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All Journal Jurnal Teknologi Dan Industri Pangan Jurnal Veteriner Microbiology Indonesia Journal of the Medical Sciences (Berkala Ilmu Kedokteran) The Indonesian Biomedical Journal Jurnal Locus Penelitian dan Pengabdian eJournal Kedokteran Indonesia Journal of Clinical Microbiology and Infectious Diseases

Pratiwi Pujilestari Sudarmono

Departemen Mikrobiologi, Fakultas Kedokteran, Universitas Indonesia, Jakarta

Author-ID : 5611275

Aerospace Engineering Agriculture, Biological Sciences & Forestry Automotive Engineering Biochemistry, Genetics & Molecular Biology Decision Sciences, Operations Research & Management Electrical & Electronics Engineering Immunology & microbiology Industrial & Manufacturing Engineering Mathematics Medicine & Pharmacology Neuroscience Public Health Veterinary

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Lactobacillus plantarum PADA FESES INDIVIDU DEWASA SEHAT YANG MENGONSUMSI Lactobacillus plantarum IS-10506 DARI DADIH [Lactobacillus plantarum in Stool of Apparently Healthy Adults Consuming Lactobacillus plantarum IS-10506 from Dadih] Azmier Adib; Mardiastuti H Wahid; Pratiwi Sudarmono; Ingrid S. Surono
Jurnal Teknologi dan Industri Pangan Vol. 24 No. 2 (2013): Jurnal Teknologi dan Industri Pangan
Publisher : Departemen Ilmu dan Teknologi Pangan, IPB Indonesia bekerjasama dengan PATPI

A placebo double blind pre-post human study was conducted in apparently healthy adults. There were two treatment groups consisting of Group A and B representing probiotic and placebo group, respectively. Twenty four participants were randomly assigned, each supplemented with either placebo or probiotic Lactobacillus plantarum IS-10506. The micro encapsulated powder was given at a dose of 2.6x1010 CFU/day for 21 consecutive days. Stool samples were collected before and after the supplementation. The fresh stool samples were analyzed for the viability of Lactobacillus sp. by conventional plate count method in MRS agar. Some stool samples were kept frozen to be analyzed by using real time PCR to trace back the availability of Lactobacillus plantarum with species specific primer. The Lactobacillus sp. in stools of healthy adults given microencapsulated probiotic Lactobacillus plantarum IS-10506 powder was significantly more than those who consumed microencapsulated placebo powder. Molecular detection by qPCR confirmed the availability of Lactobacillus plantarum in fecal samples of the probiotic group after given the supplementation for 21 days. The molecular detection validation confirmed that probiotic Lactobacillus plantarum was available in the fecal samples of the probiotic group of healthy adults. However, the availability and viability of Lactobacillus plantarum were not consistently found in the intestinal tract.

Bacterionomics and vironomics in carcinogenesis Pratiwi Sudarmono
Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Vol 48, No 4 (2016): SUPPLEMENT
Publisher : Journal of the Medical Sciences (Berkala Ilmu Kedokteran)

