Epidemiological Characterization of Respiratory Pathogens Using the Multiplex PCR FilmArray™ Respiratory Panel.

Various pathogens can cause upper respiratory tract infections, presenting challenges in accurate diagnosis due to similar symptomatology. Therefore, rapid and precise diagnostic tests are crucial for effective treatment planning. Traditional culture-based methods for diagnosis are limited by their reliance on skilled personnel and lengthy processing times. In contrast, multiplex polymerase chain reaction (PCR) techniques offer enhanced accuracy and speed in identifying respiratory pathogens. In this study, we aimed to assess the efficacy of the FilmArray™ Respiratory Panel (RP), a multiplex PCR test capable of simultaneously screening 20 pathogens. This retrospective analysis was conducted at Dankook University Hospital, South Korea, between January 2018 and December 2022. Samples from patients with upper respiratory tract infections were analyzed. Results revealed adenovirus as the most prevalent pathogen (18.9%), followed by influenza virus A (16.5%), among others. Notably, a 22.5% co-infection rate was observed. The FilmArray™ RP method successfully identified 20 pathogens within 2 h, facilitating prompt treatment decisions and mitigating unnecessary antibiotic prescriptions. This study underscores the utility of multiplex PCR in respiratory pathogen identification, offering valuable insights for epidemiological surveillance and diagnosis.

Changes in Respiratory Pathogens before and after the COVID-19 Pandemic (2018-2021).

Objective: This study is aimed at investigating the pattern of change occurring in respiratory pathogens before and after the outbreak of COVID-19, a type of viral pneumonia for which a pandemic was declared (March 2020). The results were analyzed by gender and age to identify the association between personal hygiene and prevention of infection by respiratory pathogens. Methods: A retrospective analysis was performed on 39,814 sputum, bronchial aspirate, and transtracheal aspirate samples obtained from 15,398 patients visiting a university hospital, located in Chungcheongnam-do, South Korea, between January 2018 and December 2021. From 4,454 patients whose samples were culture positive for bacteria, 6,389 strains were isolated and further cultured. Results: The mean age of the outpatients with respiratory pathogens was 66.2 years, and the comparison of the culture test results by gender showed that 64.9% (2,892/4,454) were male and 35.1% (1,562/4,454) were female. Compared to the pre-COVID-19 pandemic period, the number of outpatients with a request for respiratory microbial cultures after the onset of the pandemic was reduced by 20.7% and the number of outpatients with a positive culture result was reduced by 23.0%. The number of respiratory samples received was reduced by 6.7% after the pandemic, while the sample positive rate was reduced by 18.3%. Among the isolated microbial strains, there was a significant decrease of 43.1% for the Acinetobacter baumannii complex, 60.5% for Streptococcus pneumoniae, 67.2% for Haemophilus influenzae, and 78.1% for Moraxella catarrhalis when compared with pre-COVID-19 levels. The distribution of respiratory microbial strains by age group showed that the highest percentage of isolated strains was in patients in their 70s. Conclusions: The improvements in personal hygiene due to the COVID-19 pandemic exerted a substantial influence on the pattern of change in other common respiratory microorganisms, which highlights the importance of personal hygiene management in the prevention of respiratory infections.

Performance evaluation of four rapid antibody tests for the detection of severe acute respiratory syndrome coronavirus 2.

BACKGROUND: The prompt detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is important in the therapeutic management of infected patients. Rapid diagnostic tests are widely used for this purpose. This study aimed to evaluate the clinical performance of four SARS-CoV-2 immunoglobulin IgG/IgM rapid diagnostic tests in the detection of SARS-CoV-2. METHODS: Nasopharyngeal and oropharyngeal swabs and/or sputum were collected from 30 patients infected with SARS-CoV-2 and 30 healthy volunteers. All specimens were tested using four SARS-CoV-2 IgG/IgM rapid diagnostic tests and real-time polymerase chain reaction. We assessed the clinical sensitivity and specificity of the tests. RESULTS: The clinical sensitivity of FREND™, SsmarTest™, BIOCREDIT™, and IVDLAB™ was 96.67%, 100.00%, 100.00%, and 96.67%, respectively, compared to real-time polymerase chain reaction. The clinical specificity was 96.67%, 100.00%, 86.67%, and 96.67%, respectively. CONCLUSION: These findings could expedite the detection of SARS-CoV-2 and thus reduce the risk of further transmission of the virus.

Pattern of change of C-reactive protein levels and its clinical implication in patients with acute poisoning.

