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  • Brief Communication2021-11-01
    Clinical Microbiology

    Clinical Performance of the Standard Q COVID-19 Rapid Antigen Test and Simulation of its Real-World Application in Korea

    Jaehyeon Lee , M.D., So Yeon Kim , M.D., Hee Jae Huh , M.D., Namsu Kim , M.D., Heungsup Sung , M.D., Hyukmin Lee , M.D., Kyoung Ho Roh , M.D., Taek Soo Kim , M.D., and Ki Ho Hong , M.D.

    Ann Lab Med 2021; 41(6): 588-592

    Abstract : The rapid antigen test (RAT) for coronavirus disease (COVID-19) represents a potent diagnostic method in situations of limited molecular testing resources. However, considerable performance variance has been reported with the RAT. We evaluated the clinical performance of Standard Q COVID-19 RAT (SQ-RAT; SD Biosensor, Suwon, Korea), the first RAT approved by the Korean Ministry of Food and Drug Safety. In total, 680 nasopharyngeal swabs previously tested using real-time reverse-transcription PCR (rRT-PCR) were retested using SQ-RAT. The clinical sensitivity of SQ-RAT relative to that of rRT-PCR was 28.7% for all specimens and was 81.4% for specimens with RNA-dependent RNA polymerase gene (RdRp) threshold cycle (Ct) values ≤23.37, which is the limit of detection of SQ-RAT. The specificity was 100%. The clinical sensitivity of SQ-RAT for COVID-19 diagnosis was assessed based on the Ct distribution at diagnosis of 33,294 COVID-19 cases in Korea extracted from the laboratory surveillance system of Korean Society for Laboratory Medicine. The clinical sensitivity of SQ-RAT for COVID-19 diagnosis in the Korean population was 41.8%. Considering the molecular testing capacity in Korea, use of the RAT for COVID-19 diagnosis appears to be limited.

  • Original Article2022-03-01
    Clinical Microbiology

    Clinical Differences in Patients Infected with Fusobacterium and Antimicrobial Susceptibility of Fusobacterium Isolates Recovered at a Tertiary-Care Hospital in Korea

    Myungsook Kim , Ph.D., Shin Young Yun , M.D., Yunhee Lee , B.D., Hyukmin Lee , M.D., Dongeun Yong , M.D., Kyungwon Lee , M.D.

    Ann Lab Med 2022; 42(2): 188-195

    Abstract : Background: Fusobacterium species are obligately anaerobic, gram-negative bacilli. Especially, F. nucleatum and F. necrophorum are highly relevant human pathogens. We investigated clinical differences in patients infected with Fusobacterium spp. and determined the antimicrobial susceptibility of Fusobacterium isolates. Methods: We collected clinical data of 86 patients from whom Fusobacterium spp. were isolated from clinical specimens at a tertiary-care hospital in Korea between 2003 and 2020. In total, 76 non-duplicated Fusobacterium isolates were selected for antimicrobial susceptibility testing by the agar dilution method, according to the Clinical and Laboratory Standards Institute guidelines (M11-A9). Results: F. nucleatum was most frequently isolated from blood cultures and was associated with hematologic malignancy, whereas F. necrophorum was mostly prevalent in head and neck infections. Anti-anaerobic agents were more commonly used to treat F. nucleatum and F. varium infections than to treat F. necrophorum infections. We observed no significant difference in mortality between patients infected with these species. All F. nucleatum and F. necrophorum isolates were susceptible to the antimicrobial agents tested. F. varium was resistant to clindamycin (48%) and moxifloxacin (24%), and F. mortiferum was resistant to penicillin G (22%) and ceftriaxone (67%). β-Lactamase activity was not detected. Conclusions: Despite the clinical differences among patients with clinically important Fusobacterium infections, there was no significant difference in the mortality rates. Some Fusobacterium spp. were resistant to penicillin G, ceftriaxone, clindamycin, or moxifloxacin. This study may provide clinically relevant data for implementing empirical treatment against Fusobacterium infections.

