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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 51 Documents
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Post-Bronchoscopy Infections: A Literature Review: A Literature Review Permatasari, Tri Wijayanti; Karuniawati, Anis
Journal of Clinical Microbiology and Infectious Diseases Vol. 4 No. 2 (2024): Available online : 1 December 2024
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.v4i2.61

Abstract

Post-bronchoscopy infections are a critical concern in respiratory medicine, given their potential to exacerbate patient morbidity, particularly among immunocompromised individuals or those with pre-existing lung conditions, one of which is infection. The infection arises from lower respiratory tract pathogens, and most infections originate from reprocessing practices. Infection can occur when the bronchoscope comes into contact with the mucosa and blood vessels of the respiratory tract. Bacteremia is a more often post-bronchoscopy infection complication rather than pneumonia. It is commonly involving Coagulase-negative or positive Staphylococcus, non-hemolytic or hemolytic Streptococcus, Citrobacter species, and Klebsiella. However, in general, the incidence of post-bronchoscopy infection is mainly caused by gram-negative bacteria. Various risks can affect post-bronchoscopy infection that can increase the severity of the disease to death. It is important to increase obedience and precaution against the transmission of infection. Reducing bacterial pathogens and controlling infection are important steps to reduce the post-bronchoscopy infection mortality rate. Therefore, this study aimed to review the post-bronchoscopy infections in detail.
Rare case of human Streptococcus suis purpura fulminans at Prof. Ngoerah Hospital, Denpasar, Bali Nara Dhany, Henri; Tarini, Ni Made Adi; Putrawan, Ida Bagus Putu; Pinatih, Komang Januartha Putra
Journal of Clinical Microbiology and Infectious Diseases Vol. 4 No. 2 (2024): Available online : 1 December 2024
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.v4i2.63

Abstract

Background: Streptococcus suis (S. suis) is a zoonotic bacterium capable of causing severe infections in humans, particularly those with occupational exposure to pigs or pork products. Notable manifestations include meningitis, endocarditis, sepsis, and distinct skin conditions such as purpura and necrotic lesions. Southeast Asia reports the highest incidence, correlating with prevalent pig farming practices. Though infrequent, S. suis infections can lead to severe outcomes if not promptly diagnosed and treated. Case Presentation: We present a case involving a 73-year-old Balinese man without recent exposure to pigs or pork but with a history of pork consumption six months prior. He was admitted with symptoms including skin discoloration, respiratory distress, and loss of consciousness. Physical and laboratory examinations revealed pleural effusion, pneumonia, and high procalcitonin levels. Blood cultures identified S. suis, confirmed by VITEK® 2 system with susceptibility to multiple antibiotics, except tetracycline. Despite initial treatment with ceftriaxone, azithromycin, and levofloxacin; the patient’s condition deteriorated, resulting in a fatal outcome. Conclusion: This case underscores the importance of early diagnosis and rapid antibiotic intervention in S. suis infection. Delay in hospitalization significantly impacts prognosis, and timely, targeted treatment could improve survival rates. Enhanced awareness and preventive strategies in high-risk areas are vital to reducing the incidence and mortality associated with this infection.
Non-dermatophytic onychomycosis caused by Fusarium spp. in a 58-year-old agricultural worker: a case report Aminy, Sayyidah A.; Amaia, Devika N.; Soebono, Hardyanto; Nuryastuti, Titik
Journal of Clinical Microbiology and Infectious Diseases Vol. 4 No. 2 (2024): Available online : 1 December 2024
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.v4i2.66

Abstract

Introduction: Onychomycosis is a nail infection caused by dermatophytes, non-dermatophytes, and yeast. Fusarium spp. is one of the non-dermatophyte molds that can cause onychomycosis. A superficial infection with these fungi can lead to an invasive infection. Few case reports of onychomycosis caused by Fusarium spp. in Indonesia have been documented. Case description: We present a case of a 58-year-old male patient with a history of hepatitis B, atopic dermatitis, and corticosteroid consumption. Hyperkeratosis with a yellowish color was observed, and small particles of cornified material were discovered beneath both of his great toenails. Onychomycosis is assessed based on clinical symptoms. Mycological examinations were done by KOH examination and culture. Macroscopic examination of the culture revealed a white, cottony-looking mold with a non-pigmented reverse. Microscopic examination showed the septate hyphae, the canoe-shaped macroconidia, and the oval microconidia. We diagnosed onychomycosis caused by Fusarium spp. Based on macroscopic and microscopic examination. The antifungal susceptibility test showed a high MIC against several antifungal agents. Conclusion: It is important to be cautious for onychomycosis caused by Fusarium spp. infection as superficial infection can progress to invasive disease. Given the high prevalence of Fusarium spp. resistance to the antifungal group, antifungal treatment selection should be carefully considered.
Neisseria gonorrhoeae and Chlamydia trachomatis coinfection in a 20-year-old man with recurrent urethritis: a case report Prawarni, Vidyadhari Puspa; Prameshwara, Almarissa Ajeng; Susetiati, Devi Artami; Nuryastuti, Titik
Journal of Clinical Microbiology and Infectious Diseases Vol. 4 No. 2 (2024): Available online : 1 December 2024
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.v4i2.67

