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All Journal HAYATI Journal of Biosciences Microbiology Indonesia Media Penelitian dan Pengembangan Kesehatan Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Jurnal Biotek Medisiana Indonesia Medical Journal of Indonesia Sari Pediatri Paediatrica Indonesiana Indonesian Journal of Obstetrics and Gynecology (Majalah Obstetri dan Ginekologi Indonesia) The Indonesian Journal of Infectious Diseases Eksakta : Berkala Ilmiah Bidang MIPA Journal of the Indonesian Medical Association : Majalah Kedokteran Indonesia JKKI : Jurnal Kedokteran dan Kesehatan Indonesia Makara Journal of Science Journal of Clinical Microbiology and Infectious Diseases Jurnal Kefarmasian Indonesia

Fera Ibrahim

Departemen Mikrobiologi Fakultas Kedokteran Universitas Indonesia/KSM Mikrobiologi Klinik RSUPN Dr Cipto Mangunkusumo, Jakarta, Indonesia

Author-ID : 284826

Agriculture, Biological Sciences & Forestry Astronomy Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Computer Science & IT Decision Sciences, Operations Research & Management Earth & Planetary Sciences Education Energy Engineering Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Mathematics Mechanical Engineering Medicine & Pharmacology Neuroscience Public Health

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Perbedaan Sekuens Asam Amino Epitop Sel B dan Sel T pada Protein Hemaglutinin (H) Antara Virus Campak Liar dan Virus Vaksin di Indonesia Made Setiawan; Agus Sjahrurachman; Fera Ibrahim; Agus Suwandono
Sari Pediatri Vol 10, No 3 (2008)
Publisher : Badan Penerbit Ikatan Dokter Anak Indonesia (BP-IDAI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14238/sp10.3.2008.190-5

Latar belakang. Protein H virus campak sangat penting agar virus dapat menginfeksi sel pejamu. Selain itu, protein H dapat merangsang antibodi spesifik yang dapat menetralisasi virus campak, sehingga virus tidak dapat menginfeksi sel. Bila ada perbedaan sekuens asam amino epitop sel B dan sel T pada protein H antara virus campak liar dan virus vaksin campak, maka vaksin tidak dapat merangsang terbentuknya antibodi protektif.Tujuan. Mengetahui perbedaan sekuens asam amino epitop sel B dan sel T pada protein H antara virus campak liar (G2, G3, dan D9) dan virus vaksin CAM-70, Schwarz dan Edmonston-wt.Metode. Ekstraksi dan amplifikasi gen dilakukan di laboratorium menggunakan teknologi biologi molekuler dan analisis gen dan protein dilakukan menggunakan teknologi bioinformatika.Hasil. Ditemukan perbedaan sekuens asam amino epitop sel T pada protein H antara virus campak liar dan virus Edmonstone-wt, sedangkan antara virus campak liar dan virus vaksin (CAM-70 dan vaksin Schwarz) tidak ditemukan perbedaan. Ditemukan perbedaan sekuens asam amino pada epitop sel B protein H antara virus campak liar dan virus vaksin (CAM-70 dan Schwarz, sedangkan antara CAM-70 dan Schwarz tidak ditemukan perbedaan.Kesimpulan. Tidak ada perbedaan sekuens asam amino epitop sel T antara virus campak liar dan virus vaksin (Schwarz dan CAM-70). Perbedaan ditemukan pada epitop sel B antara virus campak liar dan virus vaksin (CAM-70 dan Schwarz).

Difference of hemaglutinins between wild-type and vaccine measles virus in Indonesia Made Setiawan; Agus Sjahrurachman; Fera Ibrahim; Agus Suwandono
Paediatrica Indonesiana Vol 48 No 1 (2008): January 2008
Publisher : Indonesian Pediatric Society

Background Hemaglutinin (H) protein of measles virus is veryimportant in the process of host cell infection. H protein is alsoable to induce specific antibodies which can neutralize measlesvirus and block the cell infection.Objective This study aimed to explore the nucleotide and aminoacid sequence differences between wild-type measles virus (G2,G3 and D9) with CAM-70, Schwarz and Edmonston-wt vaccinevirus.Methods The exctration and amplification of the gene wereconducted in the laboratory using biomolecular technology. Thegene and protein analysis were conducted using the bioinformatictechnology.Results The results showed that the differences in nucleotidesequences were highest between wild-type virus and CAM-70vaccine virus (76-77 nucleotides), followed by Schwarz (61-64nucleotides) and Edmonston (60-63 nucleotides). The differencesin amino acid sequences were highest between wild-type virusand CAM-70 (24-29 residues), followed by Schwarz (13-20residues) and Edmonston (12-19 residues).Conclusion The Indonesian wild-type measles virus was geneticallycloser to Schwarz vaccine virus than CAM-70 vaccine virus,hence the neutralizing antibodies generated by Schwarz vaccinewere more specific against Indonesian wild-type virus comparedto CAM-70 vaccine.

