Most Read (Last 3 years)

  • Original Article2023-01-01 Clinical Microbiology

    Serotype Distribution and Antimicrobial Resistance of Streptococcus pneumoniae Causing Invasive Pneumococcal Disease in Korea Between 2017 and 2019 After Introduction of the 13-Valent Pneumococcal Conjugate Vaccine

    Gyu Ri Kim , Ph.D., Eun-Young Kim , Ph.D., Si Hyun Kim , Ph.D., Hae Kyung Lee , M.D., Jaehyeon Lee , M.D., Jong Hee Shin , M.D., Young Ree Kim , M.D., Sae Am Song , M.D., Joseph Jeong , M.D., Young Uh , M.D., Yu Kyung Kim , M.D., Dongeun Yong , M.D., Hyun Soo Kim , M.D., Sunjoo Kim , M.D., Young Ah Kim , M.D., Kyeong Seob Shin , M.D., Seok Hoon Jeong , M.D., Namhee Ryoo , M.D., and Jeong Hwan Shin , M.D.

    Ann Lab Med 2023; 43(1): 45-54

    Abstract : Background: Streptococcus pneumoniae is a serious pathogen causing various infections in humans. We evaluated the serotype distribution and antimicrobial resistance of S. pneumoniae causing invasive pneumococcal disease (IPD) after introduction of pneumococcal conjugate vaccine (PCV)13 in Korea and investigated the epidemiological characteristics of multidrug-resistant (MDR) isolates. Methods: S. pneumoniae isolates causing IPD were collected from 16 hospitals in Korea between 2017 and 2019. Serotyping was performed using modified sequential multiplex PCR and the Quellung reaction. Antimicrobial susceptibility tests were performed using the broth microdilution method. Multilocus sequence typing was performed on MDR isolates for epidemiological investigations. Results: Among the 411 S. pneumoniae isolates analyzed, the most prevalent serotype was 3 (12.2%), followed by 10A (9.5%), 34 (7.3%), 19A (6.8%), 23A (6.3%), 22F (6.1%), 35B (5.8%), 11A (5.1%), and others (40.9%). The coverage rates of PCV7, PCV10, PCV13, and pneumococcal polysaccharide vaccine (PPSV)23 were 7.8%, 7.8%, 28.7%, and 59.4%, respectively. Resistance rates to penicillin, ceftriaxone, erythromycin, and levofloxacin were 13.1%, 9.2%, 80.3%, and 4.1%, respectively. MDR isolates accounted for 23.4% of all isolates. Serotypes 23A, 11A, 19A, and 15B accounted for the highest proportions of total isolates at 18.8%, 16.7%, 14.6%, and 8.3%, respectively. Sequence type (ST)166 (43.8%) and ST320 (12.5%) were common among MDR isolates. Conclusions: Non-PCV13 serotypes are increasing among invasive S. pneumoniae strains causing IPD. Differences in antimicrobial resistance were found according to the specific serotype. Continuous monitoring of serotypes and antimicrobial resistance is necessary for the appropriate management of S. pneumoniae infections.

  • Guideline2022-09-01 Clinical Microbiology

    Guidelines for Mobile Laboratories for Molecular Diagnostic Testing of COVID-19

    Kyoung Ho Roh , M.D., Ki Ho Hong , M.D., Myung-Hyun Nam , M.D., Taek Soo Kim , M.D., Moon-Woo Seong , M.D., Jin Kyung Lee , M.D., Sookyoung Bae , M.D., Hee Jae Huh , M.D., Jeong-Yeal Ahn , M.D., Jinsook Lim , M.D., Gab Jung Kim , Ph.D., Jae Sun Park , Ph.D., Hyun Yeong Kim , Ph.D., Cheon Kwon Yoo , Ph.D., and Hyukmin Lee , M.D. on behalf of Korean Society for Laboratory Medicine, COVID-19 Task Force, and the Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency

    Ann Lab Med 2022; 42(5): 507-514

    Abstract : With the rapid spread of the coronavirus disease (COVID-19), the need for rapid testing and diagnosis and consequently, the demand for mobile laboratories have increased. Despite this need, there are no clear guidelines for the operation, maintenance, or quality control of mobile laboratories. We provide guidelines for the operation, management, and quality control of mobile laboratories, and specifically for the implementation and execution of COVID-19 molecular diagnostic testing. These practical guidelines are primarily based on expert opinions and a laboratory accreditation inspection checklist. The scope of these guidelines includes the facility, preoperative evaluation, PCR testing, internal and external quality control, sample handling, reporting, laboratory personnel, biosafety level, and laboratory safety management. These guidelines are useful for the maintenance and operation of mobile laboratories not only in normal circumstances but also during public health crises and emergencies.

