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All Journal HAYATI Journal of Biosciences SAINS MEDIKA : JURNAL KEDOKTERAN DAN KESEHATAN Jurnal Ilmiah Aplikasi Isotop Radiasi Microbiology Indonesia Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Journal of Biomedicine and Translational Research The Indonesian Biomedical Journal Biomedical Journal of Indonesia Universa Medicina Indonesian Journal of Biotechnology and Biodiversity The Indonesian Journal of Infectious Diseases Eksakta : Berkala Ilmiah Bidang MIPA Majalah Kedokteran Andalas Health Information : Jurnal Penelitian Jurnal Ners East Asian Journal of Multidisciplinary Research (EAJMR) Journal of Comprehensive Science Makara Journal of Health Research Makara Journal of Science Journal of Clinical Microbiology and Infectious Diseases Indonesian Journal of Biomedicine and Clinical Sciences

Andi Yasmon

Department Of Microbiology, Faculty Of Medicine Universitas Indonesia, Cipto Mangunkusumo Hospital, Jakarta

Author-ID : 422494

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Optimizing Real-Time PCR methods for detection of ssaN gene Salmonella enterica subsp.enterica in the blood specimen Oktania Sandra Puspita; Andi Yasmon; Beti Ernawati Dewi
Journal of Biomedicine and Translational Research Vol 6, No 2 (2020): Augusts 2020
Publisher : Faculty of Medicine, Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jbtr.v6i2.7120

Background Typhoid fever caused by Salmonella typhi is a common acute infection of the reticuloendothelial system, intestinal lymphoid tissue, and gall bladder. Detection of Salmonella spp. is still based on cultures and serological methods.Widal test is one of the serological tests that is still widely used, especially in developing countries including Indonesia.Widal tests have low sensitivity and specificity. They often produce false positive or false negative results.ObjectiveThe aim of this study were i) real time PCR optimization to develop a Salmonella enterica detection system. ii) molecular detection of new target gene (ssaN gene) from blood specimens in typhoid fever patients.Methods An experimental laboratory study was performed from March to October 2016. Extraction of Salmonella typhi DNA is used as templates for the optimization of real time PCR reaction.The blood sample was from patients suspected with typhoid fever obtained from the Menteng Sub-district Health Center according to the inclusion criteria.ResultsSpecificity test of real time PCR showed that the primers and probes used are not cross-react against other microorganisms. Sensitivity test obtained minimal detection is at least 10 cfu/ml of blood specimen. In blood clinical specimens, real time PCR could detect 19 (38%) positive samples of 50 blood specimen from suspected typhoid fever patients. Eleven samples with negative Widal serology gives positive results in real time PCR.ConclusionReal time PCR used in this study can increase the level of rate of positive testing by 22% of the total specimens.Keywords : Salmonella enterica subsp.enterica, typhoid fever, ssaN gene, real time PCR

PREVALENSI ISOLAT MRSA PENGHASIL PANTON-VALENTINE LEUKOCIDIN PADA PASIEN ICU RUMAH SAKIT TERSIER Linosefa Linosefa; Delly Chipta Lestari; Ardiana Kusumaningrum; Anis Karuniawati; Andi Yasmon
Majalah Kedokteran Andalas Vol 39, No 1 (2016): Published in April 2016
Publisher : Faculty of Medicine, Universitas Andalas

