Immune Responses After Vaccination With Primary 2-Dose ChAdOx1 Plus a Booster of BNT162b2 or Vaccination With Primary 2-Dose BNT162b2 Plus a Booster of BNT162b2 and the Occurrence of Omicron Breakthrough Infection

Background@#Before the omicron era, health care workers were usually vaccinated with either the primary 2-dose ChAdOx1 nCoV-19 (Oxford-AstraZeneca) series plus a booster dose of BNT162b2 (Pfizer-BioNTech) (CCB group) or the primary 2-dose BNT162b2 series plus a booster dose of BNT162b2 (BBB group) in Korea. @*Methods@#The two groups were compared using quantification of the surrogate virus neutralization test for wild type severe acute respiratory syndrome coronavirus 2 (SVNT-WT), the omicron variant (SVNT-O), spike-specific IgG, and interferon-gamma (IFN-γ), as well as the omicron breakthrough infection cases. @*Results@#There were 113 participants enrolled in the CCB group and 51 enrolled in the BBB group. Before and after booster vaccination, the median SVNT-WT and SVNT-O values were lower in the CCB (SVNT-WT [before-after]: 72.02–97.61%, SVNT-O: 15.18–42.29%) group than in the BBB group (SVNT-WT: 89.19–98.11%, SVNT-O: 23.58–68.56%; all P < 0.001). Although the median IgG concentrations were different between the CCB and BBB groups after the primary series (2.677 vs. 4.700 AU/mL, respectively, P < 0.001), they were not different between the two groups after the booster vaccination (7.246 vs. 7.979 AU/mL, respectively, P = 0.108). In addition, the median IFN-γ concentration was higher in the BBB group than in the CCB group (550.5 and 387.5 mIU/mL, respectively, P = 0.014). There was also a difference in the cumulative incidence curves over time (CCB group 50.0% vs. BBB group 41.8%; P = 0.045), indicating that breakthrough infection occurred faster in the CCB group. @*Conclusion@#The cellular and humoral immune responses were low in the CCB group so that the breakthrough infection occurred faster in the CCB group than in the BBB group.

Positivity of Rapid Antigen Testing for SARS-CoV-2 With Serial Followed-up Nasopharyngeal Swabs in Hospitalized Patients due to COVID-19

Despite the accuracy of nucleic acid amplification tests (NAATs), rapid antigen tests (RATs) for severe acute respiratory syndrome coronavirus-2 are widely used as point-of-care tests. A total of 282 pairs of reverse transcription-polymerase chain reaction and Standard Q COVID-19 Ag tests were serially conducted for 68 patients every 3–4 days until their discharge. Through a field evaluation of RATs using direct nasopharyngeal swabs, the sensitivities were 84.6% and 87.3% for E and RNA-dependent RNA polymerase (RdRp) genes, respectively, for specimens with cycle thresholds (Cts) < 25. The Ct values of E and RdRp genes for 95% detection rates by RATs were 16.9 and 18.1, respectively. The sensitivity of RAT was 48.4% after the onset of symptoms, which was not sufficient. RAT positivity gradually decreased with increased time after symptom onset and had continuously lower sensitivity than NAATs.

A Novel Species of the Genus Arsenicicoccus Isolated From Human Blood Using Whole-Genome Sequencing

Whole-genome sequencing (WGS) is an easily accessible and valuable tool in clinical microbiology, which can be used for identifying novel and rare species. We isolated grampositive cocci from the blood of a pediatric patient, which could not be phenotypically identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) (BioMérieux, Marcy-l’Étoile, France). We could not identify the isolate to the species level using 16S ribosomal RNA (rRNA) sequencing. WGS was performed using the Illumina MiSeq platform (Illumina, San Diego, CA, USA); however, the subsequent genomic sequence database search using the TrueBac ID-Genome system (ChunLab, Inc., Seoul, Korea) did not yield any hits with an average nucleotide identity value > 95.0%, which is the cut-off for species-level identification. Phylogenetic analysis suggested that the isolate belonged to a new Arsenicicoccus species, forming a subcluster with Arsenicicoccus bolidensis. Our data demonstrate that WGS allows a more accurate annotation of microbial genomes than other clinical microbiology tools, such as MALDITOF MS and 16S rRNA sequencing. This is the first report of the isolation of a novelArsenicicoccus species from a clinical sample.

