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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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ANALISIS GEN HAEMAGGLUTININ PADA VIRUS CAMPAK LIAR Subangkit, Subangkit; Mursinah, Mursinah; Bela, Budiman; Ibrahim, Fera
Media Penelitian dan Pengembangan Kesehatan Vol 25, No 1 Mar (2015)
Publisher : Badan Penelitian dan Pengembangan Kesehatan

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (360.115 KB)

AbstrakPenyakit Campak disebabkan oleh virus campak yang termasuk genus Morbilivirus dan Family Paramyxoviridae. Penyakit campak masih menjadi masalah kesehatan karena masih ditemukan Kejadian Luar Biasa (KLB) di Indonesia. Salah satu penyebab terjadinya KLB tersebut diduga sebagaiakibat perbedaan antigenesitas antara strain vaksin yang digunakan dengan strain virus campak liar yang beredar di Indonesia. Penelitian ini bertujuan mendapatkan gambaran tentang karakteristik genetik gen Haemagglutinin virus campak liar yang ada di Indonesia. Spesimen yang digunakan sebanyak 27 isolat virus penyebab KLB dari 17 propinsi selama periode tahun 2003-2010. Isolat virus dilakukan pemeriksaan secara RT-PCR dan sekuensing dengan metode Sanger. Hasil sekuensing dianalisis dengan menggunakan perangkat lunak Bioedit 7.0 dan MEGA 4.0. Hasil penelitian didapatkan perbedaan 10 asam amino antara virus campak strain vaksin CAM-70 dan virus campak liar pada posisi D416N; K424T; V451M; N455T; V466I; I473T; F476L; Y481S atau Y481N; H495N; G505D. Kesimpulan penelitian ini adalah terdapat perbedaan karakteristik genetik antara virus campak liar di Indonesia berbeda dengan strain virus vaksin CAM-70.Kata kunci : Campak, Analisis Molekuler, Hemagglutinin, CD46AbstractMeasles is caused by virus belonging to the genus Morbilivirus and Family Paramyxoviridae. Measles is still a public health problem because outbreak of measles still found in Indonesia. Outbreak is suspected as a result of differences in antigenicity between vaccine strains used with wild-type measles virus strains circulating in Indonesia. This study aims to get genetic characteristics of wild-type measles virus haemagglutinin gene in Indonesia. The specimens were used 27 viral isolates from 17 provinces period 2003-2010. Viral isolates examined by RT-PCR and sequencing with Sanger method. Sequencing analysis were conducted using Bioedit 7.0 and MEGA 4.0 software. The results showed 10 amino acid differences between the vaccine strain measles virus CAM-70 and wild-type measles virus in position D416N; K424T; V451M; N455T; V466I; I473T; F476L; Y481S or Y481N; H495N; G505D. Conclusion: There is a difference between the genetic characteristics of wild-type measles virus in Indonesia and vaccine strain CAM-70.Keywords : Measles, Molecular Analisys, Haemagglutinin, CD46

Profil Candida penyebab kandidemia dan pola kepekaan terhadap anti jamur pada pasien sakit kritis di Rumah Sakit Cipto Mangunkusuno Mursinah, Mursinah; Ibrahim, Fera; Wahid, Mardiastuti
Jurnal Biotek Medisiana Indonesia Vol 5, No 2 (2016): :
Publisher : Puslitbang Biomedis dan Teknologi Dasar Kesehatan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22435/jbmi.v5i2.7706.105-111

Candida spesies is important cause of nosocomial infection that lead to death and prolonged hospital stay. Guideline management of candidiasis by Infectious Diseases Society of America (IDSA) in 2009 proposed early antifungal therapy in critical patient with the risk of invasive candidiasis. Early identification ofÂ sepsis patien with high risk of fungal infection is challenging becauseÂ long and low result from blood culture. Antifungal usage without appropriate indication can cause resistance to antifungal. The aim of the study is obtain data candida species that caused candidemia in Cipto Mangunkusuno hospital (RSCM) and sensitivity pattern to antifungal. This retrospective study used patient medical record from 2011-2014. This study had 117 candidemia case in RSCM during 2011-2014. Every year candidemia was dominated by CandidaÂ tropicalis, CandidaÂ albicans, and CandidaÂ parapsilosis with trend the increase number of CandidaÂ tropicalis since 2013. Susceptibility pattern of Candida that cause candidemia in RSCM from 71 isolat tested the result was86% spesies Candida flukonazol sensitive, 99% vorikonazol sensitive, 97% amfoterisin B sensitive and 100% flusitosin sensitive.

