Guidelines2020-11-01 Clinical Microbiology

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Abstract : Coronavirus disease 2019 (COVID-19) is a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Early detection of COVID-19 and immediate isolation of infected patients from the naive population are important to prevent further pandemic spread of the infection. Real-time reverse transcription (RT)-PCR to detect SARS-CoV-2 RNA is currently the most reliable diagnostic method for confirming COVID-19 worldwide. Guidelines for clinical laboratories on the COVID-19 diagnosis have been recently published by Korean Society for Laboratory Medicine and the Korea Centers for Disease Control and Prevention. However, these formal guidelines do not address common practical laboratory issues related to COVID-19 real-time RT-PCR testing and their solutions. Therefore, this guideline is intended as a practical and technical supplement to the “Guidelines for Laboratory Diagnosis of COVID-19 in Korea”.

Original Article2020-07-01 Clinical Chemistry

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Abstract : BackgroundHigh-density lipoprotein cholesterol (HDL-C) is a complex mixture of subclasses with heterogeneous atheroprotective activities. We analyzed HDL-C subclass in relation to cardiovascular risk and metabolic syndrome (MetS) in a population with high HDL-C levels.MethodsA total of 300 Korean individuals with high HDL-C levels (≥2.331 mmol/L) were enrolled following a comprehensive general medical examination including body composition analysis. HDL3-C levels were measured using the HDL3-EX SEIKEN kit (Randox Ltd., Crumlin, UK) and non-HDL3-C levels were calculated by subtracting HDL3-C levels from total HDL-C levels.ResultsHDL3-C levels and HDL3-C proportion had a weak positive correlation with low-density lipoprotein cholesterol (LDL-C) and triglycerides (r=0.21, r=0.25; r=0.26, r=0.34, respectively, all P<0.001); in contrast, non-HDL3-C levels had a weak negative correlation with these parameters (r=?0.17 and r=?0.25, respectively, both P<0.005). HDL3-C levels and HDL3-C proportion were significantly higher in the MetS group (N=8) than in the non-MetS group (0.71 vs 0.63 mmol/L, P=0.001; 29.7 vs 25.8%, P=0.001, respectively); these were the only predictors of MetS among the lipid variables (areas under the curves [AUC]=0.84 and 0.83, respectively, both P=0.001).ConclusionsIn populations with high HDL-C levels, HDL-C subclass may provide a greater amount of information on cardiovascular risk and MetS than HDL-C levels alone.

Original Article2020-07-01 Clinical Microbiology

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Abstract : Background Colistin has become a last-resort antibiotic for the management of multidrug-resistant gram-negative bacteria. The disk diffusion test is cheap and easy to perform but may be unreliable for colistin susceptibility testing due to poor diffusion of the large colistin molecule. An improved agar diffusion test would increase the reliability of colistin susceptibility testing. This study aimed to modify Muller-Hinton agar (MHA) to improve colistin diffusion in agar. Methods MHA was modified by reducing the agar concentration from 100% to 30% and supplementing with protamine. We tested 60 gram-negative clinical isolates of Pseudomonas aeruginosa (N=27) and Acinetobacter calcoaceticus-baumannii complex (N=33). Disk diffusion test results were interpreted based on minimum inhibitory concentrations determined by broth microdilution. Results The modified MHA yielded the best performance metrics, including 94.7% sensitivity, 100% specificity, and an area under the curve of 0.995 (95% confidence interval, 0.982?1.000), P

Review Article2019-09-01 Diagnostic Genetics

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Abstract : In 2015, the American College of Medical Genetics and Genomics (ACMG), together with the Association for Molecular Pathology (AMP), published the latest guidelines for the interpretation of sequence variants, which have been widely adopted into clinical practice. Despite these standardized efforts, the degrees of subjectivity and uncertainty allowed by the guidelines can lead to inconsistent variant classification across clinical laboratories, making it difficult to assess the pathogenicity of identified variants. We describe the critical elements of variant interpretation processes and potential pitfalls through practical examples and provide updated information based on a review of recent literature. The variant classification we describe is meant to be applicable to sequence variants for Mendelian disorders, whether identified by single-gene tests, multi-gene panels, exome sequencing, or genome sequencing. Continuing efforts to improve the reproducibility and objectivity of sequence variant interpretation across individuals and laboratories are needed.

