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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.

Analysis of Klebsiella Pneumonia and Resistance Genes Coding and Carbapenemase Production in National Referral Hospital Wastewater Simanjuntak, Glory Gelarich; Karuniawati, Anis; Saharman, Yulia Rosa; Muziasari, Windi
Jurnal Kesehatan Vol 14 No 3 (2023): Jurnal Kesehatan
Publisher : Poltekkes Kemenkes Tanjung Karang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26630/jk.v14i3.4147

Hospitals, as a source of transmission and spread of bacteria carrying antibiotic-resistant genes (ARGs) as well as a high source of antibiotic compounds, are a significant reservoir of antibiotic-resistant gene transfer that causes bacteria to develop multidrug resistance (MDR). Klebsiella pneumonia is a bacterium often found in wastewater with a high level of Extended Spectrum Î²-lactamase (ESBL) and carbapenemase resistance. This study aimed to determine Klebsiella pneumonia and resistance genes encoding ESBL and carbapenemase in hospital wastewater to obtain primary Antimicrobial Resistance (AMR) data in the environment, which was first conducted in Indonesia. The resistance gene detection method was developed using High Throughput Real-Time and conventional Real-Time (HT-RT PCR). The data obtained were relative abundance and copy number. The results showed that blaTEM and blaNDM were the highest ARGs. Conventional Real-Time PCR results showed better sensitivity in detecting K. pneumoniae and ARGs than HT-RT PCR. The detection of K. pneumoniae and ARGs in RSCM wastewater in Indonesia indicates the need to improve the handling of RSCM WWTP to monitor the number of microbial resistances to antibiotics.

Optimizing Gram-Negative Bacteria Isolation from Children Diarrheal Stool Samples in Jakarta: A Comparative Analysis of Six Culture Media Abdelrazig, Omnia Amir Osman; Fadilah, Fadilah; Prasetyo, Dimas Seto; Saharman, Yulia Rosa; Hegar, Badriul
Al-Hayat: Journal of Biology and Applied Biology Vol 7, No 1 (2024)
Publisher : Fakultas Sains dan Teknologi, UIN Walisongo Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21580/ah.v7i1.20528

The prevalence of diarrheal illnesses in Indonesia remains a significant concern among children under the age of five, evident through diagnostic findings and symptomatic manifestations, leading to increased rates of mortality and morbidity. This study aimed to identify, isolate, and culture gram-negative bacteria responsible for childhood diarrhea. Twenty stool samples were collected from children under the age of 5 with acute diarrhea in Jakarta health centres and hospitals between October 2023 to January 2024. These samples were inoculated onto selective agars to facilitate the growth of gram-negative bacteria. After a 24-hour incubation period, colonies suspected to be E. coli, K. pneumoniae, Salmonella, Shigella, or Vibrio were identified using the Vitek-2 compact system. The results revealed a notable presence of Gram-negative bacteria in all the fecal samples from diarrheal children, with Escherichia coli (E. Coli) and Klebsiella pneumoniae (Klebsiella p) as the predominant species. In conclusion, our study, utilizing various cultures and the Vitek-2 compact system, elucidates the microbial landscape driving diarrheal morbidity in Indonesian children under five, with E. Coli and klebsiella pneumoniae emerging as prevalent contributors to childhood diarrhea in this population.

Comparison Study of Bacterial Profile, Wound Healing, and Cost Effectiveness in Pressure Injury Patients Using Treatment Honey Dressing and Hydrogel Putri, Nandita Melati; Margareta Lumbuun, Ruth Fitri; Kreshanti, Prasetyanugraheni; Saharman, Yulia Rosa; Tunjung, Narottama
Jurnal Plastik Rekonstruksi Vol. 9 No. 1 (2022): Jurnal Plastik Rekonstruksi
Publisher : Lingkar Studi Bedah Plastik Foundation