Effectiveness of Platelet Function Analyzer-100 for Laboratory Detection of Anti-Platelet Drug-Induced Platelet Dysfunction

BACKGROUND: High on-treatment platelet reactivity (HTPR) is the phenomenon wherein patients exhibit normal platelet activity in laboratory testing despite adequate adherence to anti-platelet treatment. We investigated the detection rates of Platelet Function Analyzer (PFA)-100 (Dade Behring AG, Düdingen, Switzerland) for drug-induced platelet dysfunction and analyzed potential contributors to HTPR with practical PFA-100 data over six years. METHODS: We used data from 6,957 patients who underwent PFA-100 testing after receiving aspirin, clopidogrel, or non-steroidal anti-inflammatory drugs (NSAIDs). Of these, 6,163 patients were tested with only the collagen/epinephrine cartridge (Col/EPI) of PFA-100; 794 were tested with both Col/EPI and the collagen/ADP cartridge (Col/ADP). We calculated PFA-100 closure time (CT) for each drug and compared the clinical and laboratory characteristics of the patients with prolonged CTs and normal CTs (i.e., HTPR). RESULTS: In Col/EPI, 73.2% (365/499), 72.6% (390/537), and 55.3% (3,442/6,228) patients showed prolonged CTs for aspirin, clopidogrel, and NSAIDs, respectively. In Col/ADP, prolonged CTs were observed in 37.4% (34/91), 43.2% (35/81), and 29.6% (200/676) of patients receiving aspirin, clopidogrel, and NSAIDs, respectively. Of the patients tested with both cartridges, 88.9% (48/54), 95.3% (41/43), and 89.0% (577/648) of the patients receiving aspirin, clopidogrel, and NSAIDs had prolonged CTs, and 10.0% (79/794) showed normal CTs regardless of drugs. For clopidogrel users (both cartridges), there were more patients with malignancies in the normal CT than prolonged CT group. CONCLUSIONS: PFA-100 is not sufficiently effective for laboratory screening of drug-induced platelet dysfunction. Malignancy may contribute to clopidogrel-related HTPR in PFA-100.

Age-related Reference Intervals for Total Collagen-I-N-terminal Propeptide in Healthy Korean Population

BACKGROUND: Procollagen type I N-terminal propeptide (PINP) is one of the most clinically useful bone formation biomarkers. Therefore, the purpose of this study was to independently evaluate the performance of automated total PINP assay and established age- and gender-specific reference intervals for PINP in healthy Korean population. METHODS: The imprecision, linearity, and detection capability of Elecsys total PINP assay was determined and reference interval was established using 599 serums from Korean population with normal bone mineral densities based on bone densitometry. Age groups were divided into 20s, 30s, 40s, 50s, 60s and over. RESULTS: Elecsys total PINP had excellent performance in imprecision, linearity, and detection capability. When partitioning age groups in Korean male and female populations, there was significant difference in total PINP between different age groups. In male populations, PINP level was decreased with increasing age, then it remained steady after middle-age. In female populations, there was a decreasing tendency similar to that in the male population with a sharp increase in the 50 to 59 age group. CONCLUSIONS: Elecsys total PINP assay showed precise and reliable performance in our study. We established age-related PINP reference intervals for Korean male and female population with normal bone mineral densities.

Prevalence and Antimicrobial Susceptibility of Mycoplasma hominis, Ureaplasma urealyticum and Ureaplasma parvum in Individuals With or Without Symptoms of Genitourinary Infections

