Annals of Clinical Microbiology, The official Journal of the Korean Society of Clinical Microbiology
Hae-Sun Chung
Ann Clin Microbiol 2025 September, 28(3):19. Published on 20 September 2025.
Si Hyun Kim, Jeong Hwan Shin
Ann Clin Microbiol 2025 September, 28(3):16. Published on 11 September 2025.
Accurate identification of the Mycobacterium tuberculosis complex (MTBC) and nontuberculous mycobacteria (NTM) is crucial for effective patient management. With declining tuberculosis and rising NTM infections in South Korea, rapid diagnostics are essential. This review provides a comprehensive overview of current diagnostic methods for mycobacterial identification used in Korean clinical laboratories. The field has shifted from conventional methods, such as acid-fast bacilli staining, culture, and biochemical tests, toward rapid technologies. In Korea, immunochromatographic assays (ICA) targeting the MPT64 antigen are widely used to differentiate MTBC from NTM. For species-level NTM identification, laboratories employ advanced techniques including mycolic acid analysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and diverse molecular assays. Prominent molecular diagnostics include real-time PCR, PCR-restriction fragment length polymorphism (RFLP), line probe assays (LPA), and DNA sequencing of genes like 16S rRNA and rpoB. These modern techniques offer significantly improved speed and accuracy, replacing traditional approaches in routine diagnostics. In South Korea, modern tools have supplanted conventional methods for mycobacterial identification. Real-time PCR and antigen detection are the primary assays for identifying MTBC in cultures. For NTM species, laboratories use a range of techniques including PCR-RFLP, HPLC, LPA, MALDI-TOF MS, and sequencing. Next-generation sequencing is poised to become a pivotal future tool, offering comprehensive species identification and simultaneous profiling of drug resistance. Those modern techniques will transform diagnostic and surveillance strategies for mycobacterial diseases.
Minh Phuong Trinh, Min-Kyoung Shin
Ann Clin Microbiol 2025 September, 28(3):18. Published on 20 September 2025.
(This article belongs to the Special Issue on Current Trends in Laboratory Diagnosis and Public Health of Mycobacterial Diseases in Korea.)
Mycobacterium tuberculosis (MTB) and nontuberculous mycobacteria (NTM) present distinct clinical and epidemiological challenges and thus require tailored genotyping approaches. MTB is a globally transmissible pathogen for which diagnostic and surveillance infrastructures are well defined, whereas NTM infections are environmentally acquired, taxonomically diverse, and increasingly prevalent among vulnerable populations. Molecular genotyping is indispensable for both pathogen groups, supporting outbreak investigation and drug resistance prediction for MTB and species-level identification and relapse-versusreinfection distinction for NTM. In this review, the evolution of strategies for genotyping mycobacteria are outlined, and traditional techniques (e.g., spoligotyping and mycobacterial interspersed repetitive unit–variable number tandem repeat genotyping) and advanced methods (multilocus sequence typing and whole-genome sequencing) are compared. We highlight the divergent drivers of genotyping between MTB and NTM, examine key technical and interpretive challenges, and discuss how cross-learning between these two fields can accelerate innovation. Emerging technologies such as portable sequencing platforms, artificial intelligence-assisted analysis, and curated genomic databases are expanding access to high-resolution genotyping. However, significant gaps remain, particularly in standardizing NTM genomic analyses and integrating genotypic data into global surveillance systems. By exploring the intersections between MTB and NTM molecular epidemiology, a synergistic pathway for more precise, accessible, and effective mycobacterial genotyping is highlighted.
Ha-eun Cho, Young Jin Kim
Ann Clin Microbiol 2025 September, 28(3):17. Published on 20 September 2025.
(This article belongs to the Special Issue on Current Trends in Laboratory Diagnosis and Public Health of Mycobacterial Diseases in Korea.)