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14228/jprjournal.v9i1.334

Background : Pressure injury is a localized soft tissue injury caused by prolonged pressure over bony prominence. Most published papers used Manuka honey as dressing, while this product is expensive. As this reason, this study will use local product honey called Nusantara honey, to prove the use of local honey has better healing process, bacterial profile, and cost effectiveness, compared to the standard dressing, hydrogel.Method : This is a one-month experimental study conducted in patients with pressure injury that referred to our division. Parameter of the bacterial profile was taken from deep-tissue specimen. The healing process was examined with Pressure Ulcer Scale for Healing (PUSH) Tool. Cost was accumulated after all the treatment. Data was analysed with t-Test or Mann Whitney (if the distribution is not normal), with statistical significance was define as p<0.05..Result : Of 26 wounds, 12 were randomized to hydrogel and 14 to honey dressing. Characteristics were determined by sex, age, body mass index, level of consciousness, mobilization status, immobilization etiology, comorbidities, grade and location of ulcer, hemoglobin, leukocytes, and albumin level. There was clinically significant wound size reduction in honey dressing according to PUSH Tool (p=0.118). The bacterial profile and reduction were similar. Honey dressing appeared to be more cost effective in terms of dressing cost (p<0.001) and lower total cost.Conclusion: The local honey dressing has better wound healing outcome, although it is not statistically significant. Its capability of decreasing pathogens is similar with hydrogel, with lower cost, particularly the dressing cost. This local honey dressing could be a good choice as wound dressing in areas where the modern dressings are not available.

Mobile Genetic Elements Contributing to Carbapenem Resistance in Acinetobacter baumannii: Current Insights Mardhiyah, Azzahrah Khairunnisa; Saharman, Yulia Rosa; Sjatha, Fithriyah
EKSAKTA: Berkala Ilmiah Bidang MIPA Vol. 25 No. 04 (2024): Eksakta : Berkala Ilmiah Bidang MIPA (E-ISSN : 2549-7464)
Publisher : Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Negeri Padang, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/eksakta/vol25-iss04/534

Acinetobacter baumannii has become a major cause of hospital-acquired infections with the rapid development of resistance to multiple antibiotics, including critical carbapenems. This resistance challenge limits treatment options and increases morbidity and mortality. The genetic plasticity of A. baumannii facilitates the mobilization of resistance genes via mobile genetic elements (MGE). Addressing this crisis requires a deeper understanding of the mechanisms by which MGE propagates carbapenem resistance. This paper provides a solution by systematically reviewing recent research on the role of MGE in disseminating resistance genes. Following PRISMA guidelines, a comprehensive literature review was conducted across various databases. The review revealed that resistance mechanisms primarily involve carbapenem-hydrolyzing enzymes and MGE, such as integrons, transposons, insertion sequences, and plasmids. Notably, genes like blaOXA-23 and blaNDM are frequently mobilized by these elements, facilitating horizontal gene transfer and persistence. Understanding the mechanisms of MGE-mediated gene transfer is crucial for developing strategies to control the spread of antibiotic resistance inÂ A. baumannii.

Analisis Xpert® -Carba-R pada Skrining Enterobacterales Resisten Karbapenem di Unit Perawatan Intensif di Rumah Sakit Rujukan Nasional di Jakarta Saharman, Yulia Rosa; Sania, Nina; Aditianingsih, Dita
Majalah Kedokteran Indonesia Vol 74 No 5 (2024): Journal of The Indonesian Medical Association - Majalah Kedokteran Indonesia, Vo
Publisher : PENGURUS BESAR IKATAN DOKTER INDONESIA (PB IDI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.47830/jinma-vol.74.5-2024-1696

Introduction: Carbapenem-resistant Enterobacterales (CRE) represent a significant global health problem due to their high resistance to antibiotics. Traditional methods for identifying resistance genes, such as Real-Time PCR (RT-PCR), are accurate but time-consuming and involve complex techniques. This study aimed to compare the Cepheid Xpert® Carba-R test with RT-PCR, used as the gold standard, to determine its effectiveness in rapidly identifying carbapenem resistance genes in CRE. Method: The study was performed from January to June 2022, involving patients admitted to the Intensive Care Unit (ICU) at Dr. Cipto Mangunkusumo National Hospital. Rectal or perirectal swabs were collected upon ICU admission. If patients tested negative for CRE upon admission, repeat swabs were taken at discharge or death, with a maximum length of stay (LOS) of 14 days in the ICU. Genotypic identification of carbapenem resistance genes, including KPC, NDM, OXA-48, VIM, and IMP, was performed using the Cepheid Xpert® Carba-R and compared to RT-PCR. Additionally, phenotypic identification through bacterial culture was performed using the Vitek method. Result: Out of 102 ICU patients, 10.23% (22/215 isolates) were found to be positive for CRE, with the most common bacterial isolates being Escherichia coli (148/215, 68.83%) and Klebsiella pneumoniae (53/215, 24.65%). CRE was found in 1 of 148 E. coli isolates (0.67%) and in 21 of 53 K. pneumoniae isolates (39.62%). The most frequently detected carbapenem resistance gene was OXA-48 (16/22, 72.73%), followed by NDM (6/22, 27.27%). The Xpert® Carba-R test demonstrated a sensitivity and specificity of 100%, with positive predictive value (PPV) and negative predictive value (NPV) both equal to 1. A discrepancy was observed between the phenotypic and genotypic identification, with 27 phenotypically identified CRE isolates compared to 22 genotypically confirmed ones. Conclusion: The Cepheid Xpert® Carba-R test provides a reliable, rapid alternative for identifying carbapenem resistance genes in CRE, demonstrating perfect sensitivity and specificity in this study. This study indicates that Xpert® Carba-R can be an alternative in the rapid identification of CRE resistance genes.

