Original Article2022-03-01 Clinical Microbiology
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.
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.
Original Article2022-03-01 Clinical Microbiology
Bongyoung Kim , M.D., Ph.D., Jin-Hong Kim , M.D., and Yangsoon Lee , M.D., Ph.D.
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
Guideline2022-07-01 Clinical Microbiology
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.
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.
Brief Communication2022-01-01 Clinical Microbiology
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.
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.
Original Article2023-01-01 Clinical Microbiology
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.
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.
Brief Communication2022-03-01 Clinical Microbiology
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.
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
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
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.
Letter to the Editor2022-01-01 Clinical Microbiology
Young-gon Kim , M.D., Hyunwoong Park , M.D., Ph.D., So Yeon Kim , M.D., Ph.D., Ki Ho Hong , M.D., Ph.D., Man Jin Kim , M.D., Jee-Soo Lee , M.D., Sung-Sup Park , M.D., Ph.D., and Moon-Woo Seong , M.D., Ph.D.
Original Article2022-01-01 Clinical Microbiology
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.
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.
Brief Communication2022-07-01 Clinical Microbiology
Tae Yeul Kim , M.D., Ji-Youn Kim , M.T., Hyang Jin Shim , M.T., Sun Ae Yun , M.T., Ja-Hyun Jang , M.D., Hee Jae Huh , M.D., Jong-Won Kim , M.D., and Nam Yong Lee , M.D.
Abstract : Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and influenza viruses may pose enormous challenges to our healthcare system. We evaluated the performance of the PowerChek SARS-CoV-2, Influenza A & B Multiplex Real-time PCR Kit (PowerChek; Kogene Biotech, Seoul, Korea) in comparison with the BioFire Respiratory Panels 2 and 2.1 (RP2 and RP2.1; bioMérieux, Marcy l’Étoile, France), using 147 nasopharyngeal swabs. The limit of detection (LOD) of the PowerChek assay was determined using SARS-CoV-2, influenza A, and B RNA standards. The LOD values of the PowerChek assay for SARS-CoV-2 and influenza A and B were 1.12, 1.24, and 0.61 copies/μL, respectively. The positive and negative percent agreements of the PowerChek assay compared with RP2 and RP2.1 were 97.5% (39/40) and 100% (107/107) for SARS-CoV-2; 100% (39/39) and 100% (108/108) for influenza A; and 100% (35/35) and 100% (112/112) for influenza B, respectively. The performance of the PowerChek assay was comparable to that of RP2 and RP2.1 for detecting SARS-CoV-2 and influenza A and B, suggesting its use in diagnosing SARS-CoV-2 and influenza infections.
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