Virus and bacteria are microbes which are very common cause human infection. Most of the bacterial infection can be eradicated by antibiotics and infection symptoms disappear. But for virus infection, once infected, the virus will persistently stay in the host, even undergo not only a lytic cycle but also integrated into host genome. Nowadays, at least 6 virus type are consistently related to human cancer, such as EBV,HPV,HTLV,HBV,HCV,HKSV, and the new one Merkel Virus (MCV). Although not every infected people will get cancer, but around 20% of the whole cancer in human are caused by viral oncogene.Class one oncogenic bacterial is Helicobacter pylori. Infection with this bacteria can cause persistent gastro duodenal inflammation which cause some alteration in gastric cell growth into transformation. Expression of Cag gene and Vac gene and some expression of OMP protein usually link to gastric cancer.Molecular mechanisms of carcinogenesis for every virus which cause infection is a very complex , which include several processes caused by cell transformation. Besides, other host and environmental factors are also play a significant role in cancer development. Some scientist put a Hallmark analysis as a model to quickly summarize what pathobiology process will happen and what gene or protein caused the process. The Hallmark analysis comprise of several process which may happen simultaneously because some of the Hallmark is caused by the same protein. The Hallmark consists of various virus strategies in oncogenesis such as promoting angiogenesis, avoiding immune destruction, genome instability and mutation, deregulating cellular energetic, resisting cell death, sustaining proliferative signaling, evading growth suppressors, enabling cellular immortality, promoting inflammation and activation metastasis. For example, infection by HPV, will cause low grade dysplasia which can continue to invasive cervical cancer. After host cell transformation, in the long control region genes, E6 and E7 protein will cause several strategies in oncogenesis including resisting cell death and evading growth suppressors. HBV infection will end without any serious liver damage, but after cell transformation, almost all Hallmark strategies of viral oncogenesis are happening step by step in line with the severity of liver cell damage.As the onset of cancer development after infection can last years, there are an opportunity to design either vaccine or genetic therapy to minimalize further risk of cancer in human

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.

Identifikasi Brucella abortus Isolat Lokal dengan Brucella abortus Strain Specific-Polymerase Chain Reaction (IDENTIFICATION OF LOCAL ISOLATES OF BRUCELLA ABORTUS USING BRUCELLA ABORTUS STRAIN SPECIFIC-POLYMERASE CHAIN REACTION ASSAY) Susan Maphilindawati Noor; Pratiwi Pujilestari Sudarmono; Asmarani Kusumawati; Anis Karuniawati
Jurnal Veteriner Vol 15 No 3 (2014)
Publisher : Faculty of Veterinary Medicine, Udayana University and Published in collaboration with the Indonesia Veterinarian Association

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (132.165 KB)

Brucella abortus Strain Specific-Polymerase Chain Reaction (BaSS-PCR) is a single multiplex PCRtechnique which able to identify and differentiate between Brucella abortus field strains (biovar 1, 2, and4), B. abortus vaccine strains, Brucella species, and non-Brucella species. In this study, BaSS-PCR wasapplied to identify local isolates of B. abortus in order to investigate the B. abortus strains that infectedcattle in Indonesia. Fifty local strains of B.abortus isolated from infected cattle in Java (Jakarta andBandung), South Sulawesi (Maros), East Nusa Tenggara (Kupang and Belu) were used in this study. TheDNA bands were observed by agarose gel in the presence of ethidium bromide. Identification was performedbased on the size and number of DNA products amplified by PCR from each isolates. The results showedthat the 50 isolates were of B. abortus field strains. This finding showed that the cause of bovine brucellosisin Indonesia is B. abortus field strains.

Hospital Acquired Bacterial Infection in Burns Unit at Cipto Mangunkusumo Hospital, Jakarta PRATIWI SUDARMONO; VERONICA WIWING
Microbiology Indonesia Vol. 1 No. 1 (2007): April 2007
Publisher : Indonesian Society for microbiology

Burn injury causes mechanical disruption to the skin, which allows environmental microbes to invade the deeper tissues. A prospective study of infections in burn patients has shown that the incidence of hospital acquired bacterial infection in burn wounds was high. In the Burns Unit, Cipto Mangunkusumo Hospital, Jakarta, 94 patients were hospitalized from January to July 2004. The objective of this study was to evaluate the hospital acquired infections in burn wounds. Using a cross sectional study, 49 patients were included. The specimens for bacterial investigation were obtained from clean eschar which has healthy tissue taken at day 1, day 5 and day 10. At the same time, bacterial investigations were conducted from the air and the water, as well as from the hand and nasal swabs of hospital personnel. The results show that Klebsiella pneumoniae is the most prominent bacterium found in the wounds, but it is also found in the air. Pseudomonas aeruginosa was the number two causative bacteria which caused a change of the bacterial infectivity on day 5 and 10. These bacteria were always found when we conducted bacterial investigations from the water resource of the burns unit. Methicillin Resistant Staphylococcus aureus is also found in the nasal swab of hospital personnel. Using the antibiogram pattern, there were similarities between bacteria found in the wounds and in bacteria found in the air and water. In conclusion, hospital acquired burn wound infection in Burns Unit, Cipto Mangunkusumo Hospital is as high as 62%. The surveillance data are very important for developing good clinical practice guidelines in burn injury treatment and management