Optimizing Gram-Negative Bacteria Isolation from Children Diarrheal Stool Samples in Jakarta: A Comparative Analysis of Six Culture Media Abdelrazig, Omnia Amir Osman; Fadilah, Fadilah; Prasetyo, Dimas Seto; Saharman, Yulia Rosa; Hegar, Badriul
Al-Hayat: Journal of Biology and Applied Biology Vol. 7 No. 1 (2024)
Publisher : Fakultas Sains dan Teknologi, UIN Walisongo Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21580/ah.v7i1.20528

The prevalence of diarrheal illnesses in Indonesia remains a significant concern among children under the age of five, evident through diagnostic findings and symptomatic manifestations, leading to increased rates of mortality and morbidity. This study aimed to identify, isolate, and culture gram-negative bacteria responsible for childhood diarrhea. Twenty stool samples were collected from children under the age of 5 with acute diarrhea in Jakarta health centres and hospitals between October 2023 to January 2024. These samples were inoculated onto selective agars to facilitate the growth of gram-negative bacteria. After a 24-hour incubation period, colonies suspected to be E. coli, K. pneumoniae, Salmonella, Shigella, or Vibrio were identified using the Vitek-2 compact system. The results revealed a notable presence of Gram-negative bacteria in all the fecal samples from diarrheal children, with Escherichia coli (E. Coli) and Klebsiella pneumoniae (Klebsiella p) as the predominant species. In conclusion, our study, utilizing various cultures and the Vitek-2 compact system, elucidates the microbial landscape driving diarrheal morbidity in Indonesian children under five, with E. Coli and klebsiella pneumoniae emerging as prevalent contributors to childhood diarrhea in this population.

Optimizing Gram-Negative Bacteria Isolation from Children Diarrheal Stool Samples in Jakarta: A Comparative Analysis of Six Culture Media Abdelrazig, Omnia Amir Osman; Fadilah, Fadilah; Prasetyo, Dimas Seto; Saharman, Yulia Rosa; Hegar, Badriul
Al-Hayat: Journal of Biology and Applied Biology Vol. 7 No. 1 (2024)
Publisher : Fakultas Sains dan Teknologi, UIN Walisongo Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21580/ah.v7i1.20528

The prevalence of diarrheal illnesses in Indonesia remains a significant concern among children under the age of five, evident through diagnostic findings and symptomatic manifestations, leading to increased rates of mortality and morbidity. This study aimed to identify, isolate, and culture gram-negative bacteria responsible for childhood diarrhea. Twenty stool samples were collected from children under the age of 5 with acute diarrhea in Jakarta health centres and hospitals between October 2023 to January 2024. These samples were inoculated onto selective agars to facilitate the growth of gram-negative bacteria. After a 24-hour incubation period, colonies suspected to be E. coli, K. pneumoniae, Salmonella, Shigella, or Vibrio were identified using the Vitek-2 compact system. The results revealed a notable presence of Gram-negative bacteria in all the fecal samples from diarrheal children, with Escherichia coli (E. Coli) and Klebsiella pneumoniae (Klebsiella p) as the predominant species. In conclusion, our study, utilizing various cultures and the Vitek-2 compact system, elucidates the microbial landscape driving diarrheal morbidity in Indonesian children under five, with E. Coli and klebsiella pneumoniae emerging as prevalent contributors to childhood diarrhea in this population.

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