Level of Retinol Deposit and Cervical Cancer Utami, Tofan W; Ibrahim, Fera; Purwoto, Gatot; Tiffani, Wely L; Aziz, Muhammad F; 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

DAYA ANTI BAKTERI KOMBINASI FOSFOMISIN DAN SULBAKTAM-SEFOPERAZON TERHADAP BAKTERI PSEUDOMONAS AERUGINOSA Agus Syahrurachman; Fera Ibrahim; Atna Permana
Majalah Kedokteran Indonesia Vol 69 No 12 (2019): Journal of The Indonesian Medical Association Majalah Kedokteran Indonesia Volu
Publisher : PENGURUS BESAR IKATAN DOKTER INDONESIA (PB IDI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.1234/jinma.v69i12.164

Pendahuluan: Pseudomonas aeroginosa dapat merupakan penyebab infeksi diberbagai organ. Pilihan antibiotika tunggal untuk itu menjadi lebih sedikit.Tujuan: Menilai daya antibakteri kombinasi fosfomisin dan sulbaktkam-sefoperazon in vitro terhadap isolat klinis Pseudomonas aeruginosa.Metode: Uji kerentanan 30 isolat klinis Pseudomonas aeruginosa terhadap fosfomisin dan sefoperazone-sulbactam sebagai obat tunggal dan kombinasinya dilakukan pada media cair. Daya antibakteri kombinasi fosmisin dan sulbactam sefoperazon ditentukan dengan menghitung Fraction Inhibition Index (FIC). Time-kill curve dinilai pasca paparan bakteri terhadap antibiotika selama waktu tertentu. Hasil: Proporsi isolat yang sensitif sulbactam-sefoperazon sebanyak 66,7% dan meningkat menjadi 90% terhadap kombinasi antibiotika. Proporsi isolat yang sensitif fosfomisin hanya 10% dan meningkat dua kali lipat terhadap kombinasi antibiotika. Efek sinergis, indifferent dan antagonis masing-masing ditemukan pada 60%, 36.7% dan 3.3% isolat. Dari curva time kill disimpulkan bahwa kematian bakteri yang cepat terjadi dalam 4 jam pertama. Kesimpulan: kombinasi sulbaktam sepoferazon dan fosfomisin pada sebagian besar isolat Pseudomonas aeruginosa bersifat sinergis dan hanya 1 galur yang menunjukkan efek antagonis.

The H5N1 influenza virus in Indonesia has caused more than 100 people died due to the virus infections. Cases in humans were mostly due to the virus spread from the infected birds. This study characterized molecularly the H5N1 virus from birds around the H5N1 infection cases in humans in Indonesia. Result from this study revealed that in several cases, waterfowl species could become the source of H5N1 infections in human. We found that the one of six viruses used in this study probably was a fi NI LUH PUTU INDI DHARMAYANTI; FERA IBRAHIM; . DARMINTO; AMIN SOEBANDRIO
HAYATI Journal of Biosciences Vol. 18 No. 2 (2011): June 2011
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.18.2.82

The H5N1 influenza virus in Indonesia has caused more than 100 people died due to the virus infections. Cases in humans were mostly due to the virus spread from the infected birds. This study characterized molecularly the H5N1 virus from birds around the H5N1 infection cases in humans in Indonesia. Result from this study revealed that in several cases, waterfowl species could become the source of H5N1 infections in human. We found that the one of six viruses used in this study probably was a first antigenic shift virus in Indonesia. This study shows that the AI viruses isolated from birds around humans infected by H5N1 virus has specific characteristics namely the presence of several amino acid substitutions especially on the M1 and M2 proteins. The substitutions are similar in most of H5N1 human cases in Indonesia.