Abstract

Introduction: Neisseria gonorrhoeae and Chlamydia trachomatis are the two pathogens most commonly reported to cause sexually transmitted infections (STIs) worldwide. Coinfection between these two pathogens has been widely reported, but the incidence is still rarely reported due to challenges in diagnosis to prove the involvement of the two pathogens simultaneously. The molecular diagnostic approach is an effective option for this case and optimizing this method will able to help clinicians deciding management for the patients and prevent the spreading of the disease. This study aimed to present a case of N. gonorrhoeae and C. trachomatis coinfection in a 20-year-old man with recurrent urethritis. Case Description: A 20-year-old man presented to the Dermatology and Venereology clinic at Dr. RSUP. Sardjito with purulent discharge from the penis started a week prior. From the anamnesis and physical examination, the doctors suspected this patient with N. gonorrhoeae infection. N. gonorrhoeae was detected by microscopic examination, culture, and Real-Time Polymerase Chain Reaction (RT-PCR) examination, while C. trachomatis was also detected in RT-PCR. The patient was treated with azithromycin 1-gram single dose and cefixime 400 mg single dose. Discussion: The World Health Organization (WHO) reported that the incidence of STIs is always increasing. Most STIs are usually asymptomatic, but it can be presented as urethritis in male patients. For females, it can be given as leucorrhoea, pelvic inflammatory disease (PID), or other pregnancy complications. N. gonorrhoeae and C. trachomatis are the two main pathogens always reported annually and often found as coinfection. Due to the virulence factors of these bacteria, N. gonorrhoeae and C. trachomatis are very hard to diagnose with conventional culture methods, and the molecular approach is now an effective option to detect them and help prevent recurrence. Conclusion: Coinfection of N. gonorrhoeae and C. trachomatis is a case that is quite often encountered in clinical practice, but the incidence is rarely reported due to supporting examination methods to help confirm the presence of these two microorganisms are still limited. In cases of suspected infection by N. gonorrhoeae, C. trachomatis, or both simultaneously, the most recommended microbiological examination is to use molecular diagnostics such as PCR.
Ceftriaxone-and-cefixime-resistant Neisseria gonorrhoeae in a 26-year-old-male with gonococcal urethritis: a case report Prameshwara, Almarissa Ajeng; Prawarni, Vidyadhari Puspa; Susetiati, Devi Artami; Nuryastuti, Titik
Journal of Clinical Microbiology and Infectious Diseases Vol. 4 No. 2 (2024): Available online : 1 December 2024
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.v4i2.68

Abstract

Introduction: Gonorrhoea is the most prevalent sexually transmitted infection (STI) in Indonesia. The increasing resistance of Neisseria gonorrhoeae to antibiotics has prompted the World Health Organization (WHO) to classify gonorrhoea as an urgent public health threat. Reports of resistance to third generation extended-spectrum cephalosporins (ESCs), such as cefixime and ceftriaxone, against N. gonorrhoeae are rare in Indonesia. This study aims to present a case of cefixime and ceftriaxone resistance in a 26-year-old man with gonococcal urethritis. Case Description: A 26-year-old man presented to an STI clinic with a two-week history of increased urethral discharge. He reported a history of sexual activity with multiple partners. Physical examination revealed mucopurulent exudate and thick greenish-white pus from the external genitalia. Microscopic examination of a urethral smear identified numerous polymorphonuclear cells (>10 PMN/high-power field) and Gram-negative intracellular diplococci. Bacterial culture confirmed the presence of Gram-negative diplococci consistent with N. gonorrhoeae. Polymerase chain reaction (PCR) testing further confirmed N. gonorrhoeae. Susceptibility testing revealed resistance to both cefixime and ceftriaxone. The patient was treated with dual therapy, consisting of a single oral dose of azithromycin (1 g) and cefixime (400 mg). Complete symptom resolution was achieved within one week. Conclusion: Third-generation ESCs, including injectable ceftriaxone and orally administered cefixime, are the most commonly used antibiotics for gonorrhoea treatment. Resistance to these drugs represents a significant global health threat. Discrepancies between antibiotic susceptibility test results and clinical outcomes highlight the need for further investigation into underlying factors contributing to treatment efficacy.
Identification of Methicillin-Resistant Staphylococcus aureus (MRSA) carriers in the nasal passages of healthcare workers at Universitas Udayana Hospital Winaya, Made Illene; Made Agus Hendrayana; Ni Nyoman Sri Budayanti; Ni Nengah Dwi Fatmawati
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.v5i1.82

