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Journal of Clinical Microbiology and Infectious Diseases
Published by Perhimpunan Dokter Spesialis Mikrobiologi Klinik Indonesia
ISSN : -     EISSN : 28089405     DOI : https://doi.org/10.51559/jcmid
Core Subject : Science,
Immunology & microbiology
Journal of Clinical Microbiology and Infectious Diseases; peer-reviewed journal aiming to communicate high-quality research articles, reviews, and general articles in the field. JCMID publishes articles that encompass basic research/clinical studies related to microbiology and infectious disease. The Journal aims to bridge and integrate the intellectual, methodological, and substantive diversity of medical scholarship and encourage a vigorous dialogue between medical scholars and practitioners.
Arjuna Subject : Kedokteran - Mikrobiologi (Medis)
Articles 63 Documents
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Molecular characteristics of the gyrA gene among rifampicin-resistant Mycobacterium tuberculosis isolates Aquaresta, Febriana; Kuntaman, Kuntaman; Dewi, Lisa; Syaiful, Irbasmantini
Journal of Clinical Microbiology and Infectious Diseases Vol. 5 No. 1 (2025): Available online : 1 June 2025
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.v5i1.96

Abstract

Background: Drug-resistant tuberculosis (TB) remains a public health threat, especially during this pandemic. Meanwhile, fluoroquinolone is used as a second-line multidrug-resistant TB (MDR-TB) treatment since this drug was previously prescribed for respiratory, urinary, and genital tract infections. However, unregulated and excessive use of fluoroquinolones leads to resistance. Methods: The design of this study is a descriptive observational study with a cross sectional approach. This study aims to determine the pattern of gyrA gene mutation in fluoroquinolone resistance among rifampicin-resistant Mycobacterium tuberculosis isolates during the COVID-19 pandemic in Sumatra, Indonesia. The Mycobacterium tuberculosis isolates were stored in the Palembang Health Center Laboratory as the referral laboratory in Sumatra from January to December 2020. Out of the 233 isolates that were tested phenotypically by BACTEC MGIT, 8 isolates of fluoroquinolone resistance (ofloxacin or moxifloxacin or both) were obtained and sequenced using an ABI PRISM 3730XL analyzer for Single Nucleotide Polymorphism analysis (SNP). Results: Among the six fluoroquinolone-resistant Mycobacterium tuberculosis isolates, the gyrA mutations were identified in 5/6 isolates (84%), A90V (34%), D94A (16%), and D94G (34%), while 1/6 isolates (16%) had no mutation in gyrA gene among Mycobacterium tuberculosis that were fluoroquinolone resistance. Conclusion: The gyrA gene mutation in fluoroquinolone resistance among rifampicin-resistant Mycobacterium tuberculosis was commonly present in codon 90 (2/6 isolates =32%) and 94 (3/6 isolates=68%).
Comparison between cytomegalovirus and HIV viral load among HIV patient who underwent antiretroviral therapy Tulle, Andrew; Santosaningsih, Dewi; Hastuti, Nurima Diyah Puji
Journal of Clinical Microbiology and Infectious Diseases Vol. 5 No. 2 (2025): Available online : 1 December 2025
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.v5i2.75

Abstract

Introduction: Cytomegalovirus (CMV) is one of the most prevalent viral infections in humans. The prevalence is approximately 20 percent among children and nearly 100 percent among adults. Among immunocompetent individuals, CMV infection remains predominantly asymptomatic. However, in immunocompromised patients such as people with HIV (PWH), it can cause end-organ diseases that may be life-threatening. With the increasing administration of antiretroviral therapy (ART), HIV infection can be controlled, and complications from CMV infection have been decreasing. One critical method for monitoring CMV infection is identifying CMV viremia. This study aims to investigate whether CMV viremia persists in PWH undergoing ART and to explore its relationship with HIV viral load. The research seeks to provide insights to guide clinical management of CMV reactivation in this patient population Methods: This cross-sectional study analysed archived plasma samples to detect and compare CMV viral load and HIV viral load among PWH undergoing ART. The samples were archived biological materials collected for HIV viral load detection. All samples were previously tested by PCR to detect CMV. Data were analysed using the Mann-Whitney test and Spearman correlation test. Result: Among 67 total samples, seven were identified as CMV positive, displaying various viral load concentrations. Analysis using the Mann-Whitney test demonstrated a statistically significant difference between variables, while the Spearman correlation test showed no correlation between them. This indicated that CMV viremia may not be directly influenced by HIV infection. Conclusion: Despite the significant difference between variables, the CMV viral load among PWH undergoing ART was not correlated with HIV viral load status. These findings suggest that CMV monitoring should be considered independently of HIV viral load status. However, the limited sample size suggests caution in generalizing these findings.
Outbreak of Candida lusitaniae bloodstream infection in neonatal intensive care unit: case series Sri Kusuma Dewi, Ida Ayu; Saputra, I Wayan Agus Gede Manik; Tanaya, Putu Wahyu Dyatmika; Tangkas, Made Refika Widya Apsari; Mahendra, I Putu; Handayani, Lidya
Journal of Clinical Microbiology and Infectious Diseases Vol. 5 No. 2 (2025): Available online : 1 December 2025
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.v5i2.87