Original Article2019-09-01 Diagnostic Hematology

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Abstract : BackgroundParoxysmal nocturnal hemoglobinuria (PNH) is an acquired pluripotent hematopoietic stem cell disorder associated with an increase in the number of glycosyl-phosphatidyl inositol (GPI)-deficient blood cells. We investigated PNH clonal proliferation in the three cell lineages?granulocytes, T lymphocytes, and red blood cells (RBCs)?by analyzing PIGA gene mutations and T-cell receptor (TCR) clonality.MethodsFlow cytometry was used on peripheral blood samples from 24 PNH patients to measure the GPI-anchored protein (GPI-AP) deficient fraction in each blood cell lineage. PIGA gene mutations were analyzed in granulocytes and T lymphocytes by Sanger sequencing. A TCR clonality assay was performed in isolated GPI-AP deficient T lymphocytes.ResultsThe GPI-AP deficient fraction among the three lineages was the highest in granulocytes, followed by RBCs and T lymphocytes. PIGA mutations were detected in both granulocytes and T lymphocytes of 19 patients (79.2%), with a higher mutation burden in granulocytes. The GPI-AP deficient fractions of granulocytes and T lymphocytes correlated moderately (r_s=0.519, P=0.049) and strongly (r_s=0.696, P=0.006) with PIGA mutation burden, respectively. PIGA mutations were more frequently observed in patients with clonal rearrangements in TCR genes (P=0.015). The PIGA mutation burden of T lymphocytes was higher in patients with clonal TCRB rearrangement.ConclusionsPIGA mutations were present in approximately 80% of PNH patients. PNH clone size varies according to blood cell lineage, and clonal cells may obtain proliferation potential or gain a survival advantage over normal cells.

Original Article2019-09-01 Clinical Chemistry

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Abstract : BackgroundThe use of liquid chromatography-tandem mass spectrometry (LC-MS/MS) has substantially increased in clinical laboratories worldwide. To assess the status of clinical LC-MS/MS testing in Korean laboratories, a questionnaire survey was performed by the Clinical Mass Spectrometry Research Committee of the Korean Society of Clinical Chemistry.MethodsThe questionnaire was distributed to 19 clinical laboratories performing clinical LC-MS/MS from April to May 2018. It asked about general characteristics of the laboratory and commonly utilized clinical LC-MS/MS tests: newborn screening, tacrolimus test, vitamin D test, and plasma metanephrine test. Frequency analysis and other statistical analyses were performed.ResultsA total of 17 laboratories responded. The median number of LC-MS/MS instruments, laboratory medicine physicians, and technicians in each laboratory was three, one, and two, respectively. Nine laboratory directors had >10 years of experience with clinical LC-MS/MS. For each LC-MS/MS test, at least two concentrations of QC materials were measured every 24 hours during clinical testing, and all laboratories used QC acceptability criteria based on their established QC means and SDs. All laboratories participated in an external quality assessment program. However, there was inter-laboratory variability in sample preparation methods, instruments, reagents, internal standards, and calibrators.ConclusionsLC-MS/MS has been successfully introduced in Korean clinical laboratories and is used within a quality framework. Further efforts for harmonization on a nationwide basis could facilitate the widespread use of LC-MS/MS.

Review Article2019-07-01 General Laboratory Medicine

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Abstract : The platelet-to-lymphocyte ratio (PLR) has emerged as an informative marker revealing shifts in platelet and lymphocyte counts due to acute inflammatory and prothrombotic states. PLR has been extensively examined in neoplastic diseases accompanied by immune suppression and thrombosis, which can be predicted by combined blood cell counts and their ratios. Several large observational studies have demonstrated the value of shifts in PLR in evaluating the severity of systemic inflammation and predicting infections and other comorbidities, in inflammatory rheumatic diseases. The value of PLR as an inflammatory marker increases when its fluctuations are interpreted along with other complementary hematologic indices, particularly the neutrophil-to-lymphocyte ratio (NLR), which provides additional information about the disease activity, presence of neutrophilic inflammation, infectious complications, and severe organ damage in systemic lupus erythematosus. PLR and NLR have high predictive value in rheumatic diseases with predominantly neutrophilic inflammation (e.g., Behçet disease and familial Mediterranean fever). High PLR, along with elevated platelet count, is potentially useful in diagnosing some systemic vasculitides, particularly giant-cell arteritis. A few longitudinal studies on rheumatic diseases have demonstrated a decrease in PLR in response to anti-inflammatory therapies. The main limitations of PLR studies are preanalytical faults, inadequate standardization of laboratory measurements, and inappropriate subject selection. Nonetheless, accumulating evidence suggests that PLR can provide valuable information to clinicians who encounter multisystem manifestations of rheumatic diseases, which are reflected in shifts in platelet, lymphocyte, neutrophil, or monocyte counts. Interpretation of PLR combined with complementary hematologic indices is advisable to more accurately diagnose inflammatory rheumatic diseases and predict related comorbidities.

