Strong SARS-CoV-2 Antibody Response After Booster Dose of BNT162b2 mRNA Vaccines in Uninfected Healthcare Workers

Despite strict guidelines for coronavirus disease 2019 (COVID-19), South Korea is facing its fourth pandemic wave. In this study, by using an automated electrochemiluminescence immunoassay assay, we tracked anti-spike protein receptor-binding domain (anti-S-RBD) antibody titer from the second dose to 2 weeks after the booster dose vaccination. After the second dose, 234 participants had their anti-S-RBD antibody titers decrease over time. We also showed the booster dose (the third dose) increased antibody titer by average 14 (min–max, 2–255)-fold higher compared to the second dose among the 211-booster group participants, therefore, the booster dose could be recommended for low responders to the second dose. Our findings showed a distinct humoral response after booster doses of BNT162b2 mRNA vaccines and may provide further evidence of booster vaccination efficacy. These data will also be helpful in vaccination policy decisions that determine the need for the booster dose.

Positivity of SARS-CoV-2 Antibodies among Korean Healthy Healthcare Workers 1 and 2 Weeks after Second Dose of Pfizer-BioNTech Vaccination

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.

Positivity of SARS-CoV-2 Antibodies among Korean Healthy Healthcare Workers 1 and 2 Weeks after Second Dose of Pfizer-BioNTech Vaccination

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.

Facklamia hominis Isolated from a Wound: A Case Report and Review of the Literature / 대한임상미생물학회지

Facklamia hominis is a facultative anaerobic Gram-positive coccus generally displaying weak alpha-hemolysis and negativity for catalase and oxidase. Facklamia species are part of the normal flora of the female genitourinary tract and have been reported in invasive diseases such as meningitis and infective endocarditis, albeit rarely. A 67 year-old-man presented to hospital with a tender, erythematous epidermal cyst on the right side of his upper back. Simple excision of the cyst was performed and the pus was taken with a sterile swab for culture, yielding no growth. One week later, discharge was observed in the patient's wound site and a sterile swab for culture was taken. The colonies grown were identified as F. hominis by the Vitek 2 system (bioMérieux, France), and the result was then reported to clinicians, and later confirmed by 16S rRNA gene sequencing and matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry. To the best of our knowledge, this is the first reported case of F. hominis isolation from a clinical specimen in Korea.

Evaluation of the SD Bioline Strep A Ultra Test in Relation With Number of Colony Forming Units and Color Intensity

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.

Application of Multigene Panel Sequencing in Patients with Prolonged Rate-corrected QT Interval and No Pathogenic Variants Detected in KCNQ1, KCNH2, and SCN5A

Long QT syndrome (LQTS) is an inherited cardiac disease characterized by a prolonged heart rate-corrected QT (QTc) interval. We investigated the genetic causes in patients with prolonged QTc intervals who were negative for pathogenic variants in three major LQTS-related genes (KCNQ1, KCNH2, and SCN5A). Molecular genetic testing was performed using a panel including 13 LQTS-related genes and 67 additional genes implicated in other cardiac diseases. Overall, putative genetic causes of prolonged QTc interval were identified in three of the 30 patients (10%). Among the LQTS-related genes, we detected a previously reported pathogenic variant, CACNA1C c.1552C>T, responsible for cardiac-only Timothy syndrome. Among the genes related to other cardiac diseases, a likely pathogenic variant, RYR2 c.11995A>G, was identified in a patient with catecholaminergic polymorphic ventricular tachycardia. Another patient who developed dilated cardiomyopathy with prolonged QTc interval was found to carry a likely pathogenic variant, TAZ c.718G>A, associated with infantile dilated cardiomyopathy. Comprehensive screening of genetic variants using multigene panel sequencing enables detection of genetic variants with a possible involvement in QTc interval prolongation, thus uncovering unknown molecular mechanisms underlying LQTS.

Molecular Epidemiological Features and Antibiotic Susceptibility Patterns of Streptococcus dysgalactiae subsp. equisimilis Isolates from Korea and Japan