Abstract

Introduction: Neonatal sepsis remains a significant health challenge, particularly in low- and middle-income countries (LMICs), where inadequate healthcare infrastructure and sanitation contribute to its high incidence. Sepsis is defined as life-threatening organ dysfunction resulting from a dysregulated immune response to infection. Neonates are particularly vulnerable due to immature immune systems. Candida species, especially Candida albicans and Candida parapsilosis, are common pathogens, but Candida lusitaniae has also emerged as a notable cause of neonatal sepsis, with increased resistance to Amphotericin B. This case series highlights an outbreak of Candida lusitaniae bloodstream infections in a neonatal intensive care unit (NICU), emphasizing the diagnostic and management challenges of rare fungal infections. Case Description: In this report, we describe five neonatal sepsis cases caused by Candida lusitaniae in our NICU. All patients exhibited respiratory distress, pneumonia, and elevated procalcitonin levels, and were treated with Voriconazole. The neonates had varying risk factors, including prematurity, low birth weight, and asphyxia. Blood cultures identified Candida lusitaniae in all cases, with susceptibility testing confirming sensitivity to Voriconazole, Amphotericin B, and Flucytosine. Environmental sampling revealed contamination in the NICU, specifically from a sink, suggesting nosocomial transmission. In response, the NICU was decontaminated, infection control protocols were reinforced, and environmental surveillance was intensified. All patients improved clinically and were discharged without major complications, except for mild encephalopathy in one case. Conclusion: This outbreak underlines the importance of timely identification and appropriate therapy in managing rare fungal infections in neonates. It also highlights the critical role of environmental sources in nosocomial infections and the need for robust infection control measures in NICUs. Strict infection prevention strategies, including enhanced cleaning, staff training, and surveillance, are essential to preventing such outbreaks in high-risk settings.
Demographic influence on COVID-19 reinfection at the Integrated Laboratory of Syarif Hidayatullah State Islamic University Jakarta Fiena Febriyana; Suwarsono, Erike A.
Journal of Clinical Microbiology and Infectious Diseases Vol. 5 No. 2 (2025): Available online : 1 December 2025
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.v5i2.91

Abstract

Background: COVID-19 can reinfect the same person, or it can be called reinfection. Reinfection that occurs has a slightly higher severity level, characterised by the need for ventilation and intensive care in the ICU, than the first infection. This study aimed to determine the influence of demographics on COVID-19 reinfection cases in the Integrated Laboratory of the Faculty of Medicine, Syarif Hidayatullah State Islamic University Jakarta, in 2020-2022. Methods: The study was an observational analytical study using a cross-sectional design conducted on patients in the Integrated Laboratory of the Faculty of Medicine, Syarif Hidayatullah State Islamic University Jakarta, who were selected by consecutive sampling. Results: The study aims to understand the relationship between gender, age, occupation, blood type, and source of sample with cases of COVID-19 reinfection. This study collected 396 samples. It was found that the majority of samples had the characteristics of women (57.8%), young adults (35.9%), unknown occupation (45.7%), unknown blood type (39.4%), hospital patients (90.2%), and experienced reinfection (31.8%). The results of the bivariate analysis showed a significant relationship between gender and age with cases of COVID-19 reinfection. Conclusions: A significant relationship was found between gender and age with cases of COVID-19 reinfection at the Integrated Laboratory of the Faculty of Medicine, Syarif Hidayatullah State Islamic University Jakarta.
Progressivity of in vitro resistance of Klebsiella pneumoniae ESBL to meropenem and amikacin therapy in specimens from the intensive care unit of Saiful Anwar Hospital, Malang Tri Irmawati, Anistia
Journal of Clinical Microbiology and Infectious Diseases Vol. 5 No. 2 (2025): Available online : 1 December 2025
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.v5i2.72