  • Brief Communication2022-01-01
    Clinical Microbiology

    Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay

    Ki Ho Hong , M.D., Ji Won In , M.D., Jaehyeon Lee , M.D., So Yeon Kim , M.D., Kyoung Ah Lee , M.T., Seunghyun Kim , M.T., Yeoungim An , M.T., Donggeun Lee , M.T., Heungsup Sung , M.D., Jae-Seok Kim , M.D., and Hyukmin Lee , M.D.

    Ann Lab Med 2022; 42(1): 96-99

    Abstract : The sensitivity of molecular diagnostics could be affected by nucleotide variants in pathogen genes, and the sites affected by such variants should be monitored. We report a single-nucleotide variant (SNV) in the nucleocapsid (N) gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), i.e., G29179T, which impairs the diagnostic sensitivity of the Xpert Xpress SARS-CoV-2 assay (Cepheid, Sunnyvale, CA, USA). We observed significant differences between the threshold cycle (Ct) values for envelope (E) and N genes and confirmed the SNV as the cause of the differences using Sanger sequencing. This SNV, G29179T, is the most prevalent in Korea and is associated with the B.1.497 virus lineage, which is dominant in Korea. Clinical laboratories should be aware of the various SNVs in the SARS-CoV-2 genome and consider their potential effects on the diagnosis of coronavirus disease 2019.

  • Guideline2022-07-01
    Clinical Microbiology

    Update of Guidelines for Laboratory Diagnosis of COVID-19 in Korea

    Ki Ho Hong , M.D., Gab Jung Kim , Ph.D., Kyoung Ho Roh , M.D., Heungsup Sung , M.D., Jaehyeon Lee , M.D., So Yeon Kim , M.D., Taek Soo Kim , M.D., Jae-Sun Park , Ph.D., Hee Jae Huh , M.D., Younhee Park , M.D., Jae-Seok Kim , M.D., Hyun Soo Kim , M.D., Moon-Woo Seong , M.D., Nam Hee Ryoo , M.D., Sang Hoon Song , M.D., Hyukmin Lee , M.D., Gye Cheol Kwon , M.D., and Cheon Kwon Yoo , Ph.D.

    Ann Lab Med 2022; 42(4): 391-397

    Abstract : Korean Society for Laboratory Medicine and the Korea Disease Prevention and Control Agency have announced guidelines for diagnosing coronavirus disease (COVID-19) in clinical laboratories in Korea. With the ongoing pandemic, we propose an update of the previous guidelines based on new scientific data. This update includes recommendations for tests that were not included in the previous guidelines, including the rapid molecular test, antigen test, antibody test, and self-collected specimens, and a revision of the previous recommendations. This update will aid clinical laboratories in performing laboratory tests for diagnosing COVID-19.

  • Letter to the Editor2021-09-01
    Clinical Microbiology

    Serological Evidence of Coxiella burnetii and SARS-CoV-2 Co-infection: A Case Report

    Hee Sue Park , M.D., Ph.D., Pan Kee Bae , Ph.D., Hye Won Jeong , M.D., Ph.D., Bo Ra Son , M.D., Ph.D., and Kyeong Seob Shin , M.D., Ph.D.

    Ann Lab Med 2021; 41(5): 510-513
  • Original Article2022-03-01
    Clinical Microbiology

    Virulence Factors Associated With Escherichia coli Bacteremia and Urinary Tract Infection

    Bongyoung Kim , M.D., Ph.D., Jin-Hong Kim , M.D., and Yangsoon Lee , M.D., Ph.D.

