BACKGROUND: The SD Bioline Strep A Ultra (SD, Yongin, Korea) is a recently developed rapid antigen detection test (RADT) for diagnosing bacterial pharyngitis caused by Group A Streptococcus, We evaluated the performance of SD Bioline Strep A Ultra, using the number of colony forming units and color intensity. METHODS: Three throat swabs each were taken from 343 children with pharyngitis who visited pediatric clinics. We evaluated the performance of SD Bioline Strep A Ultra and compared its positive rate with the number of colony forming units, using the Fisher exact test. RESULTS: The sensitivity, specificity, positive predictive value, and negative predictive value (95% confidence interval) were 97.4% (94.0–99.1%), 90.8% (85.0–94.9%), 93.0% (88.5–96.1%), and 96.5% (92.0–98.9%), respectively. Positive rate significantly differed by number of colony forming units (P=0.021). ROC plot for color intensity showed 0.938 of AUC (area under curve). CONCLUSIONS: SD Bioline Strep A Ultra showed excellent performance, and its positive rate differed by the number of colony counts. This RADT could be used as a sensitive and semi-quantitative method detecting bacterial pharyngitis.
Area Under Curve ; Child ; Gyeonggi-do ; Humans ; Methods ; Pharyngitis ; Pharynx ; Sensitivity and Specificity ; Stem Cells* ; Streptococcus

Background: In the coronavirus disease 2019 (COVID-19) pandemic era, the simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza virus (Flu), and respiratory syncytial virus (RSV) is important in the rapid differential diagnosis in patients with respiratory symptoms. Three multiplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assays have been recently developed commercially in Korea: PowerChek™ SARS-CoV-2, Influenza A&B Multiplex Real-time PCR Kit (PowerChek; KogeneBiotech); STANDARD™ M Flu/SARS-CoV-2 Real-time Detection Kit (STANDARD M; SD BioSensor); and Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay (Allplex; Seegene). We evaluated the analytical and clinical performances of these kits. Methods: A limit of detection tests were performed and cross-reactivity analysis was executed using clinical respiratory samples. Ninety-seven SARS-CoV-2-positive, 201 SARS-CoV-2-negative, 71 influenza A-positive, 50 influenza B-positive, 78 RSV-positive, and 207 other respiratory virus-positive nasopharyngeal swabs were tested using the three assays. The AdvanSure™ respiratory viruses rRT-PCR assay (AdvanSure; LG Life Sciences) was used as a comparator assay for RSV. Results: Except in influenza B, in SARS-CoV-2 and influenza A, there were no significant differences in detecting specific genes of the viruses among the three assays. All three kits did not cross-react with common respiratory viruses. All three kits had greater than 92% positive percent agreement and negative percent agreement and ≥ 0.95 kappa value in the detection of SARS-CoV-2 and flu A/B. Allplex detected RSV more sensitively than AdvanSure. Conclusion The overall performance of three multiplex rRT-PCR assays for the concurrent detection of SARS-CoV-2, influenza A/B, and RSV was comparable. These kits will promote prompt differential diagnosis of COVID-19, influenza, and RSV infection in the COVID-19 pandemic era.