Development of a SYBR Green real-time PCR-based assay system for detection of Neisseria gonorrhoeae Andi Yasmon; Rela Febriani; Louisa Ivana Utami; Fithriyah Fithriyah; Yeva Rosana; Fera Ibrahim; Pratiwi Sudarmono
Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Vol 54, No 1 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19106/JMedSci005401202201

Diagnosis of Neisseria gonorrhoeae infection is needed for patient therapy and for reducing this bacterial transmission in the population. The culture method is a gold standard method for N. gonorrhoeae detection, however it has low sensitivity. Among molecular methods with high sensitivity and specificity, SYBR Green real-time PCR is the potential method for N. gonorrhoeae detection. In this study, we developed an SYBR Green real-time PCR-based system assay for N. gonorrhoeae detection. Several PCR conditions were optimized and analyzed including primer annealing temperature, DNA template volume, the limit of detection (LoD), cross-reaction with others (bacteria, viruses, fungus, protozoa), and quality assurance. The results showed that the annealing temperature and DNA template volume were 60oC and 5 µL, respectively. The LoD was 29 DNA copies corresponding to 3 bacterial cells per reaction. No cross-reaction was detected for other bacteria, viruses, fungus and protozoa. The external quality assurances enrolled in 2019 and 2021 showed 100% concordance. The preliminary testing for clinical samples was also 100% concordance. In conclusion, the SYBR Green real-time PCR-based system assay developed in this study is promising for application in clinical laboratories.

Amantadine Resistant of Indonesian H5N1 Subtype Influenza Viruses During 2003-2008 NI LUH PUTU INDI DHARMAYANTI; FERA IBRAHIM; AMIN SOEBANDRIO
Microbiology Indonesia Vol. 4 No. 1 (2010): April 2010
Publisher : Indonesian Society for microbiology

The M2 protein of 146 avian influenza (AI) viruses data available in public database (NCBI), including 20 AI isolates used in this study, were sequenced at the M2 protein to find out the probability of mutation and the increase of resistance to amantadine after more than 5 years of their circulation in Indonesia. The results showed that during 2003-2008, around 62.58% (92/147) AI viruses in Indonesia have showed resistance to amantadine and 10 of them have dual mutations at V27A and S31N.

The Genetic Drift of Indonesian Avian Influenza A H5N1 Viruses During 2003-2008 NI LUH PUTU INDI DHARMAYANTI; GINA SAMAAN; FERA IBRAHIM; RISA INDRIANI; . DARMINTO; AMIN SOEBANDRIO
Microbiology Indonesia Vol. 5 No. 2 (2011): June 2011
Publisher : Indonesian Society for microbiology

The avian influenza A H5N1 outbreaks started in 2003 and Indonesia introduced a vaccination campaign in 2004 to control the disease. In 2007, anecdotal reports about reduced vaccine effectiveness were received from commercial farmers. This paper describes the evolution of viruses in Indonesia up till 2008 and focus on viruses from vaccinating farms reporting vaccine failure were compared to viruses isolated from outbreak areas with no vaccination program. Result of the study revealed that viruses from vaccinated chickens had more extensive mutation at the HA molecule compared to chicken and other avian species without vaccination. Substitutions occurred at the HA gene level as well as at NA, M1 and NS1 genes. Viruses isolated and characterized form 2008 vaccinated flocks had substitutions that were unique and different with the old viruses. The recommendation arising from this study to the avian influenza disease control program in Indonesia is that continuous monitoring of genetic character of viruses and the vaccine seed strain should be updated periodically and matched with the virus circulated in the field.

Five Unique Amino Acid Residues of Hemagglutinin (HA) Proteins of Swine Influenza A (H1N1) Detected in 2009 in Jakarta, Indonesia ANDI YASMON; YULIANTY MUHAYAR; VIVI SETIAWATY; BETI ERNAWATI DEWI; BUDIMAN BELA; FERA IBRAHIM
Microbiology Indonesia Vol. 6 No. 2 (2012): June 2012
Publisher : Indonesian Society for microbiology

