strategy and obstacles of peer educator in providing education about the reproductive health. The strategy of peer educator in providing education on reproductive health is: 1) through Compulsion, 2) through Counsel, 3) through persuasion, while barriers found in peer educator in providing education on reproductive health are: 1) The lack of time availability of peer educator in providing education for women's sex workers, 2) difficulty in communicating, 3) The Imprompia raid of Satpol PP, 4) The unbelief of female sex worker against peer educator.
Keywords: Strategy, Peer Educator, female sex worker, reproductive health, HIV/AID
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
Biological science 3D modelling
Get PDFFunded by the Government of Ontario.This project creates 3D printable models that instructors can use to illustrate lecture content, and students and teaching assistants can manipulate the models to better facilitate understanding of the physical space and relationships of biological systems, organs, and cells. It supports experiential learning for biological science courses and increases access to enhanced learning for diverse groups of students. In order to help learning in biological science courses, we will offer a library of 3D-printable files for significant biology models. These files can be used to both augment textbook content and improve hands-on learning in the lab.The views expressed in this publication are the views of the author(s) and do not necessarily reflect those of the Government of Ontario or the Ontario Online Learning Consortium (eCampusOntario)
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
Pengembangan Kunci Pintu Pintar Berbasis Radio Frequency Identification (RFID)
No full textIn this design, the author plans to give a little new touch in the area of access control, automatic open system. This design is planned to provide system access with security. Where security is made using a card and password. However, the main focus of this research is the access that is developed using a card, more specifically the e-KTP.The methodology used in this research is library research. This study was conducted to find, collect and study data from books related to the problems discussed in this study. library research and home research using C programming. By utilizing Arduino, it is hoped that it will facilitate and increase security in accessing the doo
Towards an Information System of Modeling and Monitoring of Cikapundung River, Bandung, Indonesia
No full textAbstractGrowing recognition of the need for water safety makes river water quality monitoring information and modelling usage more important to be accessed by many stakeholders. Cikapundung River which is located in the heart of Bandung City has its water for many purposes. In the other hand, the water of this river suffers as a result of wastes disposal from existing activities on its banks. Several agencies conduct regular monitoring, both discharge and water quality of this river. However, the monitoring results are not published openly. The data can only be obtained by visiting the monitoring agency. This procedure may result a non-optimal usage of the data, and can even be harmful when unsafe water is used for consumption need. An information system of monitoring data and modelling of Cikapundung River water quality is proposed to improve the method of data publication. Modelling of Cikapundung River water quality is also developed to have simple software for DO and BOD calculation simulation. The modelling is using Streeter-Phelps equation for DO calculation and first-order reaction of Phelps law for BOD calculation. The deoxygenation rates used in the software were obtained from the laboratory experiments, i.e. 0.01-0.37 per day
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