BACKGROUND: The aim of this study was to determine the prevalence and antimicrobial susceptibility of Mycoplasma hominis, Ureaplasma urealyticum, and Ureaplasma parvum among patients displaying symptoms of genitourinary infections and asymptomatic volunteers. METHODS: Genitourinary samples were collected from 897 participants (365 symptomatic patients and 532 asymptomatic volunteers). The samples were analyzed using multiplex real-time PCR (Anyplex™ II, Seegene, Korea), multiplex PCR (Seeplex®, Seegene), and Mycoplasma IST 2 Kit (bioMerieux, France). RESULTS: The prevalence of M. hominis, U. urealyticum, and U. parvum in the genitourinary samples of symptomatic patients compared with asymptomatic volunteers was 9.9% vs. 5.5%, 12.3% vs. 9.0%, and 36.4% vs. 30.8%, respectively. After eliminating cases of co-infections with other pathogens, there was a significant difference in the prevalence of M. hominis between symptomatic patients and asymptomatic volunteers (9.1% vs. 5.2%, P<0.05), but not in the prevalence of U. urealyticum and U. parvum organisms. When tested for antimicrobial susceptibility, more than 95.5% of each species were susceptible to tetracycline, doxycycline, josamycin, and pristamycin. More than 78.9% of Ureaplasma spp. were susceptible to azithromycin, erythromycin, and clarithromycin; however less than 4.2% of M. hominis were susceptible to these antibiotics. When tested with ofloxacin and ciprofloxacin, 40.9-58.9% and 9.1-25.0% of the three species were susceptible to these drugs, respectively. CONCLUSIONS: M. hominis is the leading causative pathogen for genitourinary infection; however the involvement of Ureaplasma spp. is debatable. For optimal antimicrobial therapy, the accurate detection of these organisms and determination of antimicrobial susceptibility is crucial considering their diverse antimicrobial susceptibility patterns.

Survey of Clinical Laboratory Practices for 2015 Middle East Respiratory Syndrome Coronavirus Outbreak in the Republic of Korea

BACKGROUND: It is crucial to understand the current status of clinical laboratory practices for the largest outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infections in the Republic of Korea to be well prepared for future emerging infectious diseases. METHODS: We conducted a survey of 49 clinical laboratories in medical institutions and referral medical laboratories. A short questionnaire to survey clinical laboratory practices relating to MERS-CoV diagnostic testing was sent by email to the directors and clinical pathologists in charge of the clinical laboratories performing MERS-CoV testing. The survey focused on testing volume, reporting of results, resources, and laboratory safety. RESULTS: A total of 40 clinical laboratories responded to the survey. A total of 27,009 MERS-CoV real-time reverse transcription PCR (rRT-PCR) tests were performed. Most of the specimens were sputum (73.5%). The median turnaround time (TAT) was 5.29 hr (first and third quartile, 4.11 and 7.48 hr) in 26 medical institutions. The median TAT of more than a half of the laboratories (57.7%) was less than 6 hr. Many laboratories were able to perform tests throughout the whole week. Laboratory biosafety preparedness included class II biosafety cabinets (100%); separated pre-PCR, PCR, and post-PCR rooms (88.6%); negative pressure pretreatment rooms (48.6%); and negative pressure sputum collection rooms (20.0%). CONCLUSIONS: Clinical laboratories were able to quickly expand their diagnostic capacity in response to the 2015 MERS-CoV outbreak. Our results show that clinical laboratories play an important role in the maintenance and enhancement of laboratory response in preparation for future emerging infections.

Two Cases of Enterobacter hormaechei Infection Misidentified as Cedecea davisae Infection

Enterobacteriaceae is a family of gram-negative, rod-shaped bacteria that consists of various species. Among these, members of the genus Cedecea has been reported as relatively rare causative pathogens of human infections. Commercially available automated identification systems that use biochemical reactions are known to accurately identify Enterobacteriaceae species. However, the accurate identification of some organisms with diverse biochemical profiles by these automated identification systems may be problematic. In this study, we report two cases of isolate misidentification, from patients with acute cholecystitis and deep vein thrombosis, as Cedecea davisae with VITEK II system. Both the isolates were correctly identified as Enterobacter hormaechei using gyrB gene sequence analysis. We also performed 16S rRNA sequence analyses and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analyses; however, indeterminate results were obtained from both the assays. Therefore, the sequence analysis of alternative genes, like gyrB, might be useful for accurate identification of species that belong to the family of Enterobacteriaceae.