Original Article2019-07-01 Clinical Microbiology

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Abstract : BackgroundHuman astroviruses (HAstVs) are one of the major causes of acute gastroenteritis. Classic HAstVs can be classified into eight genotypes. We investigated the positive rate of HAstVs and the distribution of HAstV genotypes in strains isolated from patients with acute gastroenteritis in Hwaseong, Korea, in 2013?2017.MethodsBetween November 2013 and December 2017, 3,519 stool samples were collected from patients with symptoms of acute gastroenteritis and tested for HAstV using multiplex PCR. For HAstV-positive samples, the ORF2 gene, which encodes a capsid protein, was genotyped by reverse-transcription PCR and sequencing. Phylogenetic analysis was performed to determine whether the sequences of the HAstVs differed by year.ResultsThe positive rate of HAstV was 1.9% (67 samples). HAstV Type 1 was the most prevalent genotype (82.4%), and Types 4, 5, and 8 were also detected. Infection occurred year-round, with no distinct seasonal variation. Infection occurred at nearly all ages (55 days?81 years; median: 3 years), and the positive rate was substantially higher in children younger than five years. Phylogenetic analysis revealed three distinct clades of HAstV Type 1 according to the collection time.ConclusionsOur results provide recent epidemiological data on HAstVs in Korea between 2013 and 2017. The finding of three distinct clades of HAstV Type 1 according to collection time suggests genetic evolution of HAstVs. These findings can enhance our knowledge on HAstV infection and viral evolution.

Original Article2019-05-01 Diagnostic Genetics

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Abstract : BackgroundTo validate the clinical application of chromosomal microarray analysis (CMA) as a first-tier clinical diagnostic test and to determine the impact of CMA results on patient clinical management, we conducted a multicenter prospective study in Korean patients diagnosed as having developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), and multiple congenital anomalies (MCA).MethodsWe performed both CMA and G-banding cytogenetics as the first-tier tests in 617 patients. To determine whether the CMA results directly influenced treatment recommendations, the referring clinicians were asked to complete a 39-item questionnaire for each patient separately after receiving the CMA results.ResultsA total of 122 patients (19.8%) had abnormal CMA results, with either pathogenic variants (N=65) or variants of possible significance (VPS, N=57). Thirty-five well-known diseases were detected: 16p11.2 microdeletion syndrome was the most common, followed by Prader-Willi syndrome, 15q11-q13 duplication, Down syndrome, and Duchenne muscular dystrophy. Variants of unknown significance (VUS) were discovered in 51 patients (8.3%). VUS of genes putatively associated with developmental disorders were found in five patients: IMMP2L deletion, PTCH1 duplication, and ATRNL1 deletion. CMA results influenced clinical management, such as imaging studies, specialist referral, and laboratory testing in 71.4% of patients overall, and in 86.0%, 83.3%, 75.0%, and 67.3% of patients with VPS, pathogenic variants, VUS, and benign variants, respectively.ConclusionsClinical application of CMA as a first-tier test improves diagnostic yields and the quality of clinical management in patients with DD/ID, ASD, and MCA.

Review Article2019-01-28 Clinical Chemistry

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Abstract : New technological advances have paved the way for significant progress in automated urinalysis. Quantitative reading of urinary test strips using reflectometry has become possible, while complementary metal oxide semiconductor (CMOS) technology has enhanced analytical sensitivity and shown promise in microalbuminuria testing. Microscopy-based urine particle analysis has greatly progressed over the past decades, enabling high throughput in clinical laboratories. Urinary flow cytometry is an alternative for automated microscopy, and more thorough analysis of flow cytometric data has enabled rapid differentiation of urinary microorganisms. Integration of dilution parameters (e.g., creatinine, specific gravity, and conductivity) in urine test strip readers and urine particle flow cytometers enables correction for urinary dilution, which improves result interpretation. Automated urinalysis can be used for urinary tract screening and for diagnosing and monitoring a broad variety of nephrological and urological conditions; newer applications show promising results for early detection of urothelial cancer. Concomitantly, the introduction of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has enabled fast identification of urinary pathogens. Automation and workflow simplification have led to mechanical integration of test strip readers and particle analysis in urinalysis. As the information obtained by urinalysis is complex, the introduction of expert systems may further reduce analytical errors and improve the quality of sediment and test strip analysis. With the introduction of laboratory-on-a-chip approaches and the use of microfluidics, new affordable applications for quantitative urinalysis and readout on cell phones may become available. In this review, we present the main recent developments in automated urinalysis and future perspectives.