Amplification Failure by the Cepheid Xpert Xpress SARS-CoV-2 Assay due to a Single-Nucleotide Variant of the N Gene in the Omicron Variant.

BACKGROUND: Rapid identification of SARS-CoV-2 infection using molecular testing has played an important role in preventing the spread of COVID-19. However, the failure of SARS-CoV-2 N gene amplification in the Cepheid Xpert SARS-CoV-2 assay could lead to the failed detection of infections, possibly leading to spread. In this study, we examined N gene amplification failure due to a single-nucleotide variant (SNV) in the N2 region of the gene. METHODS: Xpert assay results obtained at our hospital since March 2021 were retrospectively reviewed and samples with strong E gene and failed N gene amplification were selected. Whole-genome sequencing was performed using the Illumina platform. Lineage analyses were conducted and the N2 target region of the US CDC 2019-nCoV real-time PCR primer sequence, used in PCR assays of SARS-CoV-2 infection, was compared with the reference SARS-COV-2 sequence (Wuhan-Hu-1, NC_045512.2). RESULTS: The two samples eligible for this study were classified as BA.5.2 (22B, Omicron) and included two synony-mous SNVs, C29197T and C29200T, respectively. Both variants resulted in synonymous mutation of the N gene encoding alanine. The distribution of variants varied across different countries. CONCLUSIONS: Clinical laboratories performing molecular tests targeting the N gene of SARS-CoV-2 should consider the probability of N gene amplification failure when reporting the test results.

Clinical and Microbiological Characteristics of Chryseobacterium indologenes Bacteremia: A 20-Year Experience in a Single University Hospital.

BACKGROUND: Chryseobacterium indologenes is ubiquitous in nature and rarely causes infections. However, the clinical impact of C. indologenes has increased in recent years, especially in immunocompromised patients, and has resulted in high mortality rates. We aimed to investigate the clinical and microbiological characteristics of C. indologenes bacteremia. MATERIALS AND METHODS: We retrospectively reviewed medical records of a 642-bed university-affiliated hospital in Korea, dating from January 2001 to December 2020, to investigate C. indologenes bacteremia. RESULTS: A total of 22 C. indologenes isolates were identified from blood culture records. All patients were hospitalized at the time of bacteremia, and the most common manifestation was primary bacteremia. A sizable majority of the patients (83.3%) had underlying diseases, and all patients received intensive care unit care during their admission. The 14-day and 28-day mortality rates were 8.3% and 16.7%, respectively. Importantly, all C. indologenes isolates were 100% susceptible to trimethoprim-sulfamethoxazole. CONCLUSION: In our study, most of the infections were hospital-acquired, and the susceptibility pattern of the C. indologenes isolates showed multidrug resistance. However, trimethoprim-sulfamethoxazole is a potentially useful antibiotic for C. indologenes bacteremia treatment. More attention is required to identify C. indologenes as one of the most important nosocomial bacteria with detrimental effects in immunocompromised patients.

A 20-year trend of prevalence and susceptibility to trimethoprim/sulfamethoxazole of Stenotrophomonas maltophilia in a single secondary care hospital in Korea.

Stenotrophomonas maltophilia is a Gram-negative opportunistic pathogen that can cause serious infection. We aimed to analyze the prevalence and susceptibility rates to trimethoprim/sulfamethoxazole of S. maltophilia. We conducted a retrospective study of S. maltophilia isolates from a university hospital from 2001 to 2020. Clinical information, the numbers of isolates and susceptibility rates were analyzed by year. Susceptibility rates and changes in respiratory and non-respiratory samples were compared. 1805 S. maltophilia isolates were identified, of which 81.4% (1469/1805) were from respiratory samples. There was a male predominance and 52% of the isolates were from general wards. The average susceptibility rate was 87.7% and there was no significant annual trend (P = .519). The susceptibility rate was 88.7% in respiratory samples and 84.1% in non-respiratory samples (P = .018). Susceptibility analyses using clinical data over long periods can guide the choice of antimicrobials especially for pathogen whose treatment options are limited.

Human granulocytic anaplasmosis combined with rhabdomyolysis: a case report.