Penilitian ini bertujuan untuk mengetahui prevalensi MRSA penghasil Panton-Valentine leukocidin (PVL) dan pola kepekaannya. Sampel penelitian adalah isolat MRSA dari 315 pasien Rumah Sakit Umum Pusat Nasional Cipto Mangunkusumo (RSUPNCM) selama tahun 2011 dan 2014, dengan melakukan identifikasi, uji kepekaan dan uji molekuler terhadap isolat tersebut. Penelitian ini menunjukkan sebanyak 59% dari koloni MRSA yang ditemukan masih sensitif terhadap antibiotik golongan selain β-laktam, sehingga masih dapat diduga sebagai community-associated MRSA (CA-MRSA). CA-MRSA sepertinya mulai ditransmisikan di fasilitas kesehatan. Uji molekuler terhadap isolat MRSA memberikan hasil 8,3% isolat MRSA menghasilkan PVL. Berdasarkan tipe pola kepekaannya isolat MRSA penghasil PVL tersebut masih dapat digolongkan sebagai CA-MRSA. MRSA penghasil PVL ditemukan di RSUPNCM sebagai kolonisasi. Surveilan perlu dilakukan untuk memahami interaksi antara MRSA di komunitas dan rumah sakit, terutama untuk mengurangi transmisi di fasilitas kesehatan.

IDENTIFICATION OF INTESTINAL MICROBES IN CHILDREN WITH DIARRHEA ANDNON-DIARRHEA USING POLYMERASE CHAIN REACTION / ELECTROSPRAY IONIZATION-MASS SPECTROMETRY (PCR / ESI-MS) Teguh Sarry Hartono; Dewi Murniati; Andi Yasmon; Lucky H Moehario
The Indonesian Journal of Infectious Diseases Vol 2, No 2 (2015): THE INDONESIAN JOURNAL OF INFECTIOUS DISEASES
Publisher : Rumah Sakit Penyakit Infeksi Prof Dr. Sulianti Saroso

Abstract :Microbiota present in human intestinal are diverse, and imbalance in composition of intestinal flora may cause diarrhea.This study aimed to obtain a profile of intestinal bacteria in children with and without diarrhea and assess their presence with incidence of diarrhea. An analitical descriptive with cross sectional design study was carried out. A stool specimen was collected from each children of 2-12 years old with and without diarrhea who lived in North Jakarta. DNA extraction was performed prior to detection of microbes using Polymerase Chain Ceaction/Electrospray Ionization-Mass Spectrometry.Eighty stool specimens consisted of 33 and 47 specimens from children with and without diarrhea were included in the study. Thirty single and 6 multiple matches were detected in 30 specimens of the diarrhea group; 28 single and 8 multiple matches were found in 34 specimens of the non-diarrhea.Escherechiacoli and Klebsiella pneumonia were predominant in both groups. Firmicutes, Proteobacteria and Bacteroidetes were deteced in the diarrhea group, while Actinobacteria, Proteobacteria and Verrucomicrobia were in the non-diarrhea. The relationship of incidence of diarrhea and the present of enteropathogens in the stool was not significant, however, there was a strong correlation of the risk of suffering diarrhea due to the presence of enteropathogens (OR = 0.724 with 95%, CI: 0.237-2.215).In conclusion, most bacteria detected in both groups were similar, nonetheless, Actinobacteria was present only in the non-diarrhea. The chance to have diarrhea was higher when enteropathogen was detected in the stool.

Infections of Chlamydia trachomatis and Mycoplasma hominis as Risk Factors for Abnormal Cervical Cells Mardhia, Mardhia; Effiana, Effiana; Irsan, Abror; Natalia, Diana; Rahmayanti, Sari; Indarti, Junita; Rachmadi, Lisnawati; Yasmon, Andi
Makara Journal of Health Research Vol. 22, No. 1
Publisher : UI Scholars Hub