Differences of nucleotide and amino acid sequences of nucleoprotein (N) gene between wild-type measles virus and vaccine virus in Indonesia Made Setiawan; Agus Sjahrurachman; Fera Ibrahim; Agus Suwandono
Paediatrica Indonesiana Vol 48 No 2 (2008): March 2008
Publisher : Indonesian Pediatric Society

Background Measles virus is a member of genus morbiliviruswhich belongs to family paramyxovirus with negative, single-strand RNA genome. RNA is packed by nucleocapsid (N) protein.The N protein is very important for RNA replication andtranslation. Abnormality in N protein will induce abnormality invirus replication.Objective This study aimed to explore the differences ofnucleotide sequence of N gene and amino acid sequences of Nprotein between wild-type measles virus (G2, G3 and D9) andvaccine virus (CAM-70, Schwarz and Edmonston-wt)Methods The exctraction and amplification of the gene wereconducted in the laboratory using biomolecular technology. Thegene and protein analysis were conducted using the bioinformatictechnology.Results The results showed that more differences were foundbetween nucleotide sequences of N gene of wild-type measlesvirus against CAM-70 vaccine virus (77 â€“ 79 nucleotides)compared against Schwarz and Edmonston-wt vaccine virus (71-74 nucleotides). Likewise, more differences were also observedbetween amino acid sequences of N protein of wild-type measlesvirus against CAM-70 vaccine virus (18-24 residues) comparedagainst Schwarz and Edmonston-wt vaccine virus (17-23 residues).

Critical site differences of fusion protein between wildtype and vaccine measles virus strains in Indonesia Made Setiawan; Agus Sjahrurachman; Fera Ibrahim; Agus Suwandono
Paediatrica Indonesiana Vol 51 No 3 (2011): May 2011
Publisher : Indonesian Pediatric Society

Background Measles virus can cause high morbidity andÂ mortality in infants and children. Fusion glycoprotein (F protein)Â found in the viral envelope is important for the host cell infectionÂ mechanism. F protein is immunogenic and may cause specificÂ immune responses in the host. High variability is found in the FÂ protein gene of vaccine viral strains compared to 'Wild type strains.Â This amino add sequence variability may result in a less specificÂ immune response against other strains, possibly rendering thevaccine to be less effective.Objective To detennine the amino add sequence differences inÂ critical sites of F protein in Mld type and vaccine measles virusÂ strains in Indonesia.Methods We compared amino acid sequences of three genotypesÂ of Mld type measles virus (02, 03 and D9) to those of theÂ vaccine strains, CAMô€€¸ 70, Schwarz, and Edmonstonô€€¸wt typeÂ measles virus.Resul ts Analysis showed that there were differences at Flô€€¸F2Â cleavage site, B cell epitopes, and H protein binding site betweenÂ the CAMô€€¸70 vaccine viral strains and Mld type strains. SchwarzÂ vaccine strain differed from the wild type strains at the H proteinÂ binding site. A 03 wild type strain potential glycosylation site wasÂ also different from all other strains studied.Conclusion There were differences in the critical sites of F proteinÂ between Mld type strains and the CAMô€€¸70 and Schwarz vaccineÂ strains.Â

Antigenic differences between wildtype measles viruses and vaccine viruses in Indonesia Made Setiawan; Agus Sjahrurachman; Fera Ibrahim; Agus Suwandono
Paediatrica Indonesiana Vol 48 No 3 (2008): May 2008
Publisher : Indonesian Pediatric Society

Background Measles virus has a single, negative strand RNAgenome which codes 6 structural proteins: N, F, P M, H and L.Currently there are several variances in the nucleotide sequencesof N, F, M and H genes across wild type measles viruses, hencemeasles viruses can be categorized into clades and genotypes. Theantigenicity of the previous genotype of measles is different fromthe current genotype.Objective To determine the antigenic differences between wildtype measles virus and measles vaccine virus.Methods Analysis of the antigenic differences between wild typevirus (G2, G3 and D9) and vaccine virus (CAM-70 and Schwarz)was performed by immunizing mice with the respective viruses.The serum was then tested with micro-cross-neutralizationtechnique using the G2, G3, D9 and CAM-70 virus. Tests withcross ELISA examination technique were also performed usingthe same set of virus.Results Analysis of the cross neutralization test and cross ELISAshowed that the highest antigenicity reaction was found betweenwild type virus with antibody against wild type virus, while thelowest reaction was between wild type virus with antibody againstCAM-70.Conclusions We conclude that the antigenicity of antigenic proteinfrom wild type virus is higher than antigenicity of vaccine virusprotein. In addition, it was found that the antigenicity of proteinsfrom Schwarz vaccine virus was higher than proteins CAM-70vaccine virus.