BACKGROUND: Human granulocytic anaplasmosis (HGA) is a systemic inflammatory response caused by the rickettsial bacterium Anaplasma phagocytophilum. Rhabdomyolysis and acute kidney injury (AKI) are rare complications of HGA. Here, we report a case of HGA concurrent with rhabdomyolysis and AKI in an elderly patient. CASE PRESENTATION: An 84-year old woman with a medical history of hypertension was hospitalised after two days of fever, dizziness, whole body pain, and general weakness. Laboratory investigations showed severe thrombocytopenia, leukopenia, impaired renal function, and elevated cardiac enzyme and myoglobin levels. On the day after admission, peripheral blood smear revealed morula inclusions in neutrophils, a suggestive finding of HGA. Real-time polymerase chain reaction (PCR) results indicated the presence of A. phagocytophilum. Antibiotics were de-escalated to doxycycline monotherapy. After 10 days of antibiotic treatment, laboratory tests showed complete recovery from HGA complicated with rhabdomyolysis and AKI. CONCLUSIONS: HGA can lead to serious complications in patients with associated risk factors. Therefore, in patients with HGA accompanied by rhabdomyolysis, management with antibiotics and hydration should be initiated immediately, and not delayed until diagnostic confirmation.

A case of bacterial keratitis caused by multi-drug-resistant Shewanella algae without marine exposure.

Shewanella are Gram-negative rods and marine pathogens. Here, we report a case of bacterial keratitis caused by Shewanella algae without marine exposure. A 66-year-old man with suspected pneumonia was sent to the emergency department from a nursing hospital. He had been in there for 2 years in a vegetative state and could not close his eyes voluntarily. Neither the patient nor his family had experienced any marine exposure. Keratitis was suspected in his right eye. Gram-negative rods grew from swab culture and identified as S. algae by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA sequencing. The patient was treated with topical tobramycin, moxifloxacin and ofloxacin as well as steroids for 14 days, and the keratitis improved. S. algae is a rare human pathogen, and most human infections involve marine exposure. This is the second report of bacterial keratitis caused by S. algae worldwide and the first in Asia.

Preanalytical Errors in the Central Laboratory of a University Hospital Based on the Analysis of Year-Round Data.

BACKGROUND: Preanalytical errors cause a decrease in the accuracy of clinical laboratory results. We analyzed preanalytical errors (preAEs) made in the clinical laboratory of a university hospital. METHODS: All samples received in a centralized laboratory from January 1, to December 31, 2018, were analyzed retrospectively. The categories of preAEs were improper request, incorrect labeling, improper collection/transport, inadequate sample volume, inappropriate container, hemolysis, and sample clotting. The rates of preAEs in these categories were calculated according to sample type, laboratory subunit, department, sampling place, sampling time, and patient age. RESULTS: Of 1,082,014 samples received and analyzed by the laboratory, 6,848 (0.63%) were classified as having preAEs. The most frequent categories of preAE were hemolysis (44.6%), sample clotting (30.8%), and inadequate volume (16.7%). The most frequent preAE category for whole-blood and serum/plasma was clotting and hemolysis, respectively. The most frequent preAE category in the blood bank, clinical chemistry, immunology, and test referral service laboratory subunits was hemolysis, in the hematology subunit it was sample clotting, and in the microbiology and urinalysis subunits it was inadequate sample volume. Surgical departments had a higher rate of preAEs than did non-surgical departments (p < 0.0001). Samples drawn in the sampling room showed the lowest frequencies of preAEs (0.01%). Samples drawn on general wards from 5 pm to 5 am, when duty nurses perform sampling, showed a preAE rate of 2.80%. The rate of preAEs increased with patient age. CONCLUSIONS: This analysis of preAEs is the most comprehensive to date. Our findings will promote the provision of high-quality laboratory services to clinicians and their patients.

First Case of Intracranial Mycotic Aneurysm Caused by Prevotella intermedia Associated with Chronic Sinusitis in a Korean Adult.

Intracranial infection caused by anaerobic bacteria is rare, and it is difficult to identify absolute anaerobes in the clinical laboratory, especially when the bacterial load is low. Here, we report the first case of intracranial mycotic aneurysm caused by Prevotella intermedia associated with chronic sinusitis and successful identification of the bacteria by 16S rRNA sequencing from bacterial growth in broth only.

