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.

α-Carbonyl Radicals from N-Enoxybenzotriazoles: De Novo Synthesis of 9-Phenanthrols.

Visible-light-induced energy transfer to N-enoxybenzotriazoles in the presence of hydrogen atom donors or alcoholic solvents led to α-carbonyl radicals. The utility of the α-carbonyl radicals was demonstrated in intramolecular tandem cyclization and in the synthesis of 9-phenanthrols and their analogues. The mechanistic experiments suggested that quenching of the reactive benzotriazolyl radical by the alcohol was accompanied by the formation of an α-hydroxy radical that mediated hydrogen atom transfer or, itself, oxidized into aldehydes.

Energy Transfer Photocatalytic Radical Rearrangement in N-Indolyl Carbonates.

A new type of sp3-like N-centered radical has been generated by selective energy transfer catalysis. Upon photoexcitation, homolytic N-O bond cleavage of N-indolyl carbonate in the presence of an Ir complex produced N- and O-centered radicals. The high spin density at the C3 position of indole led to radical recombination with the O-centered radical, affording valuable 3-oxyindole derivatives without decarboxylation. Transformations of the desired products into various molecules were also demonstrated.

Gibberellic acid sensitive dwarf encodes an ARPC2 subunit that mediates gibberellic acid biosynthesis, effects to grain yield in rice.

The plant hormone gibberellic acid (GA) is important for plant growth and productivity. Actin-related proteins (ARPs) also play central roles in plant growth, including cell elongation and development. However, the relationships between ARPs and GA signaling and biosynthesis are not fully understood. Here, we isolated OsGASD, encoding an ARP subunit from rice (Oryza sativa), using the Ac/Ds knockout system. The osgasd knockout (Ko) mutation reduced GA3 content in shoots as well as plant growth and height. However, GA application restored the plant height of the osgasd Ko mutant to a height similar to that of the wild type (WT). Rice plants overexpressing OsGASD (Ox) showed increased plant height and grain yield compared to the WT. Transcriptome analysis of flag leaves of OsGASD Ox and osgasd Ko plants revealed that OsGASD regulates cell development and the expression of elongation-related genes. These observations suggest that OsGASD is involved in maintaining GA homeostasis to regulate plant development, thereby affecting rice growth and productivity.

Recent Progress in Enolonium Chemistry under Metal-Free Conditions.

Umpolung approach through inversion of the polarity of conventional enolates, has opened up an unprecedented opportunity in the cross-coupling via alkylation. The enolonium equivalents can be accessed either by hypervalent iodine reagents, activation/oxidation of amides, or the oxidation of alkynes. Under umpolung conditions, highly basic conditions required for classical enolate chemistry can be avoided, and they can couple with unmodified nucleophiles such as heteroatom donors and electron-rich arenes.

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.

Characterization of dwarf and narrow leaf (dnl-4) mutant in rice.

Height and leaf morphology are important agronomic traits of the major crop plant rice (Oryza sativa). In previous studies, the dwarf and narrow leaf genes (dnl1, dnl2 and dnl3) have identified in rice. Using the Ac/Ds knockout system, we found a new dwarf and narrow leaf (dnl) mutant and identified mutated gene. The dnl-4 mutant showed reduced plant height and leaf blade width compared to the wild type, and increased leaf inclination. The morphological defects of the mutant were caused by the suppressed expression of the DNL-4 gene, which encodes a pfkB carbohydrate kinase protein. These results suggest that DNL-4 expression is involved in modulating plant height and leaf growth. Furthermore, DNL-4 expression also affects productivity in rice: the dnl-4 mutant exhibited reduced panicle length and grain width compared with the wild type. To understand DNL-4 function in rice, we analyzed the expression levels of leaf growth-related genes, such as NAL1, NAL7, and CSLD4, in the dnl-4 mutant. Expression of NAL1 and NAL7 was downregulated in the dnl-4 mutant compared to the wild type. The observation that DNL-4 expression corresponded with that of NAL1 and NAL7 is consistent with the narrow leaf phenotype of the dnl-4 mutant. These results suggest that DNL-4 regulates plant height and leaf structure in rice.

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.

The New Diagnosis-Related Group Reimbursement System and Laboratory Test Quality in Korea: Analysis of External Quality Assessment Results.

Korea introduced a new diagnosis-related group (NDRG), which is a mixed-bundle reimbursement system. We evaluated the effects of NDRGs on laboratory test quality by analyzing data over three years (2016-2018) from the Korean Association of External Quality Assessment Service (KEQAS). A total of 42 NDRG-participating hospitals (CASE), 84 non-participating similar size-hospitals (CON-1), and 42 tertiary hospitals (CON-2) were included. We assumed the proportion of KEQAS results with a larger than 2 standard deviation index (SDI) to be a bad laboratory quality marker (BLQM). CASE BLQMs were lower than CON-1 BLQMs for more than 2 years in alkaline phosphatase (ALP), alanine aminotransferase (ALT), chloride, glucose, sodium, and total protein, and higher in creatinine. CASE BLQMs were higher than CON-2 BLQMs for more than 2 years in ALP, chloride, creatinine, glucose, lactate dehydrogenase (LDH), phosphorus, potassium, sodium, total calcium, total cholesterol, triglyceride, and uric acid. Mean SDIs for general chemistry tests were not significantly different depending on NDRG participation. However, the NDRG is currently a pilot program that compensates the amount of each institution's reimbursement based on the fee-for-service system, and most participants were public hospitals. Thus, the effects of NDRGs on laboratory test quality should be re-evaluated after the NDRG program has stabilized and more private hospitals are participating.