OBJECTIVES: C-reactive protein is well known as an inflammatory indicator in injury, infection, and cancer. However, little is known about its role in poisoning. C-reactive protein levels first increase and then decrease within several days during poisoning management. This study aimed to verify the C-reactive protein change pattern and its clinical co-infection possibility in patients with poisoning. METHODS: Daily C-reactive protein levels of the patients with poisoning, who were admitted for more than 5 days, were measured. Microbial cultures were conducted, and fever (⩾38°C) and infection-related symptoms were investigated. RESULTS: In the enrolled 56 patients, the initial median C-reactive protein levels at hospital day 1, 2, 3, 4, and 5 were 0.28, 4.85, 10.91, 10.57, and 6.68 mg/dL, respectively. C-reactive protein level was the highest at hospital day 3 and decreased thereafter. No statistical difference was observed in the daily and maximal C-reactive protein levels between the culture-positive and culture-negative groups. The levels at hospital days 3-5 and the maximal level were 8.4, 9.2, 5.49, and 11.02 mg/dL, respectively, in non-fever group. The levels at hospital days 3-5 and the maximal level were 7.4, 9.2, 4.74, and 10.81 mg/dL, respectively, in non-symptoms group. Levels at hospital days 3-5 and the maximal level were 5.21, 4.93, 3.7, and 5.28 mg/dL, respectively, in all-negative (culture-negative without fever or infection symptoms) group. CONCLUSIONS: Acute rise and fall of C-reactive protein levels can be observed in the infection-unlikely patients with poisoning. The levels were similar to bacterial infection levels, possibly due to the drug reaction itself, rather than for superimposed infections.

Performance Evaluation of the BZ COVID-19 Neutralizing Antibody Test for the Culture-Free and Rapid Detection of SARS-CoV-2 Neutralizing Antibodies.

Rapid and accurate measurement of SARS-CoV-2 neutralizing antibodies (nAbs) can aid in understanding the development of immunity against COVID-19. This study evaluated the diagnostic performance of a rapid SARS-CoV-2 nAb detection test called the BZ COVID-19 nAb test BZ-nAb (BZ-nAb; BioZentech). Using the 90% plaque-reduction neutralization test (PRNT-90) as a reference, 104 serum specimens collected from COVID-19-positive and -negative patients were grouped into 40 PRNT-90-positive and 64 PRNT-90-negative specimens. The performance of the BZ-nAb was compared with that of the cPass surrogate virus neutralization test (cPass sVNT; Genscript). The BZ-nAb showed a sensitivity ranging from 92.5%-95.0% and specificity ranging from 96.9%-100%, whereas cPass sVNT showed a sensitivity of 100% (95% confidence interval (CI) 90.5%-100%) and specificity of 98.4% (95% CI, 91.6%-100%). The dilution factor obtained with PRNT-90 showed a stronger correlation with the percent inhibition of cPass sVNT (r = 0.8660, p < 0.001) compared with the test and control line ratio (T/C ratio) of the BZ-nAb (r = -0.7089, p < 0.001). An almost perfect agreement was seen between the BZ-nAb and cPass sVNT results, with a strong negative correlation between the BZ-nAb T/C ratio and cPass sVNT percent inhibition (r = -0.8022, p < 0.001). In conclusion, the diagnostic performance of the BZ-nAb was comparable to that of the cPass sVNT, although the BZ-nAb had a slightly lower sensitivity.

Prevalence and Antimicrobial Susceptibility of Streptococcus pneumoniae Isolated from Clinical Samples in the Past 8 Years in Korea.

Pneumococcal infection is the main causative agent of pneumonia, meningitis, and sepsis in immunocompromised and elderly people. The samples in this study were collected from subjects in an 800-bed hospital in Chungnam province, Korea, over the past 8 years. Of the 473,230 samples obtained for microbial culture from 2012 to 2019, Streptococcus pneumoniae was isolated from 714 samples collected from 702 patients, with a pneumococcal-positive rate of 0.15%. We investigated the temporal, demographic, and specimen-specific distributions, as well as the antibiotic susceptibility pattern for S. pneumonia. The age of patients ranged from 0 days to 98 years, with an average age of 64.7 years. The distribution among the sexes was 2.4 : 1 (male : female), with more samples isolated from male patients. We observed that spring was the predominant season in which the infection occurred, accounting for 37.6% of the cases. Pneumococci were most frequently isolated from sputum (608 cases, 85.2%). Invasive infections were detected at a rate of 66% (in blood cultures), and noninvasive infections were detected at a rate of 91% (in sputum cultures). Antimicrobial resistance to ceftriaxone, cefotaxime, erythromycin, tetracycline, clindamycin, cotrimoxazole, levofloxacin, and penicillin, based on noninvasive infections, was observed in 21.6%, 27.2%, 79.2%, 73.2%, 68.0%, 51.3%, 9.8%, and 18.1% of cases, respectively. Additionally, on average, 66.9% of multidrug-resistant bacteria showed resistance to three or more antimicrobial agents, and 2.8% showed resistance to all other antibacterial agents except vancomycin. These results might facilitate the administration of appropriate empirical antibacterial therapy for pneumococcal infections.