Real-time display of laboratory testing status improves satisfaction levels in an emergency department: A pilot study.

BACKGROUND: Clinicians need to know timelines of requested laboratory tests to provide effective patient management. We developed a real-time laboratory progress checking system and measured its effectiveness using appropriate indicators in an emergency room setting. METHODS: In our original in-house health information system display, blank spaces, which were generated for test results when tests were ordered, remained empty until the final results reported. We upgraded the laboratory reporting system to show real-time testing information. The stages included requests for test, label printing, sampling, laboratory receipts, performance of tests, verification of results, and interpretation of results and final report by laboratory physician. To assess the usefulness of the function, we measured the emergency department healthcare workers' satisfaction and compared the number of phone calls about test status before and after implementation. RESULTS: After the system upgrade, the healthcare workers' understanding of the testing process increased significantly as follows. More clinicians could estimate the time of final test results through the real-time testing status information (61.9% and 85.7%, P = .002), and respondents reported that the upgraded system was more convenient than the original system (41.3% and 22.2%, respectively, P = .022). The number of phone calls about the test status decreased after implementation of the upgrade; however, the difference was not statistically significant (before, 0.13% [63 calls/48 637 tests] and after, 0.09% [42/46 666]; P = .066). CONCLUSIONS: The real-time display of laboratory testing status increased understanding of testing process among healthcare workers in emergency room, which ultimately may increase the usefulness and efficiency of the laboratory service use.

Comparison of the Seroprevalence of Measles Antibodies among Healthcare Workers in Two Korean Hospitals in 2019.

We performed a point seroprevalence survey of measles among healthcare workers (HCWs) at two Korean teaching hospitals in 2019. A total of 2,830 HCWs underwent an antibody test. The overall seropositivity of measles was 93.1%. The seroprevalence of measles was lowest in HCWs aged 20 - 24 years (81.2%), followed by those aged 25 - 29 years (90.1%). The rates of anti-measles IgG positivity were significantly different between the two hospitals (97.0% vs. 89.4%, P <0.001). These results suggest that the seropositivity of measles in HCWs may differ depending on the hospital's vaccination policy.

Evaluation of Cumulative and Conditional Antibiotic Release from Vancomycin-Embedded Fibrin Sealant and Its Antibacterial Activity : An In Vitro Study.

OBJECTIVE: Fibrin sealants have been used for hemostasis, sealant for cerebrospinal fluid leakage, and adhesive barrier in neurosurgery. Further, as its clinical use and role of an effective drug delivery vehicle have been proposed. This study was performed to measure antibacterial activity and continuous local antibiotic release from different concentrations of vancomycin-impregnated fibrin sealant in vitro. METHODS: Antibacterial activity was investigated by disk diffusion test by measuring the diameter of the growth inhibition zone of bacteria (methicillin-resistant Staphylococcus aureus, ATCC29213) from vancomycin-embedded fibrin sealant disc diluted at five different concentrations (C1-C5; 8.33, 4.167, 0.83, 0.083, and 0.0083 mg/disc, respectively). Continuous and conditioned release of vancomycin concentration (for 2 weeks and for 5 days, respectively) were also measured using high-performance liquid chromatography (HPLC) method. To mimic the physiologic wound conditions with in vitro, conditioned vancomycin release in phosphate buffer solution (PBS) was measured and replaced PBS for five consecutive days, half a day or completely daily. RESULTS: In the disk diffusion test, the mean diameters of bacterial inhibition zone were 2.54±0.07 cm, 2.61±0.12 cm, and 2.13±0.15 cm (C1, C2, and C3 respectively) but 1.67±0.06 cm and 1.23±0.15 cm in C4 and C5, respectively. Continuous elution test elicited the peak release of vancomycin from the fibrin sealant at 48 hours, with continued release until 2 weeks. However, conditioned vancomycin release decreased to half or more on day 2, however, the sustainable release was measured over the therapeutic dose (10-20 µg/mL) for 5 days and 4 days in assays of half and total exchange of PBS. CONCLUSION: This study suggests that fibrin sealant can provide an efficient vehicle for antibiotic drug release in a wide range of neurosurgical procedures and the safe and effective therapeutic dose will be at the concentration embedded of 4.167 mg/disc or more of vancomycin.