Abstract

Introduction: Multidrug-resistant organism (MDRO) infections pose a significant global health challenge. The WHO has identified Klebsiella pneumoniae as a high-priority pathogen responsible for such infections. The presence of K. pneumoniae ESBL can lead to higher mortality rates. Currently, antibiotics like meropenem and amikacin are used to treat K. pneumoniae ESBL infections. However, there is no existing research on how antibiotic resistance develops over time. This study aimed to investigate the progression of in vitro resistance of K. pneumoniae ESBL to meropenem and amikacin in samples from the ICU at Saiful Anwar Hospital. Methods: This study uses the AZDZST method, a novel technique called the Ameri-Ziaei double antibiotic synergism test for assessing antimicrobial synergy. It functions as a disk diffusion test designed for double antibiotic synergy, with inhibition zone diameters providing data similar to other disk diffusion methods. This makes AZDAST simple to perform using the Kirby-Bauer disk susceptibility test. The method is independent and does not require reference tables like CLSI guidelines. Results are interpreted by comparing inhibition zone sizes around single and dual disks; a reduction in zone size indicates resistance. Klebsiella pneumoniae ESBL isolates, confirmed by Vitek 2, were tested for susceptibility to meropenem and amikacin. These isolates were exposed to 10 µg meropenem disks, 30 µg amikacin disks, and a combination of both disks using AZDAST over 14 days. The inhibition zones were measured after 18-24 hours of incubation at 37°C. Results: Amikacin antibiotics exhibited resistance by the fifth day of exposure, while meropenem showed resistance on the 12th day across three samples, and on the 14th day in one sample. The combination of amikacin and meropenem also exhibited resistance by day 14 of exposure. There was no significant difference in the duration of resistance between monotherapy and the combination therapy of meropenem and amikacin. Conclusion: Meropenem shows resistance by day 12, while amikacin is resistant from day 5. There is no significant difference in resistance duration between monotherapy and combination antibiotic treatments against Klebsiella pneumoniae ESBL in vitro.
Identification test of bacterial species and resistance genes from infectious patients using MDR direct flow chip molecular technique compared to conventional techniques Surjawinata, Mario; Sudarmono, Pratiwi; Lestari, Resti Hardianti
Journal of Clinical Microbiology and Infectious Diseases Vol. 5 No. 2 (2025): Available online : 1 December 2025
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.v5i2.89

Abstract

Introduction: Antimicrobial resistance poses a threat to global public health by increasing morbidity and mortality. While resistance development is a natural biological process, antibiotic use has accelerated its rise resistance. This study aimed to determine the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the MDR Direct Flow Chip Kit to detect 5 bacterial species and a total of 55 resistance gene markers. Methods: The research employed a cross-sectional design, analyzing positive samples determined by the VITEK® 2 system from various specimens, including sputum, pus, and blood. These specimens were collected from sepsis patients at the FKUI Clinical Microbiology Laboratory in 2023. They were stored in Eppendorf tubes with TSB and Glycerol fluids, then cultured on Nutrient Agar Media and incubated overnight. HybriSpot® will analyze the increasing isolates using the MDR Direct Flow Chip, an in vitro diagnostic kit that quickly detects multidrug-resistant bacteria. This kit employs multiplex PCR to identify five bacterial species—Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, Escherichia coli, and Acinetobacter baumannii—as well as 55 resistance gene markers. These markers include the primary enzymatic mechanisms associated with nine different antibiotic classes. Result: A total of 40 samples were analyzed with HybriSpot® using the MDR Direct Flow Chip, which identified 5 genus species and detected 31 resistance genes. The same samples were also tested with the VITEK® 2 system, which identified the same 5 genus species and provided antibiotic susceptibility results. The overall sensitivity was 80%, specificity was 94.2%, and conformity was 94.68%. Conclusion: The MDR Direct Flow Chip assay is a promising method for identifying pathogens in positive blood cultures of infected patients and can aid antimicrobial stewardship programs in hospitals.
Diagnostic Challenges in Non-albicans Candida Bloodstream Infection in an Immunocompromised Patient: A Case Report Valentine Hursepuny; Yunialthy Dwia Pertiwi; Utma Laela Warka; Nadyah; Baedah Madjid; Andi Rofian Sultan; Mochammad Hatta; Firdaus Hamid
Journal of Clinical Microbiology and Infectious Diseases Vol. 6 No. 1 (2026): Available online : 1 June 2026
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.v6i1.64