  • Guideline2023-03-01 Clinical Microbiology

    Guidelines for the Laboratory Diagnosis of Monkeypox in Korea

    Ki Ho Hong , M.D., Gab Jung Kim , Ph.D., Kyoung Ho Roh , M.D., Hyukmin Lee , M.D., Ok Kyu Park , M.S., Taek Soo Kim , M.D., Jae-Seok Kim , M.D., Jaehyeon Lee , M.D., Moon-Woo Seong , M.D., So Yeon Kim , M.D., Jae-Sun Park , Ph.D., Younhee Park , M.D., Hee Jae Huh , M.D., Namhee Ryoo , M.D., Hyun Soo Kim , M.D., Heungsup Sung , M.D., and Cheon Kwon Yoo , Ph.D.; On behalf of the Committee of Management of Laboratory Tests for Infectious Diseases, Korean Society for Laboratory Medicine, and the Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency

    Ann Lab Med 2023; 43(2): 137-144

    Abstract : While the coronavirus disease 2019 pandemic is ongoing, monkeypox has been rapidly spreading in non-endemic countries since May 2022. Accurate and rapid laboratory tests are essential for identifying and controlling monkeypox. Korean Society for Laboratory Medicine and the Korea Disease Prevention and Control Agency have proposed guidelines for diagnosing monkeypox in clinical laboratories in Korea. These guidelines cover the type of tests, selection of specimens, collection of specimens, diagnostic methods, interpretation of test results, and biosafety. Molecular tests are recommended as confirmatory tests. Skin lesion specimens are recommended for testing in the symptomatic stage, and the collection of both blood and oropharyngeal swabs is recommended in the presymptomatic or prodromal stage.

  • Original Article2023-09-01 Clinical Microbiology

    Comparison of Nasal Swabs, Nasopharyngeal Swabs, and Saliva Samples for the Detection of SARS-CoV-2 and other Respiratory Virus Infections

    Eun Ju Jung , M.D., Ph.D., Su Kyung Lee , M.S., Seon Hee Shin , M.D., Ph.D., Jin Soo Kim , M.D., Ph.D., Heungjeong Woo , M.D., Ph.D., Eun-Jung Cho , M.D., Ph.D., Jungwon Hyun , M.D., Ph.D., Jae-Seok Kim , M.D., Ph.D., and Hyun Soo Kim , M.D., Ph.D.

    Ann Lab Med 2023; 43(5): 434-442

    Abstract : Background: Nasal swabs and saliva samples are being considered alternatives to nasopharyngeal swabs (NPSs) for detecting severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2); however, few studies have compared the usefulness of nasal swabs, NPSs, and saliva samples for detecting SARS-CoV-2 and other respiratory virus infections. We compared the positivity rates and concentrations of viruses detected in nasal swabs, NPSs, and saliva samples using cycle threshold (Ct) values from real-time PCR tests for respiratory viruses. Methods: In total, 236 samples (48 five-rub and 10 10-rub nasal swabs, 96 NPSs collected using two different products, 48 saliva swabs, and 34 undiluted saliva samples) from 48 patients (34 patients with SARS-CoV-2 and 14 with other respiratory virus infections) and 40 samples from eight healthy controls were obtained. The PCR positivity and Ct values were compared using Allplex Respiratory Panels 1/2/3 and Allplex SARS-CoV-2 real-time PCR. Results: NPSs showed the lowest Ct values (indicating the highest virus concentrations); however, nasal and saliva samples yielded positive results for SARS-CoV-2 and other respiratory viruses. The median Ct value for SARS-CoV-2 E gene PCR using nasal swab samples collected with 10 rubs was significantly different from that obtained using nasal swabs collected with five rubs (Ct=24.3 vs. 28.9; P=0.002), but not from that obtained using NPSs. Conclusions: Our results confirm that the NPS is the best sample type for detecting respiratory viruses, but nasal swabs and saliva samples can be alternatives to NPSs. Vigorously and sufficiently rubbed nasal swabs can provide SARS-CoV-2 concentrations similar to those obtained with NPSs.

  • Original Article2023-09-01 Clinical Microbiology

    European Committee on Antimicrobial Susceptibility Testing-Recommended Rapid Antimicrobial Susceptibility Testing of Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus From Positive Blood Culture Bottles

    Jong-Min Park , Ph.D., Mijung Kwon , M.T., Ki Ho Hong , M.D., Hyukmin Lee , M.D., and Dongeun Yong , M.D.