Latent tuberculosis (TB) refers to a state in which an individual is infected with Mycobacterium tuberculosis but shows no clinical symptoms. The World Health Organization estimates that 23% of the global population has latent TB, which poses a significant public health challenge owing to the risk of progression to active TB. Diagnosis of latent TB involves tests, such as the tuberculin skin test (TST) and interferon-gamma release assays (IGRAs). The TST can yield false positives due to prior Bacillus Calmette-Guérin (BCG) vaccination, whereas IGRAs offer higher specificity and are unaffected by BCG vaccination. Factors, such as age and recent vaccinations, can affect test performance. Treatment with isoniazid and rifampicin is recommended for those diagnosed, as it has been shown to prevent 80%-90% of active TB cases, although more extended follow-up studies are needed to confirm its long-term efficacy. Indeterminate IGRA results, especially in immunocompromised individuals, add complexity to the diagnosis and treatment decisions, highlighting the need for careful interpretation. Further research is vital to improve the diagnostic accuracy, interpretation, and treatment effectiveness.
Young Ah Kim, Jaekwang Lee, Sunmin Lee
Ann Clin Microbiol 2025 September, 28(3):12. Published on 24 July 2025.
Backgrounds: The coronavirus disease 2019 (COVID-19) pandemic has retreated the years of progress that essential tuberculosis (TB) medical services provided in reducing the burden of TB. This study evaluated the clinical impact of the COVID-19 pandemic on TB management based on treatment discontinuation and mortality rates.
Methods: Two time intervals were included in this study: before the spread of COVID-19 (2018–2019) and during the pandemic phase of COVID-19 (2020–2021). Newly diagnosed patients with pulmonary TB (42,930 before and 32,094 during COVID-19) were included using the national reimbursement data from the health insurance service in Korea. Treatment discontinuation was defined as the discontinuation of treatment for more than 2 weeks during the initial intensive care phase or for more than 2 months during the maintenance phase. Mortality rates were compared before the spread and during the pandemic phase of COVID-19 in all patients and subgroups with various comorbidities. The Kaplan–Meier survival curve for each group of study participants was derived, and collective statistical significance was confirmed using the log-rank test.
Results: The treatment discontinuation rate over the entire period showed a trend of decreasing the time factor (-0.0084), decreasing the level change (-0.0166), and increasing the intersection term (0.0039). These tendencies were similar during the initial intensive care and maintenance treatment periods, suggesting that the decreasing trend over time was significant, but the level change and slope change before the spread and during the pandemic phase of COVID-19 were not in agreement. The total mortality rates increased more during the COVID-19 pandemic (14.6% increase after 1 year and 18.9% increase after 2 years, based on 2020) than before COVID-19 (12.3% increase after 1 year and 16.1% increase after 2 years, based on 2018). Regarding the impact of comorbidities on TB mortality, malnutrition and diabetes showed a strong impact on the mortality with more than 2 of relative risks both in 1-year and 2-year mortalities.
Conclusion: This study verified the clinical impact of the COVID-19 pandemic on TB management. Therefore, establishing appropriate TB management policies is urgently needed for the future COVID-19-like pandemic situation.
Heejung Kim
Ann Clin Microbiol 2025 September, 28(3):14. Published on 20 September 2025.
Background: Accurate diagnosis of Clostridioides difficile infection (CDI) requires both microbiologic confirmation and clinical correlation. Current guidelines recommend a two-step algorithm combining a sensitive screening test with a specific confirmatory assay. This study evaluated the diagnostic performance of the glutamate dehydrogenase (GDH)/toxin enzyme immunoassay (EIA) over five years and assessed its suitability as an initial screening test.
Methods: We retrospectively analyzed 8,685 C. difficile-related tests conducted between March 2020 to February 2025. The GDH/toxin EIA was performed using the C. DIFF QUIK CHEK COMPLETE (TechLab). Toxigenic culture involved alcohol-shocked stool samples plated on chromogenic agar and incubated anaerobically for 48 hours. Toxin gene polymerase chain reaction (PCR) was done using the BD MAX Cdiff assay and the Xpert C. difficile assay.
Results: The GDH test showed a sensitivity of 77.0% and negative predictive value (NPV) of 95.1% compared with culture. The toxin EIA showed 35.0% sensitivity and 96.9% positive predictive value relative to PCR. The combined GDH+Toxin EIA achieved 82.6% sensitivity and 96.9% NPV compared with PCR. Most discordant results involved low bacterial burden or non-toxigenic isolates. GDH positivity correlated with growth quantity, and toxin EIA positivity varied by ribotype. Algorithm modeling suggested the GDH/toxin test as a cost-effective first-line option.