BACKGROUND: Stool cultures are essential for diagnosing bacterial gastrointestinal infections. Laboratory procedures and target organisms for stool culture testing can vary by institute. Therefore, a nationwide survey was conducted to determine the stool culture procedures performed in clinical laboratories of Korea. METHODS: Questionnaires were delivered by electronic mail to 98 clinical microbiologists and by Google survey to the 301 institutes participating in the Korean External Quality Control Program of Bacterial Cultures. RESULTS: Of the 68 institutes sent complete responses, Gram staining and wet smears were performed in 73.5% and 64.7%, respectively. A molecular test was conducted in 32.4% of laboratories, and blood agar plates were used in 23.5%. Staphylococcus aureus , Pseudomonas aeruginosa , and Candida species were reported for predominant growth by 17.6%, 8.8%, and 7.4% of the respondents, respectively. Campylobacter culture was available only in 25.0% of laboratories, whereas Clostridium difficile could be cultivated in 38.2%. Susceptibility testing results of Salmonella-Shigella were reported for all tested antibiotics in 22.1% of laboratories, whereas 69.1% reported results for antibiotics specified by the Clinical and Laboratory Standard Institute guidelines. CONCLUSIONS: Methods and results of gram staining, wet smears, use of stool culture media, target microorganisms, and antibiotic susceptibility differed among the institutes. Further discussion is needed to develop a standardized protocol for stool culture to maximize isolation of bacterial pathogens that cause gastroenteritis.
Academies and Institutes ; Agar ; Anti-Bacterial Agents ; Campylobacter ; Candida ; Clostridium difficile ; Culture Media ; Diagnosis* ; Diarrhea ; Electronic Mail ; Gastroenteritis* ; Korea* ; Methods* ; Pseudomonas aeruginosa ; Quality Control ; Staphylococcus aureus ; Surveys and Questionnaires

BACKGROUND: Point-of-care (POC) tests are used increasingly due to fast results and simple test procedures, which enables rapid diagnosis and therapeutic monitoring. We evaluated the performance of the Piccolo xpress Chemistry Analyzer (Abaxis, USA) a POC chemistry analyzer. METHODS: Fourteen analytes, Na+, K+, Cl-, Ca2+, total carbon dioxide, AST, ALT, total bilirubin, alkaline phosphatase, blood urea nitrogen, creatinine, albumin, total protein, and glucose; were measured simultaneously with a 100 microliter of whole blood sample using a Comprehensive Metabolic Reagent disk. Within-run and total precision and linearity were evaluated according to CLSI EP15-A and EP6-A guidelines, respectively. Comparison with a central laboratory chemistry analyzer was performed using 144 patient samples. RESULTS: The coefficients of variations of within-run and total precision were all within 5% for three levels except for total carbon dioxide, ALT, alkaline phosphatase, total bilirubin, and creatinine in low level, and creatinine in middle level. The results of 14 analytes were linear within a commonly encountered range in clinical samples (r2> or =0.98). More than 10% of samples in Na+, AST, ALT, glucose, BUN did not satisfy CLIA analytical quality requirement. CONCLUSIONS: The Piccolo xpress Chemistry Analyzer can analyze multiple analytes with a minimal amount of whole blood in a short time. It showed an acceptable performance for precision, linearity and comparison with central laboratory analyzer. It can be useful as a screening tests modality in mobile clinics, ambulances, and field clinics for military use, and for pediatric patients from whom enough sample volume is difficult to obtain.
Alanine Transaminase/blood ; Alkaline Phosphatase/blood ; Aspartate Aminotransferases/blood ; Bilirubin/blood ; Blood Chemical Analysis/*instrumentation/methods/*standards ; Blood Glucose/analysis ; Calcium/blood ; Carbon Dioxide/blood ; Chlorides/blood ; Creatinine/blood ; Humans ; *Point-of-Care Systems ; Potassium/blood ; Quality Control ; Reproducibility of Results ; Serum Albumin/analysis ; Sodium/blood