Abstract

Background: Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen responsible for healthcare-associated infections (HAIs), with growing global concern due to its resistance to multiple antibiotics, including beta-lactams. Healthcare workers (HCWs), particularly those in critical care settings, are at risk of being asymptomatic carriers, facilitating MRSA transmission. This study aimed to determine the prevalence and distribution of MRSA carriers among healthcare workers (HCWs) at Universitas Udayana Hospital, Bali, Indonesia. Methods: A descriptive cross-sectional study was conducted from October to November 2024. A total of 44 nasal swab samples were collected from nurses across various hospital wards. Samples were cultured on Mannitol Salt Agar and underwent Gram staining, catalase, and coagulase testing. MRSA identification was confirmed using the cefoxitin disk diffusion method, with inhibition zones of ≤21 mm indicating methicillin resistance, as per CLSI guidelines. Data were analyzed descriptively. Results: MRSA colonization was identified in 4 out of 44 samples (9.1%), with cases distributed in the NICU (2 cases), ICU (1 case), and Surgical Ward (1 case). In addition, 12 samples (27.3%) were positive for methicillin-sensitive Staphylococcus aureus (MSSA), while 28 samples (63.6%) contained coagulase-negative staphylococci (CNS), predominantly in the outpatient and emergency departments. Conclusion: The presence of MRSA among HCWs, especially in critical units like NICU and ICU, emphasizes the importance of enhanced infection control measures. Routine screening, strict adherence to hand hygiene, appropriate use of personal protective equipment, and implementation of decolonization protocols, such as mupirocin application and chlorhexidine bathing, should be optimized to reduce MRSA transmission risks within healthcare facilities.
Trends in antimicrobial resistance of extended-spectrum beta-lactamase-producing Escherichia coli in urinary tract infections in ICU and non-ICU settings at Ngoerah Hospital, 2020-2022 Bryan Setiawan; Ni Nyoman Sri Budayanti; Fatmawati, Ni Nengah Dwi; I Putu Bayu Mayura
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.v5i1.83

Abstract

Background: Urinary Tract Infection (UTI) is one of the most common nosocomial infections, with Escherichia coli (E. coli) as the primary pathogen. The misuse and overuse of antibiotics has led to the emergence of antibiotic resistance, particularly in Extended-Spectrum Beta-Lactamase (ESBL)-producing E. coli. This resistance presents a significant challenge in managing UTIs, especially among ICU and non-ICU ward patients. This study aims to analyze trends in antibiotic resistance of ESBL-producing E. coli in UTI patients in ICU and non-ICU settings at Ngoerah Hospital during 2020–2022. Methods: A descriptive study with a cross-sectional approach was conducted. The inclusion criteria of this study were samples with identification results of E. coli bacteria with VITEK 2 Compact (bioMérieux, France), which showed E. coli with a probability greater than or equal to 90% and accompanied by sensitivity of E. coli bacteria to antibiotics. Result: Among 789 samples meeting inclusion criteria, 90% (714) were from non-ICU wards, while 10% (75) were from ICU wards. ESBL-producing E. coli accounted for 53% (416), while non-ESBL strains constituted 47% (373). The prevalence of ESBL-producing E. coli in non-ICU wards increased from 43% (96 isolates) in 2020 to 47% (129 isolates) in 2021 and 51% (149 isolates) in 2022. In ICU wards, prevalence rose from 3% (6 isolates) in 2020 to 4% (12 isolates) in 2021 and 8% (24 isolates) in 2022. Tigecycline, meropenem, and ertapenem demonstrated high sensitivity (≥96%), while beta-lactam antibiotics like ampicillin, cefixime, and cefazolin showed 100% resistance. Conclusion: The increasing resistance of ESBL-producing E. coli, particularly in non-ICU settings, highlights the need for strict antibiotic policies and monitoring to prevent further resistance.
Prevalence and antibiotic sensitivity patterns of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae in pneumonia patients at Ngoerah Hospital from 2020 to 2022 Arikandini, Dewa Ayu Putu Aisaka Rajeshi; Ni Nyoman Sri Budayanti; Ni Nengah Dwi Fatmawati; I Putu Bayu Mayura
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.v5i1.86