Abstract

Introduction: Candidemia has increased in recent years, leading to prolonged hospital stay, increased healthcare costs, and high mortality. Patients with underlying conditions such as malignancy and those requiring invasive medical devices are at higher risk of Candida bloodstream infection. Therefore, this study aims to describe a rare case of non-albicans Candida bloodstream infection in an immunocompromised patient, with emphasis on diagnostic challenges and clinical implications of discordant laboratory identification in guiding appropriate management. Case Description: A 48-year-old female with cervical cancer undergoing chemotherapy and hemodialysis via a right-thigh double-lumen catheter presented to the emergency department with prolonged vaginal bleeding, oliguria, nausea, and significant weight loss. Laboratory findings revealed leukocytosis and renal impairment. She received a combination of ceftazidime, moxifloxacin, and metronidazole in the ICU. The patient had multiple invasive devices, including intravenous catheters, parenteral nutrition, and urinary catheters. Blood culture performed on day 15 of hospitalisation identified Candida lipolytica, which was sensitive to voriconazole, amphotericin B, and flucytosine. Moreover, PCR and phylogenetic sequencing were performed to ensure accurate species identification. Despite the final identification and clinical management efforts, the patient’s clinical condition continued to deteriorate, and she eventually succumbed after three weeks of hospitalisation. Conclusion: This case highlights a rare non-albicans Candida bloodstream infection in an immunocompromised patient, emphasising the diagnostic challenges associated with accurate species identification. A stepwise diagnostic approach with culture, proteomic, and molecular confirmation, including PCR and phylogenetic analysis, is essential to ensure accurate identification and optimal clinical management.
Kodamaea ohmeri: a rare yeast infection in a neonate - a case report Putu Wila Widiastuti; Ida Ayu Sri Kusuma Dewi; I Wayan Agus Gede Manik Saputra
Journal of Clinical Microbiology and Infectious Diseases Vol. 6 No. 1 (2026): Available online : 1 June 2026
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.v6i1.88

Abstract

Background: Kodamaea ohmeri is a member of the Saccharomycetaceae family and class Ascomycota. It is a rare human pathogen that can cause fatal infections and lead to an increased risk of morbidity or mortality. This opportunistic pathogen is associated with invasive fungal infections in newborn intensive care units (NICUs). Prematurity, very low birth weight, prolonged rupture of membranes, and invasive procedures are among the key risk factors identified in affected neonates. We report a case of K. ohmeri infection in a newborn treated at Bali Mandara General Hospital, Denpasar, Bali. This study aimed to enhance the awareness and understanding of clinicians, microbiologists, and infection control professionals in the management of neonates with K. ohmeri infection. Case: A preterm infant with gestational age 30 to 31 weeks was diagnosed with respiratory distress syndrome, neonatal pneumonia, stage 1 acute kidney injury, and neonatal sepsis. The infant had very low birth weight of 1420 grams, APGAR scores of 5-6-7, premature rupture of membranes more than 24 hours, and chest retractions. The baby was then transferred to the NICU and put on a mechanical ventilator due to respiratory failure. Blood cultures collected from two sites grew K.ohmeri. Treatment with intravenous voriconazole 3 mg per day, caffeine citrate, and nebulization resulted in clear clinical and laboratory improvement. After 14 days, procalcitonin levels decreased from 54.27 ng/mL to 0.51 ng/mL. Chest retractions were no longer present, and ventilatory support was discontinued. Conclusion: This case highlights the importance of early recognition, accurate microbiological identification, and timely antifungal therapy for Kodamaea ohmeri infections in neonates. Increasing awareness among clinicians and infection control teams regarding risk factors, diagnostic considerations, and appropriate management is essential to improving outcomes and reducing the risk of transmission within NICU settings.
Profile of Candida species urinary tract infection amongst intensive care unit patients at a teaching hospital in Yogyakarta, Indonesia Vyonne Chiara Sentosa; Raden Ludhang Pradipta Rizki; Nurrokhman; Marselinus Edwin Widyanto Daniwijaya
Journal of Clinical Microbiology and Infectious Diseases Vol. 6 No. 1 (2026): Available online : 1 June 2026
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.v6i1.102