A Prospective Cohort Study of Durations of Staphylococcus aureus Bacteremia According to Different Phenotypes and a New Concept of Persistent Bacteremia.

The purpose of this study was to describe and compare the duration of Staphylococcus aureus bacteremia (SAB) according to methicillin resistance and the primary foci of infection. We also aimed to newly define persistent SAB considering these results. Nonduplicated episodes of SAB in patients aged ≥15 years from 14 hospitals in the Republic of Korea were analyzed between January 2009 and February 2018. The duration of SAB was defined as the number of days from the time of administration of an antibiotic to which the isolate was susceptible after the onset of SAB to the last day of a positive blood culture for S. aureus SAB durations were described and compared based on methicillin resistance and the primary foci of infection. Cases in the top quartile for the duration of bacteremia in the respective clinical context were classified as newly defined persistent SAB, and its association with in-hospital mortality was evaluated. A total of 1,917 cases were analyzed. The duration of SAB was longer in patients with methicillin-resistant SAB (MRSAB; n = 995) than in patients with methicillin-susceptible SAB (MSSAB; n = 922) (median duration, 1 day [interquartile range, 1 to 3 days] for MSSAB and 1 day [interquartile range, 0 to 5 days] for MRSAB; P < 0.001). The duration of bacteremia was longer in patients with endocarditis and bone and joint, endovascular, and surgical site infections and was shorter in patients with skin and soft tissue infections. Newly defined persistent SAB was independently associated with in-hospital mortality (adjusted odds ratio, 1.97; 95% confidence interval, 1.54 to 2.53; P < 0.001). The durations of SAB were dependent on methicillin resistance and the primary foci of infection, and considering these contexts, persistent SAB was significantly associated with in-hospital mortality.

Detection and characterization of an emerging type of Babesia sp. similar to Babesia motasi for the first case of human babesiosis and ticks in Korea.

Babesiosis is a tick-transmitted intraerythrocytic zoonosis. In Korea, the first mortalities were reported in 2005 due to Babesia sp. detection in sheep; herein we report epidemiological and genetic characteristics of a second case of babesiosis. Microscopic analysis of patient blood revealed polymorphic merozoites. To detect Babesia spp., PCR was performed using Babesia specific primers for ß-tubulin, 18S rDNA, COB, and COX3 gene fragments. 18S rDNA analysis for Babesia sp., showed 98% homology with ovine Babesia sp. and with Babesia infections in Korea in 2005. Moreover, phylogenetic analysis of 18S rDNA, COB, and COX3 revealed close associations with B. motasi. For identifying the infectious agent, Haemaphysalis longicornis (296) and Haemaphysalis flava (301) were collected around the previous residence of the babesiosis patient. Babesia genes were identified in three H. longicornis: one sample was identified as B. microti and two samples were 98% homologous to B. motasi. Our study is the first direct confirmation of the infectious agent for human babesiosis. This case most likely resulted from tick bites from ticks near the patient house of the babesiosis patient. H. longicornis has been implicated as a vector of B. microti and other Babesia sp. infections.

Renoprotective effects of febuxostat compared with allopurinol in patients with hyperuricemia: A systematic review and meta-analysis.

BACKGROUND: Hyperuricemia is reported to be related to rapid progression of renal function in patients with chronic kidney disease (CKD). Allopurinol, a uric acid lowering agent, protects renal progression. However, it is not widely used in patients with CKD because of its serious adverse event. Febuxostat can be alternatively used for patients who are intolerable to allopurinol. We aimed to determine renoprotective effect and urate-lowering effect between the two drugs. METHODS: We performed a systematic review and meta-analysis of randomized controlled trials to assess the effects of febuxostat compared to allopurinol in patients with hyperuricemia. MEDLINE, Embase, and Cochrane Library databases were searched to identify research publications. RESULTS: Four relevant publications were selected from among 3,815 studies. No significant differences were found in the changes in serum creatinine from baseline between the febuxostat and allopurinol groups. Changes in estimated glomerular filtration rate (eGFR) were observed between the two groups at 1 month (mean difference 1.65 mL/min/1.73 m2, 95% confidence interval [CI] 0.38, 2.91 mL/min/1.73 m2; heterogeneity χ2 = 1.25, I2 = 0%, P = 0.01); however, the changes in eGFR were not significantly different at 3 months. A significant difference did exist in the changes in albuminuria levels from baseline between the febuxostat and allopurinol groups (mean difference -80.47 mg/gCr, 95% CI -149.29, -11.64 mg/gCr; heterogeneity χ2 = 0.81, I2 = 0%, P = 0.02). A significant difference was also observed in the changes in serum uric acid from baseline between the febuxostat and allopurinol groups (mean difference -0.92 mg/dL, 95% CI -1.29, -0.56 mg/dL; heterogeneity χ2 = 6.24, I2 = 52%, P < 0.001). CONCLUSION: Febuxostat might be more renoprotective than allopurinol.