Development of a multiplex Loop-Mediated Isothermal Amplification (LAMP) assay for on-site diagnosis of SARS CoV-2.

A newly identified coronavirus, designated as severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), has spread rapidly from its epicenter in China to more than 150 countries across six continents. In this study, we have designed three reverse-transcription loop-mediated isothermal amplification (RT-LAMP) primer sets to detect the RNA-dependent RNA polymerase (RdRP), Envelope (E) and Nucleocapsid protein (N) genes of SARS CoV-2. For one tube reaction, the detection limits for five combination SARS CoV-2 LAMP primer sets (RdRP/E, RdRP/N, E/N, RdRP/E/N and RdRP/N/Internal control (actin beta)) were evaluated with a clinical nasopharyngeal swab sample. Among the five combination, the RdRP/E and RdRP/N/IC multiplex LAMP assays showed low detection limits. The sensitivity and specificity of the RT-LAMP assay were evaluated and compared to that of the widely used Allplex™ 2019-nCoV Assay (Seegene, Inc., Seoul, South Korea) and PowerChek™ 2019-nCoV Real-time PCR kit (Kogenebiotech, Seoul, South Korea) for 130 clinical samples from 91 SARS CoV-2 patients and 162 NP specimens from individuals with (72) and without (90) viral respiratory infections. The multiplex RdRP (FAM)/N (CY5)/IC (Hex) RT-LAMP assay showed comparable sensitivities (RdRP: 93.85%, N: 94.62% and RdRP/N: 96.92%) to that of the Allplex™ 2019-nCoV Assay (100%) and superior to those of PowerChek™ 2019-nCoV Real-time PCR kit (RdRP: 92.31%, E: 93.85% and RdRP/E: 95.38%).

Viral kinetics of SARS-CoV-2 over the preclinical, clinical, and postclinical period.

BACKGROUND: It is necessary to know the viral kinetics and conduct epidemiological investigations of confirmers to prevent the spread of the new infectious disease COVID-19 to the community. To date, no study has been published on viral kinetics during the preclinical and clinical periods of SARS-CoV-2. METHODS: A confirmed case was defined as a patient with positive results by real-time reverse transcription polymerase chain reaction (RT-PCR) assay for SARS-CoV-2. Both specimen types were collected over the whole clinical course in all patients. Asymptomatic patients who had been screened for COVID-19 due to a strong epidemiological link were also enrolled. The study population included 54 hospitalized patients with confirmed COVID-19. RESULTS: COVID-19 shows a very high viral load on the day of symptom development, which then decreases overall. Rapid viral proliferation was observed 0-5 days before symptoms developed. Cycle threshold (Ct) value was the lowest in the clinical course from 5 days before symptoms to 10 days after symptoms occurred (Ct < 30). The rRT-PCR results were negative approximately 3 weeks after the onset of symptoms. However, there was a continuous pattern that was negative and positive for up to 6 weeks and more. CONCLUSION: Considering the characteristic that COVID-19 has a high viral load before symptoms appear, it is necessary to consider to expand the scope of epidemiological investigations. As there is a very low possibility of transmission after 10 days of symptom occurrence, it may be considered to release isolation after 10 days of symptom occurrence in limited resource situations. This study allows for the planning of epidemiological investigations, patient's ward supply, and follow-up of patients through sequential changes in viral loads over the entire clinical course. In addition, it is possible to estimate the clinical time at which the patient is present.

Comparative evaluation of Plateletworks, Multiplate analyzer and Platelet function analyzer-200 in cardiology patients.

