Whole-genome sequencing applications for evolution of clinical microbiology
Original article Takashi Takahashi Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences and Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan Correspondence to Takashi Takahashi, E-mail: taka2si@lisci.kitasato-u.ac.jp Ann Clin Microbiol 2025;28(4):22. https://doi.org/10.5145/ACM.2025.28.4.3Received on 16 September 2025, Revised on 03 November 2025, Accepted on 03 November 2025, Published on 27 November 2025.Copyright © Korean […]
Impact of nontuberculous mycobacteria on the performance of Xpert MTB/RIF and Xpert MTB/RIF Ultra for the detection of tuberculosis and rifampin resistance: a diagnostic accuracy study
Original article Sangsoo Jung1,2, Eunsang Suh1*, Jun-Ki Lee1, Byung Woo Jhun3, Tae Yeul Kim1, Hee Jae Huh1,2, Nam Yong Lee1 1Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea 2Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Korea […]
Fig. 2. Trends in requests for bacterial cultures and antimicrobial susceptibility tests for patients suspected of (A) pneumonia, (B) sepsis, (C) UTI, (D) soft tissue infection. N, number; UTI, urinary tract infection.
Ann Clin Microbiol 2025;28(4):20. Factors influencing microbial diagnostic testing for infectious diseases in Korea: a nationwide retrospective cohort study Download image
Fig. 1. Trends in requests for tuberculosis-related tests. N, number; AFB, acid-fast bacilli; TB, tuberculosis.
Ann Clin Microbiol 2025;28(4):20. Factors influencing microbial diagnostic testing for infectious diseases in Korea: a nationwide retrospective cohort study Download image
Table 2. Factors affecting bacterial culture and antimicrobial susceptibility tests: multivariate analysis
Ann Clin Microbiol 2025;28(4):20. Factors influencing microbial diagnostic testing for infectious diseases in Korea: a nationwide retrospective cohort study Download table Characteristics Variates Pneumonia Bloodstream infection Urinary tract infection Soft tissue infection Total (n) Incidence rate (%) OR 95% CI P-value Total (n) Incidence rate (%) OR 95% CI P-value Total (n) Incidence rate (%) […]
Table 1. Factors affecting requesting tuberculosis-related tests: multivariate analysis
Ann Clin Microbiol 2025;28(4):20. Factors influencing microbial diagnostic testing for infectious diseases in Korea: a nationwide retrospective cohort study Download table Characteristics Variates Total (n) Incidence rate (%) AFB smear Mycobacterium culture Molecular diagnostic test OR 95% CI P-value OR 95% CI P-value OR 95% CI P-value Sex Male 260,824 1.01 1 – – 1 […]
Factors influencing microbial diagnostic testing for infectious diseases in Korea: a nationwide retrospective cohort study
Original article Young Ah Kim1, Jae Kwang Lee2, Hee Kyoung Choi3 1Department of Laboratory Medicine, 2Research Center, 3Department of Infectious Disease, National Health Insurance Service Ilsan Hospital, Goyang, Korea Correspondence to Young Ah Kim, E-mail: yakim@nhimc.or.kr Ann Clin Microbiol 2025;28(4):20. https://doi.org/10.5145/ACM.2025.28.4.1Received on 22 July 2025, Revised on 21 October 2025, Accepted on 23 October 2025, […]
Fig. 4. Circular visualization of MRSA complete genomes with HL21008 as a reference strain. The inner genome rings showed 100% identity (black), >= 98% (dark magenta) and >= 96% (red) for these reference isolates, reflecting similarity percentages determined by BLAST hit. Black peaks indicate GC content, and the innermost green and purple peaks denote positive and negative GC skews, respectively. MRSA: methicillin-resistant Staphylococcus aureus
Ann Clin Microbiol 2025;28(3):15. Complete genome analysis of representative methicillin-resistant Staphylococcus aureus clinical strains prevalent in Korea during 2014-2017 Download image
Fig. 3. Minimal spanning tree (MSTreeV2) based on cgMLST (left) and wgMLST (right) allelic profiles of the representative S. aureus strains, illustrating relationships between major clones. The Korean clinical MRSA strains are indicated by bolded rectangles. SCCmec II strains from Korea clustered closely with other representative SCCmec II strains. In contrast, SCCmec IVA strains of CC8 (HL16278 and HL18840) formed a distinct clade, separate from other SCCmec IV reference strains of CC8 in both allelic analysis of cgMLST and wgMLST, which is consistent with the findings of SNP-based phylogenetic tree analysis. A total of 2,009 cgMLST loci and 3,567 wgMLST loci were included in this analysis. MLST: multilocus sequence typing; SCCmec: staphylococcal cassette chromosome mec; SNP: single-nucleotide polymorphism
Ann Clin Microbiol 2025;28(3):15. Complete genome analysis of representative methicillin-resistant Staphylococcus aureus clinical strains prevalent in Korea during 2014-2017 Download image
Fig. 2. SNP-based phylogenetic tree with Snippy, Gubbins, and RAxML-NG analysis of the representative S. aureus strains, illustrating relationships between major clones. The Korean clinical MRSA strains are indicated by bolded rectangles. SCCmec II strains from Korea clustered closely with other representative SCCmec II strains. In contrast, SCCmec IVA strains of CC8 (HL16278 and HL18840) formed a distinct clade, separate from other SCCmec IV reference strains of CC8. A total of 112,574 SNP loci were included in the analysis.SNP: single-nucleotide polymorphism; MRSA: methicillin-resistant Staphylococcus aureus; SCCmec: staphylococcal cassette chromosome mec
Ann Clin Microbiol 2025;28(3):15. Complete genome analysis of representative methicillin-resistant Staphylococcus aureus clinical strains prevalent in Korea during 2014-2017 Download image