    Ann Lab Med 2022; 42(2): 203-212

    Abstract : Background: Extraintestinal pathogenic Escherichia coli (ExPEC) causes various infections, including urinary tract infection (UTI), sepsis, and neonatal meningitis. ExPEC strains have virulence factors (VFs) that facilitate infection by allowing bacterial cells to migrate into and multiply within the host. We compared the microbiological characteristics of ExPEC isolates from blood and urine specimens from UTI patients. Methods: We conducted a single-center, prospective study in an 855-bed tertiary-care hospital in Korea. We consecutively recruited 80 hospitalized UTI patients with E. coli isolates, which were isolated from blood and/or urine, and urine alone between March 2019 and May 2020. We evaluated the 80 E. coli isolates for the presence of bacterial genes encoding the sequence types (STs), antimicrobial resistance, and VFs using whole-genome sequencing (WGS). Results: We found no significant differences in STs, antimicrobial resistance patterns, or VFs between isolates from blood and urine specimens. ST131, a pandemic multidrug-resistant clone present in both blood and urine, was the most frequent ST (N=19/80, 24%), and ST131 isolates carried more virulence genes, especially, tsh and espC, than non-ST131 isolates. The virulence scores of the ST131 group and the ST69, ST95, and ST1193 groups differed significantly (P

  • Original Article2021-09-01
    Clinical Microbiology

    Risk Factors for Extended-Spectrum-β-Lactamase-Producing Escherichia coli in Community-Onset Bloodstream Infection: Impact on Long-Term Care Hospitals in Korea

    Yae Jee Baek , M.D., Young Ah Kim , M.D., Dokyun Kim , M.D., Jong Hee Shin , M.D., Young Uh , M.D., Kyeong Seob Shin , M.D., Jeong Hwan Shin , M.D., Seok Hoon Jeong , M.D., Geun Woo Lee , M.P.H., Eun Ji Lee , M.S, Dong-Sook Kim , Ph.D., Yoon Soo Park , M.D., Ph.D.

    Ann Lab Med 2021; 41(5): 455-462

    Abstract : Background: The prevalence of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) in the community has increased worldwide due to multifactorial reasons. ESBL-EC bloodstream infection (BSI) complicates the decision for proper antimicrobial administration. In this multicenter study, we investigated the prevalence, risk factors, and molecular background of community-onset (CO) ESBL-EC BSI. Methods: We included data for all episodes of ESBL-EC BSI of community origin from May 2016 to April 2017 obtained from the Korean national antimicrobial resistance surveillance system, which comprises six sentinel hospitals. Data, including previous history of admission and use of antimicrobials and medical devices before BSI, were collected, along with microbiological analysis results. Results: Among 1,189 patients with CO BSI caused by E. coli, 316 (27%) were identified as ESBL producers. History of admission, especially to a long-term care hospital (LTCH), and previous use of β-lactams/β-lactamase inhibitors, carbapenem, lincosamide, aminoglycoside, and extended-spectrum cephalosporin were independent risk factors for CO ESBL-EC BSI; admission to an LTCH showed the highest odds ratio (3.8, 95% confidence interval 2.3-6.1). The most common genotype was CTX-M-15 (N=131, 41%), followed by CTX-M-14 (N=86, 27%). ST131 was the most common sequence type among ESBL-EC groups (57%). Conclusions: In Korea, 27% of CO E. coli BSI were caused by ESBL producers. From perspectives of empirical treatment and infection control, history of admission to an LTCH and antimicrobial use should be noted.

  • Brief Communication2022-03-01
    Clinical Microbiology

    Serotype Distribution and Antimicrobial Resistance of Salmonella Isolates in Korea between 2016 and 2017

    Si Hyun Kim , Ph.D., Gyung-Hye Sung , Ph.D., Eun Hee Park , Ph.D., In Yeong Hwang , Ph.D., Gyu Ri Kim , Ph.D., Sae Am Song , M.D., Hae Kyung Lee , M.D., Young Uh , M.D., Young Ah Kim , M.D., Seok Hoon Jeong , M.D., Jong Hee Shin , M.D., Kyeong Seob Shin , M.D., Jaehyeon Lee , M.D., Joseph Jeong , M.D., Young Ree Kim , M.D., Dongeun Yong , M.D., Miae Lee , M.D., Yu Kyung Kim , M.D., Nam Hee Ryoo , M.D., Seungok Lee , M.D., Jayoung Kim , M.D., Sunjoo Kim , M.D., Hyun Soo Kim , M.D., and Jeong Hwan Shin , M.D.