Nine HA genes of influenza A (H1N1) viruses originating from swine which were detected in 2009 in Jakarta, Indonesia, were characterized in this study. Nasopharyngeal and/or pharyngeal samples were extracted to obtain viral RNA genomes. Amplification of the HA segment was performed by using the reverse transcription-polymerase chain reaction (RT-PCR), and followed by nested PCR in cases of RT-PCR negative. DNA sequencing was performed by using eight overlapping primers. All the Jakarta strains were closely related to vaccine strain A/California/07/2009. Nine amino acid changes were found in the Jakarta strains, and 5 (P100S, S220T, G239D, R240Q, and I338V) of those were unique to all Jakarta strains with respect to strain A/California/07/2009 used to produce vaccine. An I338V substitution was detected in a cleavage site of HA and no amino acid changes were detected in potential sites for N-linked glycosylation. For seven sites (positions 131, 158, 160, 183, 187, 222, and 227) playing an important role in viral attachment to host receptor, none of the expected amino acid changes was detected; however, a S220T substitution close to amino acid 222 was found in all the Jakarta strains. All amino acid changes potentially affect the pathogenicity of the viruses and the efficacy of strain A/California/07/2009 in neutralizing the Jakarta strains.

Konstruksi Plasmid Pengekspresi Antigen Gag dan Protein Penghantar VP22 untuk Pengembangan Vaksin HIV-1 Melinda Remelia; Budiman Bela; Silvia Tri Widyaningtyas; Fera Ibrahim
Media Penelitian dan Pengembangan Kesehatan Vol 31 No 2 (2021)
Publisher : Sekretariat Badan Penelitian dan Pengembangan Kesehatan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22435/mpk.v31i2.3046

The endogenous HIV-1 vaccine based on Gag protein is expected to stimulate the immune response of CD8+ T cells (cytotoxic). The Gag protein that has been produced by the E.coli prokaryote system is an exogenous antigen. The fusion of VP22 protein is expected to deliver Gag antigen into the cytoplasm of cell, observed by eGFP markers. Sequences of VP22 (114 pb), GagHIV-1 (1506 pb), and eGFP (733 pb) were inserted into the pQE80L, respectively. The recombinant protein was expressed in the E.coli system and purified by the Ni-NTA method. Antigen delivery fused with VP22 and eGFP was observed with fluorescence and confocal microscopy. The recombinant plasmid constructs of protein expression eGFP, VP22-eGFP, GagHIV-1-eGFP, VP22-GagHIV-1-eGFP were verified by DNA sequencing according to the reference. The recombinant plasmid constructs of Gag HIV-1-eGFP and VP22-GagHIV-1-eGFP still need to be optimized so they can be expressed in the E.coli system. The recombinant protein VP22-eGFP (27.02 kDa) was succesfully obtained and fluorescent green (entered) into the cytoplasm and nucleus of vero cells. In addition to the HIV-1 vaccine, this recombinant plasmids pQE80L-eGFP and pQE80L-VP22-eGFP also have the potential to be used as tools in the development of endogenous vaccines for another viruses/microbes. Abstrak Vaksin endogen HIV-1 berbasis protein Gag diharapkan dapat menstimulus respons imun sel T CD8+ (sitotoksik). Protein Gag yang telah diproduksi dengan sistem prokariota E.coli merupakan antigen yang bersifat eksogen. Fusi protein VP22 diharapkan mampumenghantarkan antigen Gag masuk ke sitoplasma sel, diamati dengan marker eGFP. Sekuens VP22 (114 pb), GagHIV1 (1506 pb), dan eGFP (733 pb) telah diinsersikan pada vektor pQE80L. Protein rekombinan diekspresikan pada sistem E.coli dan dipurifikasi dengan metode Ni-NTA. Penghantaran antigen yang difusikan dengan VP22 dan marker eGFP diamati dengan mikroskop fluoresens dan konfokal. Konstruksi plasmid rekombinan pengekspresi protein eGFP, VP22-eGFP, GagHIV1-eGFP, dan VP22-GagHIV1-eGFP telah diverifikasi dengan sekuensing DNA sesuai dengan sekuen referensi. Plasmid rekombinan pengekspresi GagHIV1-eGFP dan VP22-GagHIV1-eGFP masih perlu dioptimasi agar dapat diekspresikan di sistem E.coli. Protein rekombinan VP22-eGFP (27,02 kDa) telah berhasil diperoleh serta berpendar fluoresens hijau (masuk) ke sitoplasma dan nukleus sel vero. Selain vaksin HIV-1, plasmid rekombinan pQE80L-eGFP dan pQE80L-VP22-eGFP juga berpotensi dapat digunakan sebagai ‘tools’ dalam pengembangan vaksin endogen dari virus atau mikroba lainnya.

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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