Discrepancy between Vitamin D Total Immunoassays due to Various Cross-reactivities

BACKGROUND: The purpose of this study was to find out the cause of discrepancy between various automated immunoassays for 25-hydroxy-vitamin D (25-[OH]D). METHODS: National Institute of Standards & Technology Standard Reference Material (SRM) 972a is SRM for 25-(OH)D and consists of 4 vials of frozen serum with different concentrations of 25-(OH)D. Each concentration was measured 6 times in 3 different immunoassays: ADVIA Vitamin D Total assay (Siemens Healthcare, Erlangen, Germany), ARCHITECT 25-(OH)D (Abbott Laboratories, Abbott Park, IL, USA), and COBAS Vitamin D Total assay (Roche Diagnostics, Basel, Switzerland). RESULTS: When using the certified reference values of SRM 972a as it is, discarding the cross-reactivity of each immunoassay, for ADVIA, the coefficient of determination (R2) as a score of regression analysis was 0.8995 and maximal difference between measured value and certified reference value was 3.6 ng/mL in level 3. The R2 and maximal differences of ARCHITECT were 0.5377 and 6.9 ng/mL, respectively, in level 4. Those of COBAS were 0.3674 and 22.3 ng/mL, respectively, in level 4. When considering cross-reactivities of each immunoassays to various 25-(OH)D metabolites, the ADVIA had R2 and maximal difference of 0.9254 and 3.3 ng/mL, respectively, in level 3. For ARCHITECT, the R2 and maximal differences were 0.7602 and 5.1 ng/mL, respectively, in level 1. Those of COBAS were 0.9284 and 4.9 ng/mL, respectively, in level 1. CONCLUSIONS: The cause of discrepancies between vitamin D immunoassays was mainly on the difference in cross-reactivities to various vitamin D metabolites. The discrepancies can be considerably decreased by considering cross-reactivities of each immunoassay.

Two Cases of Bacteremias Caused by Clostridium ramosum / 대한임상미생물학회지

Clostridium ramosum is Gram-positive anaerobic bacillus and is known as a non-pathogenic enteric bacterium. It is a member of the RIC group, which is a subgroup of Clostridium having atypical characteristics. Rarely, it has been reported as a pathogen of otitis media in young children or the cause of infection in immunosuppressed adults. Here, we report the first two Korean cases of C. ramosum bacteremia in colon cancer and pressure sore cases, respectively.

Interpretation of Papanicolaou Smear Test and Gram Stain Results for the Diagnosis of Infectious Vaginitis is Affected by Knowledge of Additional Related Test Results

BACKGROUND: Infectious vaginitis is a common gynecologic disease that is primarily caused by three pathogens (Trichomonas vaginalis, Gardnerella vaginalis, and Candida species). The aim of this study was to confirm the effects of other infectious vaginitis-related test results on the interpretation of Gram stain and Papanicolaou (Pap) smear test results for disease diagnosis. METHODS: A total of 300 vaginal samples were collected from women presenting symptoms of vaginitis. The presence of the three previously mentioned pathogens was evaluated using both a Gram stain and Pap smear test, and interpreted twice by 4 different observers. The first interpretation was performed without any information, and a second interpretation was performed with knowledge of results of an Affirm VPIII test that was used to diagnose infectious vaginitis. The results from the two interpretations were compared and the sensitivity and specificity of both tests were evaluated. RESULTS: For the Gram stain samples, the detection rates of G. vaginalis were increased in the second interpretation by 6.2%, while the detection rates of Candida spp. were decreased by 0.3%. For the Pap smear test samples, the detection rates of G. vaginalis were increased in the second interpretation by 7.0%, and the detection rates of Candida spp. were increased by 2.0%. The sensitivity of both tests was increased in the second interpretation by 5.5% to 66.7%. There was no difference in the specificity between the two interpretations. CONCLUSIONS: We demonstrated that there is significant inter-observer variation when using Gram stain and Pap smear test results to diagnose infectious vaginitis. The detection rates and sensitivity of both tests changed when the results from an additional test were incorporated into the interpretation. Additional studies are needed to develop objective criteria and a standardized interpretation system for the evaluation of results from these diagnostic tests.