    Ann Lab Med 2022; 42(2): 268-273

    Abstract : Salmonella is one of the major causes of food-borne infections. We investigated the serotype distribution and antimicrobial resistance of Salmonella isolates collected in Korea between January 2016 and December 2017. In total, 669 Salmonella isolates were collected from clinical specimens at 19 university hospitals. Serotyping was performed according to the Kauffmann–White scheme, and antimicrobial susceptibility was tested using Sensititre EUVSEC plates or disk diffusion. Among the strains, C (39.8%) and B (36.6%) were the most prevalent serogroups. In total, 51 serotypes were identified, and common serotypes were S. enterica serovar I 4,[5],12:i:- (16.7%), S. Enteritidis (16.1%), S. Bareilly (14.6%), S. Typhimurium (9.9%), and S. Infantis (6.9%). The resistance rates to ampicillin, chloramphenicol, and trimethoprim-sulfamethoxazole were 32.6%, 12.1%, and 8.4%, respectively. The resistance rates to cefotaxime and ciprofloxacin were 8.1% and 3.0%, respectively, while 5.4% were multidrug-resistant. S. enterica serovar I 4,[5],12:i:- and S. Enteritidis were highly prevalent, and there was an increase in rare serotypes. Multidrug resistance and ciprofloxacin resistance were highly prevalent. Periodic investigations of Salmonella serotypes and antimicrobial resistance are needed.

  • 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.

  • Original Article2022-01-01
    Clinical Microbiology

    Genotypic Distribution and Antimicrobial Susceptibilities of Carbapenemase-Producing Enterobacteriaceae Isolated From Rectal and Clinical Samples in Korean University Hospitals Between 2016 and 2019

    Seri Jeong , M.D., Nuri Lee , M.D., Min-Jeong Park , M.D., Kibum Jeon , M.D., Han-Sung Kim , M.D., Hyun Soo Kim , M.D., Jae-Seok Kim , M.D., and Wonkeun Song , M.D., Ph.D.

    Ann Lab Med 2022; 42(1): 36-46

    Abstract : Background: The emergence of carbapenemase-producing Enterobacteriaceae (CPE) represents a major clinical problem. Recently, the occurrence of CPE has increased globally, but epidemiological patterns vary across region. We report the trends in the genotypic distribution and antimicrobial susceptibility of CPE isolated from rectal and clinical samples during a four-year period. Methods: Between January 2016 and December 2019, 1,254 nonduplicated CPE isolates were obtained from four university hospitals in Korea. Carbapenemase genotypes were determined by multiplex real-time PCR. Antimicrobial susceptibility was profiled using the Vitek 2 system (bioMérieux, Hazelwood, MO, USA) or MicroScan Walkaway-96 system (Siemens West Sacramento, CA, USA). The proportions of carbapenemase genotypes and nonsusceptibility were analyzed using Pearson’s chi-square test. Results: Among the 1,254 CPE isolates, 486 (38.8%), 371 (29.6%), 357 (28.5%), 8 (0.6%), 8 (0.6%), and 24 (1.9%) were Klebsiella pneumoniae carbapenemase (KPC), oxacillinase (OXA)-48-like, New Delhi metallo-β-lactamase (NDM), imipenemase (IMP), Verona integron-encoded metallo-β-lactamase (VIM), and multiple producers, respectively. The predominant species was K. pneumoniae (72.6%), followed by Escherichia coli (6.5%). More than 90% of the isolates harboring KPC, NDM, and OXA-48-like were nonsusceptible to cephalosporins, aztreonam, and carbapenems. Conclusions: The impact of CPE is primarily due to KPC-, NDM-, and OXA-48-like-producing K. pneumoniae isolates. Isolates carrying these carbapenemase are mostly multidrug-resistant. Control strategies based on these genotypic distributions and antimicrobial susceptibilities of CPE isolates are required.

Journal Information March, 2023
Vol.43 No.2
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