    Ann Lab Med 2023; 43(5): 443-450

    Abstract : Background: Early diagnosis and treatment are important for a good prognosis of bloodstream infections. The European Committee on Antimicrobial Susceptibility Testing (EUCAST) recommends rapid antimicrobial susceptibility testing (RAST) based on the disk diffusion methodology for 4, 6, and 8 hours of incubation. We evaluated EUCAST-RAST of Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus from positive blood culture bottles. Methods: Twenty strains of E. coli, K. pneumoniae, and S. aureus were tested using EUCAST-RAST. Ten antimicrobial agents against E. coli and K. pneumoniae and four agents against S. aureus were tested. The diameter of the inhibition zone (mm) was compared with the minimal inhibitory concentration (μg/mL) obtained using the Sensititre AST system (TREK Diagnostic Systems, East Grinstead, UK). Results: For E. coli, the percentage of total categorical agreement (CA) was 69.5% at 4 hours, and 87% at 8 hours. For K. pneumoniae, the total CA was 89% at 4 hours, and 95.5% at 6 hours. For S. aureus, the total CA was 100% after 4 hours. Discrepancies were observed mainly for E. coli with β-lactam antimicrobial agents, and the numbers of errors decreased over time. Conclusions: EUCAST-RAST for K. pneumoniae and S. aureus met the United States Food and Drug Administration criteria at 6 and 4 hours, respectively, whereas that for E. coli did not meet the criteria for up to 8 hours. RAST can shorten the turn-around testing time by more than one day; therefore, if applied accurately according to laboratory conditions, antimicrobial agent results can be reported faster.

  • Original Article2024-01-01 Clinical Microbiology

    Changing Genotypic Distribution, Antimicrobial Susceptibilities, and Risk Factors of Urinary Tract Infection Caused by Carbapenemase-Producing Pseudomonas aeruginosa

    Seri Jeong , M.D., Kibum Jeon , M.D., Nuri Lee , M.D., Min-Jeong Park , M.D., and Wonkeun Song , M.D.

    Ann Lab Med 2024; 44(1): 38-46

    Abstract : Background: Carbapenem-resistant Pseudomonas aeruginosa (CrPA) is a leading cause of healthcare-associated urinary tract infections (UTIs). Carbapenemase production is an important mechanism that significantly alters the efficacy of frequently used anti-pseudomonal agents. Reporting the current genotypic distribution of carbapenemase-producing P. aeruginosa (CPPA) isolates in relation to antimicrobial susceptibility, UTI risk factors, and mortality is necessary to increase the awareness and control of these strains. Methods: In total, 1,652 non-duplicated P. aeruginosa strains were isolated from hospitalized patients between 2015 and 2020. Antimicrobial susceptibility, carbapenemase genotypes, risk factors for UTI, and associated mortality were analyzed. Results: The prevalence of carbapenem-non-susceptible P. aeruginosa isolates showed a decreasing trend from 2015 to 2018 and then increased in the background of the emergence of New Delhi metallo-β-lactamase (NDM)-type isolates since 2019. The CPPA strains showed 100.0% non-susceptibility to all tested antibiotics, except aztreonam (94.5%) and colistin (5.9%). Carbapenems were identified as a risk and common predisposing factor for UTI (odds ratio [OR]=1.943) and mortality (OR=2.766). Intensive care unit (ICU) stay (OR=2.677) and white blood cell (WBC) count (OR=1.070) were independently associated with mortality. Conclusions: The changing trend and genetic distribution of CPPA isolates emphasize the need for relentless monitoring to control further dissemination. The use of carbapenems, ICU stay, and WBC count should be considered risk factors, and aggressive antibiotic stewardship programs and monitoring may serve to prevent worse outcomes.

  • Original Article2023-03-01 Clinical Microbiology

    Performance Comparison Between Fourier-Transform Infrared Spectroscopy–based IR Biotyper and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry for Strain Diversity

    Son Young Jun , Ph.D., Young Ah Kim , M.D., Ph.D., Suk-Jun Lee , Ph.D., Woon-Won Jung , Ph.D., Hyun-Sook Kim , Ph.D., Sung-Soo Kim , Ph.D., Hyunsoo Kim , M.D., Dongeun Yong , M.D., and Kyungwon Lee , M.D.