BACKGROUND: The molecular characterization of Streptococcus dysgalactiae subsp. equisimilis (SDSE) has not yet been performed in Korea. This study aimed to find the differences or similarities in the clinical features, molecular epidemiological findings, and antimicrobial resistance patterns of SDSE from two countries (Korea and Japan). METHODS: SDSE isolates were collected from Korea (N=69) from 2012–2016 and Japan (N=71) from 2014–2016. Clinical characteristics, emm genotypes, and sequence types (STs) were compared. Microdilution tests were performed using different antimicrobials, and their resistance determinants were screened. RESULTS: Median ages were 69 years in Korea and 76 years in Japan. The most common underlying diseases were diabetes and malignancy. Blood-derived isolates comprised 36.2% and 50.7% of Korean and Japanese isolates, respectively; mortality was not different between the two groups (5.8% vs 9.9%, P=0.53). Among Korean isolates with 20 different combined ST-emm types, ST127-stG245 (N=16), ST128-stG485 (N=10), and ST138-stG652 (N=8) were prevalent. Among Japanese isolates with 29 different combined types, ST17-stG6792 (N=11), ST29-stG485 (N=7), and ST205-stG6792 (N=6) were prevalent. Resistance rates to erythromycin, clindamycin, and minocycline were 34.8%, 17.4%, and 30.4% in Korea and 28.2%, 14.1%, and 21.4% in Japan, respectively. CONCLUSIONS: SDSE infections commonly occurred in elderly persons with underlying diseases. There was a significant difference in the distribution of ST-emm types between the two countries. Antimicrobial resistance rates were comparable with different frequencies of resistance determinants in each country.

Spectrum of MNX1 Pathogenic Variants and Associated Clinical Features in Korean Patients with Currarino Syndrome

BACKGROUND: The major genetic cause of Currarino syndrome (CS), a congenital malformation syndrome typically characterized by sacral agenesis, anorectal malformation, and presence of a pre-sacral mass, is known to be pathogenic variants in motor neuron and pancreas homeobox 1 (MNX1), which exist in almost all familial cases and 30% of sporadic cases. Less commonly, a large deletion or a complex rearrangement involving the 7q36 region is associated with CS. We investigated the spectrum of MNX1 pathogenic variants and associated clinical features in the Korean patients with CS. METHODS: We enrolled 25 patients with CS, including 24 sporadic cases and one familial case. Direct sequencing of MNX1 and multiplex ligation-dependent probe amplification were performed. We also analyzed clinical phenotypes and evaluated genotype-phenotype correlations. RESULTS: We identified six novel variants amongst a total of six null variants, one missense variant, and one large deletion. The null variants included four frameshift variants (p.Gly98Alafs*124, p.Gly145Alafs*77, p.Gly151Leufs*67, and p.Ala216Profs*5) and two nonsense variants (p.Tyr186* and p.Gln212*). The missense variant, p.Lys295Gln, was located in the highly-conserved homeobox domain and was predicted to be deleterious. A large deletion involving the 7q36 region was detected in one patient. Pathogenic variants in MNX1 were detected in 28% of all CS cases and 25% of sporadic cases. The clinical phenotype was variable in patients with and without pathogenic variants; no significant genotype-phenotype correlation was observed. CONCLUSIONS: This study revealed the spectrum and phenotypic variability of MNX1 pathogenic variants in the Korean population.

Nationwide Survey of Stool Culture Methods for the Diagnosis of Bacterial Gastroenteritis in Korea, 2016

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.

Genotyping Influenza Virus by Next-Generation Deep Sequencing in Clinical Specimens

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.

Annual Report on the External Quality Assessment Scheme for Diagnostic Genetics in Korea (2014)

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.

Non-Homologous End Joining Repair Mechanism-Mediated Deletion of CHD7 Gene in a Patient with Typical CHARGE Syndrome

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.

Molecular Characterization of the NF2 Gene in Korean Patients with Neurofibromatosis Type 2: A Report of Four Novel Mutations / 대한진단검사의학회지

BACKGROUND: Neurofibromatosis type 2 (NF2) is an autosomal dominant syndrome caused by the NF2 tumor suppressor gene. However, the NF2 mutation characteristics in Korean patients are not sufficiently understood. In this study, we conducted a comprehensive mutational analysis in 7 Korean NF2 patients by performing direct sequencing and gene-dosage assessment. METHODS: We analyzed all exons and flanking regions of NF2 by direct sequencing and screened the deletions or duplications involving NF2 by multiplex ligation-dependent probe amplification. RESULTS: Four novel NF2 mutations, including 2 splice-site mutations (c.364-1G>A and c.886-3C>G), 1 frameshift mutation (c.524delA), and 1 missense mutation (c.397T>C; p.Cys133Arg), were identified in our patients. No large deletion or duplication was identified in our series. Subsequently, we identified an abnormal splicing product by using reverse transcription-PCR and direct sequencing in 2 patients with a novel splice-site mutation. The missense mutation c.397T>C was predicted to have harmful effects on protein function. CONCLUSIONS: The detection rate of NF2 mutations in Korean patients (57%) is similar to those in other populations. Our results provided a greater insight into the mutational spectrum of the NF2 gene in Korean subjects.

Performance Evaluation of the Piccolo xpress Point-of-care Chemistry Analyzer / 대한진단검사의학회지

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.

Detection of Mutations in Chronic Hepatitis B Virus under Lamivudine Treatment: Direct Sequencing and CLIP Sequencing / 임상검사와정도관리

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.