BACKGROUND: Hepatitis B Virus (HBV) is a major risk factor for hepatocellular carcinoma, and about five to six percents of people are infected with HBV in Korea. Lamivudine is a first-line drug having good control against HBV replication, but long-term treatment by lamivudine induces drug resistance. We analyzed the rate of HBV resistance mutation for lamivudine by direct sequencing and CLIP sequencing. METHODS: HBV DNA was isolated from 371 patients who were in treatment, or were planning to be treated with lamivudine. The direct sequencing for lamivudine resistance mutation was performed in 371 patients and CLIP sequencing in 138 patients. We analyzed the mutation rate and the type of mutations for lamivudine resistance. RESULTS: The mutation was detected in 203 patients (54.7%) and (CTG) L180M (ATG) was most common (36.1%) followed by (ATG) M204I (ATT) (29.9%) and (ATG) M204V (GTG) (18.6%). According to the duration of treatment, mutation rates were as follows: 45.3% for less than one year, 71.7% for one to two years, 66.7% for two to three years, and 87.9% for more than three years. The results of the direct sequencing and CLIP sequencing agreed in 134 out of 138 patients, in whom both tests were performed. CONCLUSIONS: We confirmed that HBV mutation rates for lamivudine resistance increased as the lamivudine treatment period increased. The lamivudine resistance mutations detected were similar to the previous studies. CLIP sequencing showed good correlation with the direct sequencing and gave additional mutation information. CLIP sequencing is a promising tool for the detection of lamivudine resistance mutation in HBV that can assist treatment plans.
Carcinoma, Hepatocellular ; DNA ; Drug Resistance ; Hepatitis B virus ; Hepatitis B, Chronic ; Hepatitis, Chronic ; Humans ; Korea ; Lamivudine ; Mutation Rate ; Risk Factors

Quality control for genetic tests has become more important as testing volume and clinical demands have increased dramatically. The diagnostic genetics subcommittee of Korean Association of External Quality Assessment Service conducted two trials in 2014 based on cytogenetics and molecular genetics surveys. A total of 44 laboratories participated in the chromosome surveys, 33 laboratories participated in the fl uorescence in situ hybridization (FISH) surveys, and 130 laboratories participated in the molecular genetics surveys as a part of these trials. All laboratories showed acceptable results in the chromosome and FISH surveys. The molecular genetics surveys included various tests: Mycobacterium tuberculosis detection, hepatitis B and C virus detection and quantification, human papilloma virus genotyping, gene rearrangement tests for leukaemia and lymphomas, genetic tests for JAK2, FMS-like tyrosine kinase 3, nucleophosmin, cancer-associated genes (KRAS, EGFR, KIT, and BRAF), hereditary breast and ovarian cancer genes (BRCA1 and BRCA2), Li-Fraumeni syndrome (TP53), Wilson disease (ATP7B), achondroplasia (FGFR3), Huntington disease, spinocerebellar ataxia, spinal and bulbar muscular atrophy, mitochondrial encephalopathy with lactic acidosis and stroke like episodes, myoclonic epilepsy ragged red fibre, Prader-Willi/Angelman syndrome, Duchenne muscular dystrophy, spinal muscular atrophy, fragile X syndrome, nonsyndromic hearing loss and deafness (GJB2), multiple endocrine neoplasia 2 (RET), Leber hereditary optic neuropathy (major mutation), apolipoprotein E genotyping, methylenetetrahydrofolate reductase genotyping, ABO genotyping, and DNA sequencing analysis. Molecular genetic surveys showed excellent results for most of the participants. The external quality assessment program for genetic analysis in 2014 proved to be helpful for continuous education and the evaluation of quality improvement.
Achondroplasia ; Acidosis, Lactic ; Apolipoproteins ; Breast ; Cytogenetics ; Deafness ; Education ; Epilepsies, Myoclonic ; fms-Like Tyrosine Kinase 3 ; Fragile X Syndrome ; Gene Rearrangement ; Genetics* ; Hearing Loss ; Hepatitis B ; Hepatolenticular Degeneration ; Humans ; Huntington Disease ; In Situ Hybridization ; Korea ; Li-Fraumeni Syndrome ; Lymphoma ; Methylenetetrahydrofolate Reductase (NADPH2) ; Molecular Biology ; Molecular Diagnostic Techniques ; Multiple Endocrine Neoplasia ; Muscular Atrophy, Spinal ; Muscular Disorders, Atrophic ; Muscular Dystrophy, Duchenne ; Mycobacterium tuberculosis ; Optic Atrophy, Hereditary, Leber ; Ovarian Neoplasms ; Papilloma ; Quality Assurance, Health Care ; Quality Control ; Quality Improvement ; Sequence Analysis, DNA ; Spinocerebellar Ataxias ; Stroke