Is plasma neutrophil gelatinase-associated lipocalin a predictive biomarker for acute kidney injury in sepsis patients? A systematic review and meta-analysis.

PURPOSE: Neutrophil gelatinase-associated lipocalin (NGAL) is a useful biomarker for early diagnosis of acute kidney injury (AKI). However, the diagnostic value of NGAL for predicting AKI in sepsis patients is unclear. METHODS: MEDLINE, EMBASE, and Cochrane Library databases were searched to identify research publications. RESULTS: Twelve studies from 9 countries including a total of 1582 patients, of whom 315 (19.9%) developed AKI, were included in the study; plasma NGAL levels were significantly higher in adult sepsis patients with AKI than in those without AKI (mean difference, 274.65; 95% confidence interval [CI], 106.16-443.15; I(2) = 94%). Urine NGAL levels were not significantly different. The diagnostic odds ratio of plasma NGAL for predicting AKI in sepsis patients was 6.64 (95% CI, 3.80-11.58). The diagnostic accuracy of plasma NGAL was 0.881 (95% CI, 0.819-0.923) for sensitivity, 0.474 (95% CI, 0.367-0.582) for specificity, 0.216 (95% CI, 0.177-0.261) for positive predictive value and 0.965 (95% CI, 0.945-0.977) for negative predictive value. CONCLUSION: Plasma NGAL has a high sensitivity and a high negative predictive value for detection of AKI in adult sepsis patients. However, its low specificity and low positive predictive value could limit its clinical utility. The usefulness of urine NGAL was not revealed in this study.

Actinomyces meyeri Empyema: A Case Report and Review of the Literature.

Actinomyces meyeri is an uncommon cause of human actinomycosis. Here, we report a rare case of empyema caused by A. meyeri. A 49-year-old male presented with a history of 10 days of dyspnea and chest pain. A large amount of loculated pleural effusion was present on the right side and multiple lung nodules were documented on radiological studies. A chest tube was inserted and purulent pleural fluid was drained. A. meyeri was isolated in anaerobic cultures of the pleural fluid. The infection was alleviated in response to treatment with intravenous penicillin G (20 million IU daily) and oral amoxicillin (500 mg every 8 hours) for 4 months, demonstrating that short-term antibiotic treatment was effective.

Comparison of commercial genetic-testing services in Korea with 23andMe service.

INTRODUCTION: Genetic testing services for disease prediction, drug responses, and traits are commercially available by several companies in Korea. However, there has been no evaluation study for the accuracy and usefulness of these services. We aimed to compare two genetic testing services popular in Korea with 23andMe service in the United States. MATERIALS AND METHODS: We compared the results of two persons (one man and one woman) serviced by Hellogene Platinum (Theragen Bio Institute), DNAGPS Optimus (DNAlink), and 23andMe service. RESULTS: Among 3 services, there were differences in the estimation of relative risks for the same disease. For lung cancer, the range of relative risk was from 0.9 to 2.09. These differences were thought to be due to the differences of applied single nucleotide polymorphisms (SNPs) in each service for the calculation of risk. Also, the algorithm and population database would have influence on the estimation of relative disease risks. The concordance rate of SNP calls between DNAGPS Optimus and 23andMe services was 100% (30/30). conclusions: Our study showed differences in disease risk estimations among three services, although they gave good concordance rate for SNP calls. We realized that the genetic services need further evaluation and standardization, especially in disease risk estimation algorithm.

Clinical characteristics of vivax malaria and analysis of recurred patients.