Epithelial Cells Count and the Ratio of Leukocytes and Epithelial Cells as the Criteria to Determine Qualified Specimen for Community-Acquired Pneumonia (CAP)-causing Pathogens Identification Ade Dharmawan; Anis Karuniawati; Pratiwi Pudjilestari Sudarmono; Delly Chipta Lestari; Cleopas Martin Rumende
The Indonesian Biomedical Journal Vol 12, No 1 (2020)
Publisher : The Prodia Education and Research Institute (PERI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18585/inabj.v12i1.873

BACKGROUND: Community-acquired pneumonia (CAP) is the most common infectious with serious rate of morbidity and mortality. Recent conventional method only described 30-50% of CAP etiology. Sputum specimen quality assessment is important to obtain an accessible CAP-causing pathogens identification.METHODS: This was a prospective descriptive study involving 100 specimens from CAP-diagnosed subjects in Budhi Asih Regional General Hospital inpatien tcare. We assessed three gram-staining criteria for specimen quality determination, and continued by bacterial identification.RESULTS: All specimens were qualified according to criteria II, while only 94 and 96 specimens were qualified according to criteria I and III, respectively. Sixty-five specimens could be identified by culture and pneumoCLART polymerase chain reaction (PCR) examination, and the 35 specimens remained unknown. Ten out of those 35 specimens were positive after analyzed by Acid-fast Bacilli (AFB) test. The pathogens we identified including Klebsiella pneumoniae (29.6%), Acinetobacter baumanii (10.2%), Enterobacter cloacae (4.6%), Pseudomonas aeruginosa (4.6%), Staphyloccocus aureus (4.6%), Moraxella catarrhalis (3.7%), Enterobacter aerogenes (2.8%), Escherichia coli (2.8%), Streptococcus pneumoniae (1.9%), Mycoplasma pneumoniae (1.9%) and Citrobacter koseri (0.9%).CONCLUSION: There were no significant differences among the three criteria for sputum specimen quality assessment, based on culture and pneumoCLART examination. We suggest that criteria II could be used to avoid many specimen rejections while good quality specimens still attained for accessible bacteria identification.KEYWORDS: community-acquired pneumonia, sputum, gram stain, pathogens, bacteria

Necrotizing Fasciitis in a Leprosy Patient Nie Nie; Augustine Natasha; Sweety Pribadi; Yulia R. Saharman; Chairunissa T. Rizal; Anis Karuniawati; Pratiwi Sudarmono
eJournal Kedokteran Indonesia Vol 10, No. 1 - April 2022
Publisher : Faculty of Medicine Universitas Indonesia

Leprosy is an infection caused by Mycobacterium leprae. Disability after the infection is common and necrotizing fasciitis could deteriorate the patient current condition. We present the case of necrotizing fasciitis of the right limb inpatient with tarsal disintegration and plantar ulcer due to previous leprosy infection. The microbiology culture was inadequate in the early stage of management, which delayed the definitive antibiotic for patient and the progressive necrotic infections were uncontrolled. Amputation was done to save the patient’s life and the latter microbiology culture was able to determine the definitive antibiotic therapy. This report highlights the needs of disability management and infection control for leprosy patient after the treatment is completed.

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.