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Background: Cervical cancer is the fourth most common cancer among women across the world. Recent studies have shown that cervical cancer is not only caused by persistent infection of human papillomavirus (HPV), but sexually transmitted infections (STIs) also play a role in the pathogenesis of abnormal cervical cells. STIs frequently occur with no specific symptoms, such as the infections caused by Chlamydia trachomatis and Mycoplasma hominis. Asymptomatic STIs could lead to persistent infection. Persistent infections caused by STIs have been hypothesised to increase the access of HPV into the deeper cervical tissue and cause cervical cell abnormalities. Therefore, we conducted this study to assess the association between C. trachomatis and M. hominis infections and abnormal cervical cells. Methods: A cross-sectional study was performed on 58 outpatients at the Department of Obstetrics and Gynecology, Dr. Cipto Mangunkusumo Hospital, Jakarta, Indonesia. Abnormal cervical cells were detected by a liquid-based cytology Pap smear, and bacterial identification was done by conducting conventional duplex polymerase chain reaction (PCR). Results: 58 patients, 14 (24.1%) showed abnormal cervical cells, whereas 44 (75.9%) patients showed normal cervical cells. The conventional duplex PCR demonstrated a positive result for C. trachomatis and M. hominis bacterial infections in only 1 (7.1%) and 2 (14.3%) patients with abnormal cervical cells, respectively. The statistical analysis revealed no significant association between the bacterial infections and the abnormal cervical cytology in the patients (p > 0.05). Conclusions: Infections caused by C. trachomatis and/or M. hominis were not associated with abnormal cervical cells.

Optimization of pGEX System to Express and Isolate Mycobacterium tuberculosis Inclusion Body Protein in Combining with Modified Refolding Method Rukmana, Andriansjah; Burhanuddin, Burhanuddin; Yasmon, Andi
Makara Journal of Science Vol. 22, No. 4
Publisher : UI Scholars Hub

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Antigen sub units for vaccine studies are typically isolated from recombinant proteins in an expression system. However, not all protein expression systems are used to express the specific protein. In this study,we optimized the pGEX system combined with the modified protein refolding to express and isolate M. tuberculosis proteins, especially proteins that are expressed as an inclusion body. Resuscitation promoting factor B (RpfB) protein is one of the Resuscitation promoting factor (Rpf) family of proteins that has been studied for its ability to induce cellular immunity in animal tests. Silico analyses demonstrate how RpfB is included in cell wall and cell processes. The Rpf family proteins are promising antigens that can be used as a TB vaccine candidate. The polymerase chain reaction was briefly performed using specific primers to amplify the full length of the rpfB. PCR amplification products were then purified, cut by restriction endonucleases, and cloned into pGEX 6-P1. Protein expression was done in the Escherichia coli BL21 strain, and expressed protein was isolated using themodified protein refolding and solubilization method. The complex protein expression that appeared as inclusion bodies were successfully isolated and can be detected as complex GST-RpfB through the western blotting process. Our study results indicate that this system and our modified method are suitable for M. tuberculosis inclusion body protein expression and isolation.

A comparison study of GeneXpert and In-House N1N2 CDC Real-Time RT-PCR for detection of SARS-CoV-2 infection Andi Yasmon; Lola Febriana Dewi; Fithriyah Fithriyah; Ariyani Kiranasari; Andriansjah Rukmana; Yulia Rosa Saharman; Fera Ibrahim; Pratiwi Sudarmono
Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Vol 54, No 3 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19106/JMedSci005403202203

COVID-19 is a disease caused by SARS-CoV-2, a new virus from genus β-coronaviruses. This disease has been declared a pandemic by WHO on 11 March 2020 until now. The nucleic acid tests are the most frequently used assays because of their high sensitivity and specificity. One of the tests is the GeneXpert, a real-time reverse transcription polymerase chain reaction (rRT-PCR)-based assay platform. The use of the GeneXpert shows great public health interest because of the rapid (50 min), the minimum number of trained staff, and less infrastructure and equipment. However, there are limited data on the application of the GeneXpert for the detection of SARS-CoV-2. Therefore, we conducted a comparative study between the GeneXpert and in-house N1N2 CDC rRT-PCR assay. Of 86 samples, 17 were rRT-PCR positive while 13 were GeneXpert positive. Of rRT-PCR positive 17 samples, 7 were GeneXpert negative [58.82% (10/17] sensitivity]. We also found that 3 GeneXpert positive samples showed rRT-PCR negative (95.65% [66/69] specificity). It is concluded that negative results by the GeneXpert can not rule out the possibility of SARS-CoV-2 infection, particularly in close-contact individuals and the interpretation of the positive result should be analyzed carefully, particularly amplification with Ct>40.