Status of Quality Control for Laboratory Tests of Medical Institutions in Korea: Analysis of 10 Years of Data on External Quality Assessment Participation.

External quality assessment (EQA) is a commonly used tool to track the performance of laboratory tests. In Korea, EQA participation is not mandatory, and even basic data about EQA participation are not available. We used data of a 10-year period extracted from two databases (2009-2018): (1) the database of the National Health Insurance Service to calculate the number of medical institutions that claimed health insurance benefits, and (2) the database of the Korean Association of External Quality Assessment Service to calculate the number of medical institutions participating in EQA. The proportion of institutions that made claims for the performance of laboratory testing throughout the 10 years were 73.6%-76.0% for clinics, 91.9%-97.5% for long-term care hospitals, 97.9%-99.5% for small to medium hospitals, 99.6%-100% for general hospitals, and 100% for tertiary hospitals. The mean EQA participation rate of institutions that performed laboratory testing for the 10 years was 1.9% for clinics, 3.1% for long-term care hospitals, 27.7% for small to medium hospitals, 96.6% for general hospitals, and 100% for tertiary hospitals. The mean EQA participation of clinics, long-term care hospitals, and small to medium hospitals are increasing but is still not sufficient. Regulatory approaches are needed to increase participation rates. This result would be used for health policymaking on the quality improvement of laboratory tests.

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.

Enantioselective Synthesis of Tertiary α,α-Diaryl Carbonyl Compounds Using Chiral N,N'-Dioxides under Umpolung Conditions.

Brønsted acid-catalyzed addition of the chiral N,N'-dioxide into ynamides generated enolonium ions in situ which underwent enantioselective alkylation by indoles, pyrroles, and phenols, without racemization of the formed tertiary center. This external oxidant approach allows for the use of unmodified nucleophiles and does not leave trace groups from the oxidant, which significantly increases the synthetic efficiency and the product diversity. Furthermore, the byproduct of the N,N'-dioxide could be efficiently recycled into an optically pure form.

Fabrication and Comparison of Self-Organized Ag and Au Nanodots on Ti/MgO(001) Substrates.

We analyze and compare the differences in the dewetting phenomena and crystal structure between Ag(5.0 nm) and Au(5.0 nm) layers deposited on a Ti(1.0 nm) seed layer coated onto a MgO(001) substrate. The samples are deposited at room temperature and annealed at 350-450 °C for 5 h. The surfaces of both Ag/Ti and Au/Ti films exhibit a completely separated island structure, subsequently leading to the formation of a nanodot array after annealing. Based on atomic force microscopy (AFM) analysis, we conclude that the dewetting progression speed of Ag/Ti films is higher than that of Au/Ti films. Based on X-ray diffraction (XRD) results, the Ti thin film acts as a seed layer, assisting the epitaxial growth of fcc-Ag(001) nanodots on the MgO(001) substrate, whereas in the case of Au/Ti, the Au layer grows non-epitaxially on the MgO(001) substrate, which is related to the difference in the surface energies of Ag and Au. Furthermore, the optical absorbance spectra of the self-organized Ag and Au nanodots with the Ti seed layer are obtained in the visible light range and the optical properties of Ag and Au nanodots are compared.

Getting patient blood management Pillar 1 right in the Asia-Pacific: a call for action.

Preoperative anaemia is common in the Asia-Pacific. Iron deficiency anaemia (IDA) is a risk factor that can be addressed under patient blood management (PBM) Pillar 1, leading to reduced morbidity and mortality. We examined PBM implementation under four different healthcare systems, identified challenges and proposed several measures: (a) Test for anaemia once patients are scheduled for surgery. (b) Inform patients about risks of preoperative anaemia and benefits of treatment. (c) Treat IDA and replenish iron stores before surgery, using intravenous iron when oral treatment is ineffective, not tolerated or when rapid iron replenishment is needed; transfusion should not be the default management. (d) Harness support from multiple medical disciplines and relevant bodies to promote PBM implementation. (e) Demonstrate better outcomes and cost savings from reduced mortality and morbidity. Although PBM implementation may seem complex and daunting, it is feasible to start small. Implementing PBM Pillar 1, particularly in preoperative patients, is a sensible first step regardless of the healthcare setting.

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.

A continuous droplet electroporation system for high throughput processing.

A continuous droplet electroporation (EP) system capable of handling a billion cells has been proposed and demonstrated using a proof-of-concept prototype design. Numerical simulations were conducted to design the new system and to compare the continuous droplet EP system with the previous single droplet EP system. Through parametric studies on the applied voltage and flow rate, a much higher cyan fluorescent protein transgene expression efficiency (38.8 ± 8.9%) was accomplished over that of the previous single droplet EP system. A parallel continuous droplet EP system is also demonstrated by introducing additional electrode pairs into the continuous droplet EP system to achieve ultrahigh throughput. Finally, the significance and meaning of the present work and future development direction have been discussed.

Metal-Free Iodine-Catalyzed Oxidation of Ynamides and Diaryl Acetylenes into 1,2-Diketo Compounds.

Metal-free oxidation of ynamides is described, employing pyridine- N-oxides as oxidants under molecular iodine catalysis. In stark contrast to Brønsted acid catalysis, iodophilic activation of ynamides diverts the reaction manifold into a dioxygenation pathway. This oxidation is very rapid at room temperature with only 2.5 mol % I2. Furthermore, this protocol could be extended to nonactivated alkynes, such as diarylacetylenes, to deliver various benzil derivatives.