Rapid and accurate identification of an influenza outbreak is essential for patient care and treatment. We describe a next-generation sequencing (NGS)-based, unbiased deep sequencing method in clinical specimens to investigate an influenza outbreak. Nasopharyngeal swabs from patients were collected for molecular epidemiological analysis. Total RNA was sequenced by using the NGS technology as paired-end 250 bp reads. Total of 7 to 12 million reads were obtained. After mapping to the human reference genome, we analyzed the 3-4% of reads that originated from a non-human source. A BLAST search of the contigs reconstructed de novo revealed high sequence similarity with that of the pandemic H1N1 virus. In the phylogenetic analysis, the HA gene of our samples clustered closely with that of A/Senegal/VR785/2010(H1N1), A/Wisconsin/11/2013(H1N1), and A/Korea/01/2009(H1N1), and the NA gene of our samples clustered closely with A/Wisconsin/11/2013(H1N1). This study suggests that NGS-based unbiased sequencing can be effectively applied to investigate molecular characteristics of nosocomial influenza outbreak by using clinical specimens such as nasopharyngeal swabs.
Databases, Genetic ; Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; Influenza A Virus, H1N1 Subtype/classification/*genetics/isolation & purification ; Influenza, Human/diagnosis/*virology ; Nasopharynx/*virology ; Nucleic Acid Amplification Techniques ; Phylogeny ; RNA, Viral/analysis/metabolism ; Sequence Analysis, RNA ; Viral Proteins/genetics

CHARGE syndrome MIM #214800 is an autosomal dominant syndrome involving multiple congenital malformations. Clinical symptoms include coloboma, heart defects, choanal atresia, retardation of growth or development, genital hypoplasia, and ear anomalies or deafness. Mutations in the chromodomain helicase DNA binding protein 7 (CHD7) gene have been found in 65-70% of CHARGE syndrome patients. Here, we describe a 16-month-old boy with typical CHARGE syndrome, who was referred for CHD7 gene analysis. Sequence analysis and multiplex ligation-dependent probe amplification were performed. A heterozygous 38,304-bp deletion encompassing exon 3 with a 4-bp insertion was identified. There were no Alu sequences adjacent to the breakpoints, and no sequence microhomology was observed at the junction. Therefore, this large deletion may have been mediated by non-homologous end joining. The mechanism of the deletion in the current case differs from the previously suggested mechanisms underlying large deletions or complex genomic rearrangements in the CHD7 gene, and this is the first report of CHD7 deletion by this mechanism worldwide.
Alu Elements/genetics ; Base Sequence ; CHARGE Syndrome/diagnosis/*genetics ; DNA/chemistry/metabolism ; *DNA End-Joining Repair ; DNA Helicases/*genetics/metabolism ; DNA-Binding Proteins/*genetics/metabolism ; Exons ; Gene Dosage ; Heterozygote ; Humans ; Infant ; Male ; Multiplex Polymerase Chain Reaction ; Mutation ; Sequence Analysis, DNA ; *Sequence Deletion

The antibody titer of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was observed in 289 healthy healthcare workers who had completed the second dose of the Pfizer-BioNTech coronavirus disease 2019 (COVID-19) vaccine. Antibody tests were performed using both the automated electrochemiluminescence immunoassay (ECLIA) and the chromatographic lateral flow immunoassay (LFIA). All subjects had antibodies against the receptor binding domain of the spike protein of SARS-CoV-2 only one week after completing the vaccination, and the antibody titer became significantly higher after another week (P < 0.001). Since there was a large amount of antibody formation within two weeks after completion of vaccination, the less sensitive method, LFIA, also showed high sensitivity.There was no significant difference between whole blood and serum in detecting SARS-CoV-2 antibodies after vaccination. This is an early study of vaccinations among Koreans and is expected to contribute to the establishment of national guidelines on COVID-19 vaccination.