The objective of this study was to comparatively evaluate three commercial whole-blood platelet function analyzer systems: Platelet Function Analyzer-200 (PFA; Siemens Canada, Mississauga, Ontario, Canada), Multiplate analyzer (MP; Roche Diagnostics International Ltd., Rotkreuz, Switzerland), and Plateletworks Combo-25 kit (PLW; Helena Laboratories, Beaumont, TX, USA). Venipuncture was performed on 160 patients who visited a department of cardiology. Pairwise agreement among the three platelet function assays was assessed using Cohen's kappa coefficient and percent agreement within the reference limit. Kappa values with the same agonists were poor between PFA-collagen (COL; agonist)/adenosine diphosphate (ADP) and MP-ADP (-0.147), PFA-COL/ADP and PLW-ADP (0.089), MP-ADP and PLW-ADP (0.039), PFA-COL/ADP and MP-COL (-0.039), and between PFA-COL/ADP and PLW-COL (-0.067). Nonetheless, kappa values for the same assay principle with a different agonist were slightly higher between PFA-COL/ADP and PFA-COL/EPI (0.352), MP-ADP and MP-COL (0.235), and between PLW-ADP and PLW-COL (0.247). The range of percent agreement values was 38.7% to 73.8%. Therefore, various measurements of platelet function by more than one method were needed to obtain a reliable interpretation of platelet function considering low kappa coefficient and modest percent agreement rates among 3 different platelet function tests.

Report on the Project for Establishment of the Standardized Korean Laboratory Terminology Database, 2015.

The National Health Information Standards Committee was established in 2004 in Korea. The practical subcommittee for laboratory test terminology was placed in charge of standardizing laboratory medicine terminology in Korean. We aimed to establish a standardized Korean laboratory terminology database, Korea-Logical Observation Identifier Names and Codes (K-LOINC) based on former products sponsored by this committee. The primary product was revised based on the opinions of specialists. Next, we mapped the electronic data interchange (EDI) codes that were revised in 2014, to the corresponding K-LOINC. We established a database of synonyms, including the laboratory codes of three reference laboratories and four tertiary hospitals in Korea. Furthermore, we supplemented the clinical microbiology section of K-LOINC using an alternative mapping strategy. We investigated other systems that utilize laboratory codes in order to investigate the compatibility of K-LOINC with statistical standards for a number of tests. A total of 48,990 laboratory codes were adopted (21,539 new and 16,330 revised). All of the LOINC synonyms were translated into Korean, and 39,347 Korean synonyms were added. Moreover, 21,773 synonyms were added from reference laboratories and tertiary hospitals. Alternative strategies were established for mapping within the microbiology domain. When we applied these to a smaller hospital, the mapping rate was successfully increased. Finally, we confirmed K-LOINC compatibility with other statistical standards, including a newly proposed EDI code system. This project successfully established an up-to-date standardized Korean laboratory terminology database, as well as an updated EDI mapping to facilitate the introduction of standard terminology into institutions.

Viral shedding from diverse body fluids in a patient with severe fever with thrombocytopenia syndrome.

BACKGROUND: Severe fever with thrombocytopenia syndrome (SFTS) is a tick-borne disease characterized by high fever, thrombocytopenia, leukopenia, and multiple organ failure and is caused by a novel bunyavirus. Human-to-human transmission has been reported previously, but the mode of transmission has not been clarified thoroughly. STUDY DESIGN: We identified a case of a 73-year-old woman with SFTS and performed a semi-quantitative real-time reverse transcription PCR (real-time RT-PCR) assay on her blood, tracheal aspirate, gastric aspirate and urine to detect SFTS virus (SFTSV). RESULTS: During 7-day hospitalization, all the serum samples showed positive Ct values lower than 35 in both the S and M segments, suggesting the presence of the SFTSV RNA. After initiation of plasma exchange, serum SFTSV load markedly decreased, but still remained positive. The SFTS viral RNA was also detected in other body fluids, including tracheal aspirate and gastric aspirate. CONCLUSION: These results suggest that droplet transmission can occur through close contact with infected patients.

Performance evaluation of four rapid antigen tests for the detection of Respiratory syncytial virus.

Rapid identification of Respiratory syncytial virus (RSV) is important in the management of infected patients. Rapid diagnostic tests (RDT) are widely used for this purpose. This study aimed to evaluate the clinical performance of four RSV antigen tests including the BinaxNow RSV Card test, SD Bioline RSV test, BD Veritor RSV test, and Humasis RSV antigen test in comparison with real-time RT-PCR as the reference method. Nasopharyngeal swabs were collected from 280 patients with symptoms of lower respiratory tract infection and stored at -80°C. All swabs were tested for RSV using four rapid antigen tests and real time RT-PCR. The sensitivity of the BinaxNow RSV Card test, SD Bioline RSV test, BD Veritor RSV test, and Humasis RSV Antigen tests were 62.5%, 61.3%, 65.0%, and 67.5% for RSV A, and 61.3%, 65.0%, 61.3%, and 67.5% for RSV B compared to real time RT-PCR, respectively. The specificity of BD Veritor RSV test was 95.8% and those of the other three RDTs was 100%. Commercial RSV antigen detection assays are useful tools for the rapid diagnosis of RSV infection. However, confirmatory testing is always recommended. J. Med. Virol. 88:1720-1724, 2016. © 2016 Wiley Periodicals, Inc.