Level of Retinol Deposit and Cervical Cancer Tofan W Utami; Fera Ibrahim; Gatot Purwoto; Wely L Tiffani; Muhammad F Aziz; Andrijono Andrijono
Indonesian Journal of Obstetrics and Gynecology Volume. 5, No. 1, January 2017
Publisher : Indonesian Socety of Obstetrics and Gynecology

Objective: To analyze level of retinol deposit sufficiency in the natural history of cervical cancer. Methods: Serum retinol level was measured by ELISA from peripheral blood of subjects with normal cervix, cleared and persistent high risk human papilloma virus (HR-HPV) subclinical infection, and cervical cancer who fulfilled the inclusion and exclusion criteria. The study was held in Dr. Cipto Mangunkusumo and Fatmawati Hospital, Jakarta, within 2 years (August 2013- 2015). Blood was taken twice, consisting of post-8-hour fasting blood and 2 hours after 6000 IU retinyl palmitate oral administration. Results: Of 47 total samples, sufficient level of retinol deposit in normal cervix, cleared and persistent HR-HPV subclinical infection, and cervical cancer group was 85.0% (reference), 75.0% (OR 1.89), 33.3% (OR 11.33), and 75% (OR 1.89); respectively. Statistically, there was no significant difference from sufficiency level of retinol deposit between normal cervix and clearance HR-HPV subclinical infection (p=0.628), normal cervix and persistent HR-HPV subclinical infection (p=0.078), normal cervix and cervical cancer (p=0.433), cervical cancer and clearance HR-HPV subclinical infection (p=1.000), cervical cancer and persistent HR-HPV subclinical infection (p=0.430), persistent and clearance HR-HPV subclinical infection group (p=0.740). Conclusion: This study proves that normal cervix group has the highest level of retinol deposit sufficiency; however, it cannot be stated that cervical cancer group has less sufficiency level. Persistent HR-HPV subclinical infection group has the lowest level of retinol deposit (OR 11.33). There is no association between sufficient level of retinol deposit and clearance of HR-HPV. [Indones J Obstet Gynecol 2017; 5-1: 46-54] Keywords: cervical cancer, HR-HPV clearance, retinol deposit

Deteksi Acinetobacter baumannii Multiresisten Obat Penghasil Biofilm menggunakan Pewarnaan Berbasis Crystal Violet Ardiana Kusumaningrum; Iin Maemunah; Dimas Seto Prasetyo; Fera Ibrahim; Budiman Bela
The Indonesian Journal of Infectious Diseases Vol 5, No 2 (2019): The Indonesian Journal of Infectious Disease
Publisher : Rumah Sakit Penyakit Infeksi Prof Dr. Sulianti Saroso

Pendahuluan: Kasus infeksi terkait biofilm merupakan masalah besar pada dunia kesehatan karena sifat kekebalannya terhadap antibiotik dan respon imun, terutama pada kasus infeksi kronik akibat Acinetobacter baumannii. Saat ini terdapat berbagai metode deteksi pembentukan biofilm, namun pemeriksaan tersebut belum dilakukan secara rutin karena berbagai keterbatasan. Oleh karena itu, perlu dilakukan optimasi metode deteksi biofilm menggunakan bahan yang rutin tersedia di laboratorium serta mengukur proporsi sampel yang mengandung bakteri penghasil biofilm Metode: Desain penelitian ini adalah uji eksperimental. Pada penelitian ini dilakukan pengembangan deteksi pembentukan biofilm menggunakan metoda tabung microcentrifuse tube 1,5 ml berbahan polypropylene dengan zat warna berbasis crystal violet konsentrasi 0,1% dan 1%. Optimasi yang dilakukan meliputi media biakan, lama inkubasi, inokulum bakteri yang digunakan serta bahan pembilas. Isolat bakteri Pseudomonas aeruginosa ATCC 10145, A. baumannii ATCC 19606 dan Staphylococcus aureus ATCC 25923 digunakan sebagai kontrol positif dan kontrol negatif pemeriksaan yang dilakukan. Hasil: Pemeriksaan optimasi yang dilakukan, diperoleh kondisi optimal pembentukan biofilm menggunakan media Luria Bertani dengan besar inokulum 1 sengkelit penuh, lama inkubasi 30 jam dan pewarnaan dilakukan menggunakan crystal violet 0,1% serta bahan pembilas berupa PBS steril. Proporsi pembentukan biofilm pada A. baumannii multiresisten obat sebesar 55,3%. Kesimpulan: Metode deteksi pembentukan biofilm menggunakan metode tabung polypropylene yang dimodifikasi dan pewarnaan zat warna crystal violet 0,1% merupakan metode deteksi yang mudah dikerjakan, reproducible dan efisien, sehingga dapat dilakukan di laboratorium mikrobiologi klinik sederhana. Proporsi bakteri penghasil biofilm adalah lebih dari 50% A. baumannii resisten multiobat.