Abstract

Introduction: Candida species have been reported to be the most common fungal causative agents of urinary tract infections (UTI) in the intensive care unit (ICU), causing up to 20 - 25% of UTIs. This study aims to create profiles of patients with Candida spp. UTI, antifungal administration, Candida species accounting for UTI, and mortality rate in the ICU of a teaching hospital in Yogyakarta, Indonesia. Methods: This study was a retrospective, cross-sectional, descriptive analysis using electronic health records from ICU patients of a teaching hospital in Yogyakarta, Indonesia, with positive Candida species urine culture from January 2020 to December 2023. Result: 46 women (57.5%) and 34 men (42.5%) had positive Candida urine cultures, with the majority in the age group ≥ 60 years old (63.75%) and with prior cardiovascular disorders (17.5%). Correlation established between >7 days of ICU stay and Candida species UTI, occurring in 64 patients (80%). The majority of ICU patients with Candida species UTI received invasive procedures (60%). 77 patients (96.25%) had a primary diagnosis of non-HAIs. 35 Candida tropicalis isolates (43.75%), 31 Candida albicans isolates (38.75%), 4 Candida glabrata isolates (5%), and 3 Candida parapsilosis isolates (3.75%) were found in urine cultures of ICU patients. Fluconazole (83.75%) was identified as the most frequent antifungal administered. A mortality rate of 48.75% was demonstrated in ICU patients with Candida species UTI. Conclusions: Prevalence of Candida species UTI in ICU patients of a teaching hospital in Yogyakarta, Indonesia, increases when patients are females, ≥60 years old, have prior disease and complications of cardiovascular disease, stay >7 days in the ICU, use urinary catheters, and have a primary diagnosis of non-HAIs. Fluconazole is the most frequent antifungal administered. Candida tropicalis was identified as the most frequent causative agent of UTI in ICU patients with a mortality rate of 48.75%.
Comparison Of Modified Hodge Test (Mht), Modified Carbapenem Inactivation Method (Mcim), And Vitek-2 System For Carbapenemase Detection In Clinical Isolates Of Carbapenem-Resistant Pseudomonas aeruginosa Andina Nurdayanti; Noorhamdani; Yuyun Kusnaningrum
Journal of Clinical Microbiology and Infectious Diseases Vol. 6 No. 1 (2026): Available online : 1 June 2026
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.v6i1.103

Abstract

Introduction: Pseudomonas aeruginosa is a resilient nosocomial pathogen with intrinsic and acquired resistance to multiple antibiotics. A small percentage (2–3%) of carbapenem-resistant isolates carry mobile genetic elements encoding carbapenemases, making detection essential for therapy, infection control, and epidemiological surveillance. This study aimed to compare three phenotypic methods for detecting carbapenemase production in meropenem-resistant P. aeruginosa isolates: the Modified Hodge Test (MHT), Modified Carbapenem Inactivation Method (mCIM), and the VITEK-2 automated system. Methods: The mCIM followed standard protocols. Escherichia coli ATCC 25922 was cultured on Mueller-Hinton agar (MHA) according to CLSI 2024 guidelines. MHT steps followed the Clinical Microbiology Procedures Handbook (2016). Results from both tests were compared to those from the VITEK-2 system. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were assessed. Diagnostic accuracy was further analysed using ROC curves and AUC. Results: Of 21 meropenem-resistant P. aeruginosa isolates, 11 (52.4%) were identified as carbapenemase producers by VITEK-2 compact. MHT failed to detect any of these, showing a sensitivity of 0% and specificity of 100%. mCIM detected 10 of 11 carbapenemase producers (90.9% sensitivity) but had 50% specificity. The positive predictive value and negative predictive value were 0% and 47.6% for MHT, respectively, and 66.67% and 83.33% for mCIM, respectively. AUC values were 0.5 for MHT and 0.71 for mCIM, indicating mCIM performed more closely to VITEK-2 for carbapenemase detection. Conclusion: 52,4% of the meropenem-resistant P. aeruginosa isolates were carbapenemase producers based on VITEK-2 compact. Among phenotypic methods, mCIM demonstrated greater precision than MHT, compared with Vitek-2 compact as the standard, making it a useful screening tool. The selection of the carbapenemase detection method usage depends on each laboratory’s capabilities.

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