BACKGROUND: Plasmodium vivax malaria is an acute debilitating illness characterized by recurrent paroxysmal fever and relapses from hypnozoites in the liver. Although a few studies reported clinical characteristics of vivax malaria in civilians after reemergence in the Republic of Korea, only a small group of patients was analyzed. MATERIALS AND METHODS: We retrospectively reviewed the medical records of patients who had been diagnosed with vivax malaria by peripheral blood smear in a university-affiliated hospital located in a malaria-endemic area between January 2005 and December 2009. RESULTS: During the study period, a total of 352 malarial cases from 341 patients were diagnosed. Vivax malaria was most commonly developed in July and August, 24.7% (87/352), and 21.9% (77/352), respectively. The mean (SD) age was 42.5 (14.7) years and the number of male patients was 243 (71.3%). Six patients had a previous history of vivax malaria from 6 months to 10 years before. A total of 337 patients (98.8%) had fever and the mean (SD) body temperature was 38.3 (1.4)℃. Common associated symptoms were chills (213/341, 62.5%), headache (115/341, 33.7%), and myalgia (85/341, 24.9%). Laboratory findings included thrombocytopenia (340/341, 99.7%), anemia (97/341, 28.5%), leukopenia (148/341, 43.4%), increase of aspartate transaminase (177/341, 51.9%), and increase of alanine transaminase (187/341, 54.8%). Hypotension (14/341, 4.1%), altered mentality (3/341, 0.9%), azotemia (3/341, 0.9%), spleen infarction (2/341, 0.6%), and spleen rupture (1/341, 0.3%) developed as complications. Chloroquine was administered to all patients and primaquine was administered with mean (SD) 3.39 (0.82) mg/kg to 320 patients. There were 11 recurrent infections during the study period. The median (range) time to recurrent infection was 100 (32-285) days. Platelet counts were higher (86,550 vs. 56,910/mm(3)) and time to treatment of malaria was shorter (5 vs. 7 days) in relapsed cases compared with first occurrence cases (P=0.046). CONCLUSIONS: The overall recurrence rate of vivax malaria was 3.2% (11/341) in this study. In recurred cases, malaria was diagnosed earlier and thrombocytopenia was less severe. To evaluate the risk factors associated with recurrence and adequate dose of primaquine in Korean patients, further large-scale prospective studies will be needed.

First report of human acute acalculous cholecystitis caused by the fish pathogen Lactococcus garvieae.

We report herein the first case of acute acalculous cholecystitis caused by Lactococcus garvieae, which is known as a fish pathogen. A 69-year-old fisherman underwent laparoscopic cholecystectomy due to severe inflammation in the gallbladder. The isolate obtained from the gallbladder was identified as L. garvieae by 16S rRNA and manganese-dependent superoxide dismutase (sodA) gene sequence analysis.

New allele-specific real-time PCR system for warfarin dose genotyping equipped with an automatic interpretative function that allows rapid, accurate, and user-friendly reporting in clinical laboratories.

INTRODUCTION: The optimal dose of the oral anticoagulant warfarin varies with polymorphisms of the vitamin K epoxide reductase complex subunit 1 (VKORC1) and cytochrome P450 2C9 (CYP2C9) genes. A fast and reliable method of warfarin dose adjustment is required to prevent serious hemorrhagic or thrombotic complications. The aim of this study is to develop and validate a new warfarin dose genotyping system with an automatic interpretation function. MATERIALS AND METHODS: Four VKORC1 and two CYP2C9 SNPs were genotyped by real-time PCR using allele-specific primers and probes. Multiple reactions that included internal positive controls were performed in each well, and an automatic interpretative algorithm was developed. This system was validated using 82 clinical specimens previously genotyped by PCR-direct sequencing. The analytical time of the method was calculated. RESULTS: No interference was observed when multiple samples were included in each reaction, with all internal positive control reactions being successful. In the genotyping algorithm, Ct differences <2 and ≥2 identified heterozygotes and homozygotes, respectively. All results obtained were concordant with those of the reference method. The overall analytical time for assay of 12 specimens was around 3 hours. CONCLUSION: This rapid, accurate, and user-friendly genotyping system improves the efficacy and safety of anticoagulation therapy in clinical practice.