Abstract

Background: Pneumonia remains a major global cause of mortality, with Klebsiella pneumoniae recognized as a significant pathogen. The emergence of antibiotic resistance, particularly due to Extended-Spectrum Beta-Lactamase (ESBL) production by K. pneumoniae, complicates treatment efforts. This study aimed to determine the prevalence of ESBL-producing K. pneumoniae in pneumonia patients and assess its antibiotic sensitivity profile. Methods: A descriptive cross-sectional study was conducted retrospectively using secondary data from VITEK 2 Compact (bioMérieux) laboratory results on sputum samples collected from pneumonia patients at Ngoerah Hospital from 2020 to 2022. A total of 515 samples met the inclusion criteria out of 1,350 tested. Results: ESBL-producing K. pneumoniae was identified in 305 isolates (59.2%), with yearly prevalence rates of 63% in 2020, 52% in 2021, and 61% in 2022. Most patients were male (66.6%), aged 60 years or older (40%), and treated in non-ICU settings (69.2%), with expectorated sputum as the most common specimen type (63%). Antibiotic sensitivity testing revealed high susceptibility of ESBL-producing isolates to ertapenem (100%), meropenem (100%), amikacin (93%), and tigecycline (81%). Conclusion: ESBL-producing K. pneumoniae accounted for over half of pneumonia cases, with fluctuating prevalence across the study period. The infection predominantly affected older male patients treated in non-ICU wards. Despite resistance to many beta-lactam antibiotics, high sensitivity to carbapenems and other specific agents highlights their continued relevance in treatment. Surveillance of antibiotic resistance patterns remains essential for effective clinical management.
Appropriateness of antibiotic use and mortality risk factors in moderate to severe COVID-19 patients admitted to the intensive care unit of Bali Mandara Hospital in 2021 Saputra, I Wayan Agus Gede Manik; Laksana, Ngurah Putu Werda; Idayanti, Luh Gede Dewi; Shantivani, Made Intan; Yuliastini, Ni Luh Putu; Pratama, I Putu Agus Bayu; Laksana, Ida Ayu Candrika Widyasari
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.v5i1.69

Abstract

Introduction: The COVID-19 pandemic has been closely linked to the overuse of antibiotics, particularly in hospitalized patients. Early clinical uncertainty and lack of definitive treatments led to widespread empiric use. This study assessed the appropriateness of antibiotic use and identified mortality risk factors among moderate to severe COVID-19 patients in Bali Mandara Hospital's ICU. Methods: A retrospective cross-sectional study of 72 moderate to severe COVID-19 patients was conducted from 200 ICU admissions in 2021. Simple random sampling was used. Antibiotic appropriateness was assessed using the Gyssens method. Variables such as age, sex, severity, comorbidities (hypertension, diabetes), and culture results were analyzed using Chi-square tests. Result:  Among 322 antimicrobials, 226 were antibiotics. Gyssens' classification showed 40% appropriate use and 60% inappropriate use, mainly due to lack of indication (Category V). Age over 60, sex, and disease severity were significantly associated with mortality (p<0.05). Bacterial co-infection was confirmed in 30.6%, predominantly Enterobacteriaceae. Conclusion: Antibiotic appropriateness remains low, with substantial overuse. Mortality correlated significantly with age, sex, and disease severity. These findings underscore the need for enhanced antimicrobial stewardship and targeted clinical management in cases of severe COVID-19.
The effect of prolonged exposure to the antibiotic meropenem on the resistance characteristics of Acinetobacter baumannii in vitro Sutjipto, Yossy I.; Rahayu, Siwipeni I.; Santosaningsih, Dewi
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.v5i1.71

Abstract

Introduction: To prove the effect of prolonged exposure to the antibiotic meropenem on the emergence of Acinetobacter baumannii resistance in vitro. Methods: Meropenem-susceptible Acinetobacter baumannii isolates were exposed to 0.1 mg/ml meropenem and incubated for 8 days. The optical density and number of Acinetobacter baumannii bacterial colonies were observed every 24 hours. The average of optical density and the number of Acinetobacter baumannii bacterial colonies growing every 24 hours were analyzed using the Kruskal-Wallis test. Results: The results showed a decrease in the average optical density value and the number of Acinetobacter baumannii bacterial colonies from day 1 to day 6 of incubation. However, there was an increase in the average optical density and the number of Acinetobacter baumannii bacterial colonies starting on day 7 and day 8. Conclusions: Exposure to the antibiotic meropenem 0.1 mg/ml for 6 days might be associated with the emergence of Acinetobacter baumannii resistance in vitro.

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