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.

Multidrug Resistance and Extensively Drug-Resistance in Staphylococcus aureus, Staphylococcus epidermidis, and Staphylococcus haemolyticus Cliff Clarence Haliman; Dimas Seto Prasetyo; Conny R Tjampakasari; Fera Ibrahim; T Mirawati Sudiro
Microbiology Indonesia Vol. 16 No. 2 (2022): December
Publisher : Indonesian Society for microbiology

Antimicrobial resistance in bacteria has become a leading global public health issue. Staphylococcus sp. has an efficient mechanism to deal with antimicrobial agents that make them hard to treat in hospital-acquired and community-acquired infections. This study was conducted due to limited data about multidrug resistance and extensively drug resistance in Staphylococcus sp. in Indonesia. This study was a descriptive retrospective study using a cross-sectional design to get the prevalence and antimicrobial susceptibility of S. haemolyticus, S. aureus, and S. epidermidis. The data was secondary data extracted from WHONET 2022 software. This studyâ€™s data were from bacteria from samples sent to UKK LMK FKUI, Jakarta from 2017 to 2021 for routine diagnostic. In this study, we found that the prevalence of methicillin-resistant S.aureus was 24,9%, methicillin-resistant S.epidermidis was 65,5%, and methicillin-resistant S.haemolyticus was 86,8%. The prevalence of MDR S.aureus is less than S.epidermidis and S.haemolyticus, respectively. MDR S.haemolyticus was consistently above 85% each year, while S.epidermidis was above 50% and S.aureus was below 50%. XDR Staphylococcus was only found in S.aureus and S.haemolyticus, i.e. three and seven XDR isolates of S.aureus and S.haemolyticus respectively during 2017-2021. Although we could not find any pan-resistant isolates from all samples, we found methicillin-resistant S.aureus and S.haemolyticus isolates that were also resistant to vancomycin and linezolid. S.haemolyticus dan S. epidermidis were an important coagulase-negative Staphylococcus species that canâ€™t be neglected due to the high percentage of MDR and the discoveries of XDR in S.haemolyticus so that they have the potential to disseminate resistance plasmids to the more virulent bacteria. Therefore we need to control the use of antimicrobial agent to prevent this resistance.

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.

Co-Authors . Andriansjah . DARMINTO . DARMINTO Ade P.R. Simaremare Agus Sjahrurachman Agus Sjahrurachman Agus Sjahrurachman Agus Sjahrurachman Agus Suwandono Agus Suwandono Agus Suwandono Agus Syahrurachman Akrom, Akrom Amin Soebandrio Andi Yasmon Andrijono Andrijono Andrijono Andrijono Anna, Shoffiana Noor Ardiana Kusumaningrum Ariyani Kiranasari Aroem Naroeni Aroem Naroeni Atna Permana Beti Ernawati Dewi Betty Ernawati Budiman Bela C Rinaldi A Lesmana Cliff Clarence Haliman Conny R Tjampakasari DIAH ISKANDRIATI Dimas Seto Prasetyo Elisna Syahruddin Endang R. Sedyaningsih Fithriyah Fithriyah Fithriyah Fithriyah Gatot Purwoto GINA SAMAAN Hartiyowidi Yuliawuri Herna Herna Herna, Herna Iin Maemunah Kemal Fariz Kalista, Kemal Fariz Ketut Tuti Parwati Krisna N.A. Pangesti Kuntjoro Harimurti Lola Febriana Dewi Louisa Ivana Utami Made Setiawan Made Setiawan Made Setiawan Mardiastuti H Wahid Mardiastuti Mardiastuti Melinda Remelia Mirna Robert D.R. van Beest Holle Muhammad F Aziz Muhammad F Aziz Mursinah Mursinah Mursinah Mursinah Mursinah, Mursinah NI LUH PUTU INDI DHARMAYANTI NI LUH PUTU INDI DHARMAYANTI Ni Luh Putu Indi Dharmayanti Ni Made Adi Tarini Ni Nengah Dwi Fatmawati Pratiwi Pujilestari Sudarmono Rela Febriani Rino Alvani Gani RISA INDRIANI Samsuridjal Djauzi Scania, Alifah Evi Silvia Tri Widyaningtyas Simon Yosonegoro Liem Subangkit Subangkit Suzanna Immanuel T Mirawati Sudiro Tiffani, Wely L Tjahjani M. Sudiro Tjahyani M. Sudiro Tofan W Utami Tofan W Utami VIVI SETIAWATY Vivi Setiawaty Wely L Tiffani Yeva Rosana Yulia Rosa Saharman YULIANTY MUHAYAR Yuliar Budi Hartanto Yuyun Soedarmono

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