Peran Vitamin D Dalam Meningkatkan Respons Imunitas Terhadap Infeksi Sars-Cov-2 Diah Dwi Utami; Andi Yasmon
Journal of Comprehensive Science (JCS) Vol. 1 No. 3 (2022): Journal of Comprehensive Science (JCS)
Publisher : Green Publisher Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.36418/jcs.v1i3.47

Coronavirus disease 2019 (COVID-19) perdana ditemukan di Wuhan, Provinsi Hubei, Cina sebagai gangguan pernapasan akut. Etiologi karena varian baru SARS-CoV (SARS-CoV-2). Infeksi manusia dengan SARS-CoV-2 biasanya dikaitkan dengan penyakit pernapasan ringan hingga berat, bermanifestasi sebagai demam tinggi, peradangan parah, batuk serta disfungsi organ dalam, dan bahkan dapat menyebabkan kematian. Bentuk aktif vitamin D memberikan aktivitas pada respons imun bawaan dan didapat serta stabilitas membran endotel. Vitamin D adalah pengatur utama sistem renin-angiotensin yang digunakan oleh virus ini untuk masuk ke sel penjamu. Vitamin D meningkatkan produksi alami peptida anti mikroba dan mengaktifkan sel pertahanan seperti makrofag untuk mendegradasi SARS-CoV-2. Vitamin D memodulasi berbagai mekanisme sistem imunitas untuk menahan virus yang mencakup meredam masuk dan bereplikasi serta mengurangi konsentrasi sitokin pro-inflamasi dan meningkatkan konsentrasi sitokin anti-inflamasi. Namun literatur belum seluruhnya setuju akan hipotesis ini sehingga perlu dibuktikan dengan uji klinis dan dikaji lebih dalam lagi.

Cloning and Expression of HA1 Gene of H1N1 Influenza Virus 2009 Pandemic (H1n1pdm09) Indonesia Strain in the Pichia Pastoris Expression System for the Development of Influenza Vaccine ASRI SULFIANTI; ANDI YASMON; BUDIMAN BELA; FERA IBIRAHIM
Microbiology Indonesia Vol. 9 No. 2 (2015): June 2015
Publisher : Indonesian Society for microbiology

Among influenza viral proteins, hemagglutinin 1 (HA1) is the target for neutralizing antibodies which inhibit virus binding to receptor of target cells. This protein is widely developed as subunit recombinant vaccine. In this research, we expressed HA1 protein recombinant from DKI271/2011 Indonesian strain in Pichia pastoris. The identity of this protein was confirmed by western blotting using anti-His T ag and mouse specific antibody HAÂ H1N1pdm09. The use of yeast P . pastoris as an alternative strategy to solve the problems which commonly found in influenza vaccine productions. Expression protein in E. coli has been known to have many problems, while mammalian and insect cells requires special skills and relatively high cost. The analysis of HA1 gene sequences showed no mutation in epitope region which recognized by T dan B cells. Further, this recombinant protein can be used as vaccine candidate in influenza vaccine development.Keywords: Hemagglutinin; Pichia pastoris; vaccine; Influenza Virus; H1N1pdm09.

Limit of Detection (LOD) of in-house N1N2 CDC real-time RT-PCR assay and commercial kits to detect SARS-CoV-2 Simon Yosonegoro Liem; Fera Ibrahim; Andi Yasmon
Journal of Clinical Microbiology and Infectious Diseases Vol. 2 No. 2 (2022): Available Online: December 2022
Publisher : Indonesian Society for Clinical Microbiology (Perhimpunan Dokter Spesialis Mikrobiologi Klinik Indonesia)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.51559/jcmid.v2i2.23