Conclusion: The GDH/toxin EIA demonstrated high NPV and may be appropriate as an initial test in CDI diagnostic algorithms. These findings support its role in diagnostic stewardship and provide evidence to inform the development of national diagnostic guidelines in Korea.
Harshad Lade, Tae-Im Kim, Jung-Min Kim, Yong-Kyun Kim, Kibum Jeon, Hyun Soo Kim, Han-Sung Kim, Wonkeun Song, Jae-Seok Kim
Ann Clin Microbiol 2025 September, 28(3):15. Published on 10 September 2025.
Background: Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen responsible for various clinical infections. The investigation of representative MRSA genomes is important for understanding their molecular epidemiology and genetic evolution, as well as MRSA infections. We characterized the complete genome sequences of representative MRSA clinical strains prevalent in Korea between 2014 and 2017.
Methods: Ten representative clinical MRSA strains were selected based on the Staphylococcal Cassette Chromosome mec (SCCmec) type. Complete genomes were generated via hybrid assembly using long- and short-read sequencing. Analyses of resistance and virulence genes, whole-genome alignment, phylogenetic tree construction, and comparative genome hybridization were performed.
Results: The average chromosomal lengths were 2.916 Mb in SCCmec II (n = 6), 2.920 Mb in SCCmec IV (n = 2), and 2.777 Mb in SCCmec IVA (n = 2). The number of genome coding sequences ranged from 2,713 to 3,026, with an average of 2,946 in SCCmec II, 3,001 in SCCmec IV, and 2,740 in SCCmec IVA. Only the SCCmec IV and spa t008 strains (n = 2) harbored the Panton–Valentine leukocidin gene, which is rarely detected in Korea. The SCCmec IVA strains of ST72 showed a distinct genetic group compared with other representative SCCmec IV strains, as determined by single-nucleotide polymorphism analysis.
Conclusion: In the present study, the complete and gap-filled genome sequences of representative MRSA clones prevalent in Korea were derived and characterized by genome size, virulence, antimicrobial resistance genes, and their evolutionary relationships. Information on these clinical MRSA strains would enhance our understanding of the pathogenicity and molecular epidemiology of Korean MRSA isolates.
Yeon Chan Choi, Eun-Young Kim, Hyun Jin Choi, Si Hyun Kim, Eunkyoung You, Ja Young Lee, Jihyun Cho, Seok Hoon Jeong, Dokyun Kim, Hyun Soo Kim, Soo Hyun Kim, Young Ah Kim, Young Ree Kim, Nam Hee Ryoo, Jong Hee Shin, Kyeong Seob Shin, Young Uh, Jeong Hwan Shin
Ann Clin Microbiol 2025 September, 28(3):13. Published on 2 September 2025.
Background: Haemophilus is an important pathogen in community-acquired pneumonia and invasive diseases, such as sepsis and meningitis. We aimed to evaluate the VITEK 2 system and VITEK MS system for the identification of Haemophilus strains isolated from clinical specimens in Korea during 2023.
Methods: In total, 118 Haemophilus strains isolated from respiratory specimens (n = 107) and blood samples (n = 11) from 10 sentinel hospitals in Kor-GLASS were included in this study. All Haemophilus strains were evaluated using the VITEK 2 and VITEK MS systems. Real-time PCR and 16S rRNA sequencing were used to identify specific species.
Results: Among the 118 Haemophilus isolates, 115 were identified as H. influenzae by realtime PCR using hpd gene, and the remaining three strains were identified as H. parainfluenzae by 16S rRNA sequencing. Eighty-eight of the 115 (76.5%) and two of three (66.7%) isolates were correctly identified as H. influenzae and H. parainfluenzae, respectively, using the VITEK 2 system. The VITEK 2 system showed low discrimination (n = 22), misidentification (n = 4), and unidentified organisms (n = 2) in the 28 Haemophilus strains. The VITEK MS system achieved 100% sensitivity and specificity in identifying all 115 H. influenzae and three H. parainfluenzae isolates.
Conclusion: The VITEK MS system showed excellent performance in the identification of H. influenzae and H. parainfluenzae, whereas the VITEK 2 system showed relatively low concordance.
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