Optimization of Surfactin Production by Bacillus amyloliquefaciens MD4-12 using Response Surface Methodology AHMAD WIBISANA; WAHONO SUMARYONO; MIRAWATI SUDIRO; PRATIWI PUDJILESTARI SUDARMONO
Microbiology Indonesia Vol. 9 No. 3 (2015): September 2015
Publisher : Indonesian Society for microbiology

Surfactin is a lipopeptide biosurfactant that show potential biomedical application due to its activities such as antiviral, antibacterial, antifungi, anticancer, and antimycoplasma. Bacillus amyloliquefaciens MD4-12, isolated from oil-contaminated soil, produced promising yield of surfactin in McKeen medium. The production of surfactin was influenced by many fermentation process parameters such as carbon, nitrogen, minerals and also environmental conditions such as pH and agitation. Therefore, to obtain high yield of surfactin by Bacillus amyloliquefaciens MD4-12, optimization of process production was conducted in shake flask fermentation using response surface methodology. McKeen medium composition was used as basal medium.Â Screening of the best carbon and nitrogen source were selected in preliminary experiments followed by selection of the influencing significant parameters on surfactin production using Plackett-Burman design. Selected parameters were optimized by central composite design and for the data analysis was used response surface methodology. The result showed that the optimum medium composition contained (g/L) 45.0 glucose, 6.33 urea, 1.0 monosodium glutamate, 1.85 MgSO4.7H2O, 0.4 KCl, 0.5 K2HPO4 and 0.5 mL trace elements. The surfactin yield at optimal condition was 1.25 g/L, increased 2.4 times compared to condition prior to optimization.Â

The current trend for prosthetic joint infection diagnosis from culture to molecular: a literature review Augustine Natasha; Mardiastuti Wahid; Pratiwi Sudarmono
Journal of Clinical Microbiology and Infectious Diseases Vol. 1 No. 1 (2021): Available Online: June 2021
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.v1i1.6

Pathogen identification in prosthetic joint infection is necessary to achieve optimal patient management. The specimens for diagnosis of prosthetic joint infection could be the synovial fluid, the tissue obtained intraoperatively, and the biofilm from the implanted prosthesis. Because of the low sensitivity of the conventional specimen culture method, the preanalytic treatment of the specimen was widely studied to increase the yield of detection. This review aimed to describe the current specimen processing methods used in the clinical setting to increase the pathogen detection rate. A blood culture bottle, tissue homogenization, and explanted prosthesis sonication were the most studied methods with a good result. Molecular methods were also developed to reduce the time of pathogen detection. MALDI-TOF was studied to reduce identification time after a positive culture. Other molecular methods such as polymerase chain reaction and next-generation sequencing were studied to omit the culture step and reduce detection time. However, the impracticality and the inconsistent sensitivity of certain specimens from the molecular methods limit its application in the clinical setting. Specimen culture remains as a crucial step in the current prosthetic joint infection, with the improvement of the molecular methods toward a better prosthetic joint infection diagnosis.

Co-Authors . Andriansjah Ade Dharmawan Agus Sjahrurachman AHMAD WIBISANA Amin Soebandrio Andi Yasmon Anis Karuniawati Ariyani Kiranasari Asmarani Kusumawati Augustine Natasha Augustine Natasha Azmier Adib Betty Ernawati Chairunissa T. Rizal Cleopas Martin Rumende Delly Chipta Lestari Dewi, Intan Keumala Diniwati Mukhtar Fera Ibrahim Fera lbrahim Fithriyah Fithriyah Fithriyah Fithriyah HAK HOTTA Helwiah Umniyati Hidetaka Tsuji Holy Arief Ingrid S. Surono Leonardus B.S. Kardono Lola Febriana Dewi Louisa Ivana Utami Mardiastuti H Wahid Mardiastuti Mardiastuti Mirawati Sudiro Myrna Adianti Nie Nie Prawoto Prawoto Rela Febriani Robert Utji Shirly Kumala Susan Maphilindawati Noor Sweety Pribadi Tjahjani M. Sudiro TJAHJANI MIRAWATI SUDIRO Tomohiro Oshibe Triyani Sukarso Tunru, Insan Sosiawan VERONICA WIWING Vivi Lisdawati Wahono Sumaryono Yeva Rosana Yulia R. Saharman Yulia Rosa Saharman

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