Comparison of quantitation of cytomegalovirus DNA by real-time PCR in whole blood with the cytomegalovirus antigenemia assay.

BACKGROUND: Quantitation of cytomegalovirus (CMV) DNA using real-time PCR has been utilized for monitoring CMV infection. However, the CMV antigenemia assay is still the 'gold standard' assay. There are only a few studies in Korea that compared the efficacy of use of real-time PCR for quantitation of CMV DNA in whole blood with the antigenemia assay, and most of these studies have been limited to transplant recipients. METHOD: 479 whole blood samples from 79 patients, falling under different disease groups, were tested by real-time CMV DNA PCR using the Q-CMV real-time complete kit (Nanogen Advanced Diagnostic S.r.L., Italy) and CMV antigenemia assay (CINA Kit, ArgeneBiosoft, France), and the results were compared. Repeatedly tested patients were selected and their charts were reviewed for ganciclovir therapy. RESULTS: The concordance rate of the two assays was 86.4% (Cohen's kappa coefficient value=0.659). Quantitative correlation between the two assays was a moderate (r=0.5504, P<0.0001). Among 20 patients tested repeatedly with the two assays, 13 patients were transplant recipients and treated with ganciclovir. Before treatment, CMV was detected earlier by real-time CMV DNA PCR than the antigenemia assay, with a median difference of 8 days. After treatment, the antigenemia assay achieved negative results earlier than real-time CMV DNA PCR with a median difference of 10.5 days. CONCLUSIONS: Q-CMV real-time complete kit is a useful tool for early detection of CMV infection in whole blood samples in transplant recipients.

ABO*Ael03/O genotype with ABO discrepancy: the first case in Korea.

The Ael subgroup expresses the least amount of A antigens and could only be detected by performing the adsorption-elution test. The frequency of the Ael subgroup is about 0.001% in Koreans, and the Ael02 allele, which originates from A102, is the most frequently identified allele in the Korean population. We report a Korean family with the Ael03 allele identified by molecular genetic analysis. To the best of our knowledge, this is the first such report in Korea to date.

Detection of platelet-monocyte aggregates by the ADAM(®) image cytometer.

BACKGROUND: Inappropriate platelet activation is known to be associated with various thrombotic disorders. Platelet-monocyte aggregates (PMAs), whose formation is mediated by platelet surface P-selectin (CD62P), can be used as a reliable marker to detect platelet activation. Previous studies have generally detected PMAs through flow cytometry-based approaches. Recently, the ADAM(®) image cytometer (Nanoentek Inc., Seoul, Korea) was developed for image-based cellular analysis. In this study, we detected PMAs with the ADAM(®) cytometer, evaluated the reproducibility of the measurements made by the ADAM(®) cytometer, and compared the abilities of the ADAM(®) cytometer and a flow cytometric assay to detect PMAs. METHODS: Whole blood samples were collected from patients. Within 5 minutes of collection, anticoagulated whole blood samples were fixed in 10% paraformaldehyde and 5% glyoxal. Nineteen clinical specimens were collected; each was analyzed three times with the ADAM(®) cytometer in order to assess the reproducibility of its measurements. To compare the ability of the ADAM(®) cytometer with that of a flow cytometer to detect PMAs, each cytometer was used for 23 clinical samples and the correlation of the measurements was determined. RESULTS: The PMA measurements made by the ADAM(®) cytometer showed good reproducibility (CV < 10% for all specimens). Moreover, the PMA measurements made by the ADAM(®) cytometer exhibited a high correlation with those made by a flow cytometric assay (R = 0.944). CONCLUSIONS: The ADAM(®) cytometer is a suitable alternative method to the flow cytometry-based assays. Since the ADAM cytometer does not need specialized instrument knowledge or software proficiency (unlike flow cytometry), the ADAM(®) cytometer can be used as a rapid and reliable POCT device to measure platelet activation in peripheral blood. This, in turn, will provide valuable information regarding patient propensities to thrombotic diseases.