Introduction: There are two types of SARS-CoV-2 real-time RT-PCR (rRT-PCR) kits used in the laboratory in Indonesia, in-house and commercial kits. Our laboratory developed an in-house kit based on N1N2 CDC. In this study, we reported the In-house kit's Limit of Detection (LOD) compared with several commercial kits. Method: This report was an experimental study conducted in Clinical Microbiology Laboratory, Microbiology Department, FMUI in Jakarta. Commercial SARS-CoV-2 RNA (Vircell, Granada, Spain, Lot No. 20MBC137004-R) was used. The LoD was determined using a 2-fold dilution of the RNA in DNase/RNase-free water (Vircell®). The diluted RNA(s) were used as templates for in-house and commercial rRT-PCR kits. Result: The LOD of in-house rRT-PCR and three commercial kits (BioCoV-19 [Bio Farma], Standard M [SD Biosensor], and Real-Q [BioSewoom]) showed higher sensitivity (3.5 copies/reaction) than Power Chek [Kogenebiotech] (7 copies/reaction). Conclusion: The LOD of our In-house kit showed high performance in sensitivity and comparable with other commercial kit.

TROUBLESHOOTING IN EXPRESSION AND PURIFICATION OF RECOMBINANT SEVERE ACUTE RESPIRATORY SYNDROME-ASSOCIATED CORONAVIRUS NUCLEOCAPSID PROTEIN IN Escherichia coli BL21 Yasmon, Andi; Ibrahim, Fera; Bela, Budiman
Makara Journal of Science Vol. 14, No. 2
Publisher : UI Scholars Hub

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Co-Authors . Andriansjah Abror Irsan Ade P.R. Simaremare Agustini, Riani Anis Anis Anis Karuniawati Ardiana Kusumaningrum Ariyani Kiranasari ASRI SULFIANTI Beti Ernawati Dewi Budiman Bela Burhanuddin Burhanuddin Burhanuddin Burhanuddin Delly Chipta Lestari Delly Chipta Lestari Dewi Murniati Diah Dwi Utami Diana Natalia Diana Natalia Efendi, Ida Effendi, Ida Effiana Effiana Effiana, Effiana Elisabeth D. Harahap Elisna Syahruddin Erlina, Linda Fadilah Fadilah Fadilah FERA IBIRAHIM Fera Ibrahim Fithriyah Fithriyah Fithriyah Fithriyah Fithriyah Fithriyah Gultom, Desy A. Heri Wibowo Ibnu Agus Ariyanto Ika Ningsih Janah, Dariatul Junita Indarti Ketut Tuti Parwati Linosefa Linosefa Lisnawati Rachmadi Lola Febriana Dewi Louisa Ivana Utami Lucky H Moehario Mardhia, Mardhia Mardhia, Mardhia Mardiastuti H Wahid Maria L. Rosilawati Maria L. Rosilawati Maria Lina R. Maria Lina Rosilawati Maya Ulfah Moehario, Lucky Hartati Murti, Anissa Wari Ni Made Adi Tarini Ni Nengah Dwi Fatmawati Normasari Normasari Oktania Sandra Puspita Paramita, Rafika Indah Pramita G. Dwipoerwantoro Pratiwi Pujilestari Sudarmono Purba, Hastuti Handayani S Purnomosidi, Muhammad Abhi Rahayu, Ratih Ratnoglik, Suratno Lulut Rela Febriani Ria Kodariah Rifdah Hanifah Rosa, Yulia Rudyanto Sedono Safari, Dodi Salsabila, Korrie Samsuridjal Djauzi Sari Rahmayanti Simon Yosonegoro Liem SJATHA, FITHRIYAH Sudarmo, Fitrahwati Tafroji, Wisnu Teguh Sarry Hartono Thomas Robertus Tjampakasari, Conny Riana Utami, Diah Dwi VIVI SETIAWATY Winarti, Yayah Wresti Indriatmi B. Makes Wulandari, I Gusti Ayu Inten Yeva Rosana Yulia Rosa Saharman YULIANTY MUHAYAR Yusmaniar Yusmaniar Zaenab

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