    Ann Lab Med 2023; 43(2): 174-179

    Abstract : Background: Development of an accessible method to routinely evaluate the clonality of strains is needed in microbiology laboratories. We compared the discriminatory power of the Fourier-transform infrared (FTIR) spectroscopy–based IR Biotyper (Bruker Daltonics GmbH, Bremen, Germany) to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), using whole-genome sequencing (WGS) as the reference method. Methods: Eighty-three extended-spectrum β-lactamase–producing Escherichia coli isolates were tested using WGS, MALDI-TOF MS, and IR Biotyper. Simpson’s diversity index (SDI), a statistical analysis for testing the homogeneity of a dendrogram, and the adjusted Rand index (aRI) were used to compare the discriminatory ability between typing tests. Results: The SDI (95% confidence interval) was 0.969 (0.952–0.985) for WGS, 0.865 (0.807–0.924) for MALDI-TOF MS, and 0.974 (0.965–0.983) for IR Biotyper. Compared with WGS, IR Biotyper showed compatible diversity, whereas MALDI-TOF MS did not. The concordance and aRI improved from 66.3% to 84.3% and from 0.173 to 0.538, respectively, for IR Biotyper versus MALDI-TOF MS with WGS as the reference method. IR Biotyper showed substantially improved performance in strain typing compared with MALDI-TOF MS. Conclusions: IR Biotyper is useful for diversity analysis with improved discriminatory power over MALDI-TOF MS in comparison with WGS as a reference method. IR Biotyper is an accessible method to evaluate the clonality of strains and could be applied in epidemiological analysis during an outbreak of a health care facility, as well as for research on the transmission of resistant bacteria in community settings.

  • Original Article2023-03-01 Clinical Microbiology

    Comparative Analysis of the Molecular Characteristics of Group B Streptococcus Isolates Collected from Pregnant Korean Women Using Whole-genome Sequencing

    Yangsoon Lee , M.D., Ph.D., Hye Gyung Bae , M.D., Ph.D., Dongju Won , M.D., Ph.D., Woobin Yun , M.S., Hyukmin Lee , M.D., Ph.D., Jong Rak Choi , M.D., Ph.D., Young Uh , M.D., Ph.D., and Kyungwon Lee , M.D., Ph.D.

    Ann Lab Med 2023; 43(2): 180-186

    Abstract : Background: The incidence of early- and late-onset sepsis and meningitis in neonates due to maternal rectovaginal group B Streptococcus (GBS) colonization may differ with serotype distribution and clonal complex (CC). CC17 strains are associated with hypervirulence and poor disease outcomes. GBS serotypes are distinguished based on the polysaccharide capsule, the most important virulence factor. We determined the sequence type distribution of GBS isolates from pregnant women in Korea and validated whole-genome sequencing (WGS)-based prediction of antimicrobial susceptibility and capsular serotypes in GBS isolates. Methods: Seventy-five GBS isolates collected from pregnant Korean women visiting Wonju Severance Christian Hospital, Wonju, Korea between 2017 and 2019 were subjected to WGS using the NovaSeq 6000 system (Illumina, San Diego, CA, USA). Multilocus sequence types, serotypes, antimicrobial resistance genes, and hemolysin operon mutations were determined by WGS, and the latter three were compared with the results of conventional phenotypic methods. Results: The predominant lineage was CC1 (37.3%), followed by CC19 (32.0%), CC12 (17.3%), and CC17 (4.0%). All isolates were cps typeable (100%, (75/75), and 89.3% of cps genotypes (67/75) were concordant with serotypes obtained using latex agglutination. The cps genotypes of the 75 isolates were serotypes III (24.0%), V (22.7%), and VIII (17.3%). All isolates harboring intact ermB and tet were non-susceptible to erythromycin and tetracycline, respectively. Three non-hemolytic strains had 1-bp frameshift insertions in cylE. Conclusions: The low prevalence of CC17 GBS colonization may explain the low frequency of neonatal GBS infections. WGS is a useful tool for simultaneous genotyping and antimicrobial resistance determination.

  • Letter to the Editor2023-01-01 Clinical Microbiology

    Comparison of the Clinical Performance of the Point-of-care STANDARD M10 SARS-CoV-2 and Xpert Xpress SARS-CoV-2 Assays

    Ki Ho Hong , M.D., Jaehyeon Lee , M.D., So Yeon Kim , M.D., Yeseul Oh , M.T., Hae Weon Cho , M.D., and Hyukmin Lee , M.D.

    Ann Lab Med 2023; 43(1): 111-113
  • Letter to the Editor2023-01-01 Clinical Microbiology

    Reemergence of Parainfluenza Virus Type 3 and Respiratory Syncytial Virus Infections During the COVID-19 Pandemic

    Kuenyoul Park , M.D., Heungsup Sung , M.D., and Mi-Na Kim , M.D.

    Ann Lab Med 2023; 43(1): 114-116
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