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.

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.

Performance of Xpert MTB/RIF for the Diagnosis of Extrapulmonary Tuberculosis.

BACKGROUND: Mycobacterial burden is low in extrapulmonary specimens, making diagnosis and treatment difficult. Xpert MTB/RIF is a real-time PCR assay for the detection of Mycobacterium tuberculosis and rifampin resistance. This study evaluated the performance of the Xpert MTB/RIF assay in extrapulmonary specimens. METHODS: Acid-Fast Bacilli (AFB) smear, culture, and Xpert MTB/RIF were performed on extrapulmonary specimens. Mycobacterial culture was performed on BACTEC MGIT liquid for 6 weeks and 2% Ogawa medium for 8 weeks. Overall sensitivity and specificity of Xpert MTB/RIF was estimated using culture as a gold standard. Xpert MTB/RIF sensitivity and cycle-threshold (Ct) values according to AFB smear grade were evaluated. The sensitivity, specificity, and concordance of rifampin resistance compared to the phenotypic drug sensitivity test were evaluated. RESULTS: A total of 1,289 specimens were included in the study. The overall sensitivity and specificity of the Xpert MTB/RIF assay were 59.4% (41/69, 95% CI 46.9 - 70.9%) and 99.3% (1,212/1,220, 95% CI 98.7 - 99.7), respectively. Positive predictive value of Xpert MTB/RIF was 83.7% (41/49, 95% CI 69.8 - 92.2) and negative predictive value was 97.7% (1,212/1,240, 95% CI 96.7 - 98.5%). Xpert MTB/RIF assay sensitivity significantly increased with increases in AFB smear grade (p < 0.001). AFB smear grades and Xpert MTB/RIF Ct values were negatively correlated. Rifampin resistance results of Xpert MTB/RIF and culture showed a concordance rate of 97.2%. CONCLUSIONS: The Xpert MTB/RIF assay could be used to replace the AFB smear for the diagnosis of extrapulmonary tuberculosis, and has high specificity for the detection of rifampin resistance.

Development and Application of Computerized Risk Registry and Management Tool Based on FMEA and FRACAS for Total Testing Process.

Background and Objectives: Risk management is considered an integral part of laboratory medicine to assure laboratory quality and patient safety. However, the concept of risk management is philosophical, so actually performing risk management in a clinical laboratory can be challenging. Therefore, we would like to develop a sustainable, practical system for continuous total laboratory risk management. Materials and Methods: This study was composed of two phases: the development phase in 2019 and the application phase in 2020. A concept flow diagram for the computerized risk registry and management tool (RRMT) was designed using the failure mode and effects analysis (FMEA) and the failure reporting, analysis, and corrective action system (FRACAS) methods. The failure stage was divided into six according to the testing sequence. We applied laboratory errors to this system over one year in 2020. The risk priority number (RPN) score was calculated by multiplying the severity of the failure mode, frequency (or probability) of occurrence, and detection difficulty. Results: 103 cases were reported to RRMT during one year. Among them, 32 cases (31.1%) were summarized using the FMEA method, and the remaining 71 cases (68.9%) were evaluated using the FRACAS method. There was no failure in the patient registration phase. Chemistry units accounted for the highest proportion of failure with 18 cases (17.5%), while urine test units accounted for the lowest portion of failure with two cases (1.9%). Conclusion: We developed and applied a practical computerized risk-management tool based on FMEA and FRACAS methods for the entire testing process. RRMT was useful to detect, evaluate, and report failures. This system might be a great example of a risk management system optimized for clinical laboratories.

An Algorithmic Approach Is Superior to the 99th Percentile Upper Reference Limits of High Sensitivity Troponin as a Threshold for Safe Discharge from the Emergency Department.

Background and Objectives: High-sensitivity cardiac troponin I (hs-TnI) is an important indicator of acute myocardial infarction (AMI) among patients presenting with chest discomfort at the emergency department (ED). We aimed to determine a reliable hs-TnI cut-off by comparing various values for a baseline single measurement and an algorithmic approach. Materials and Methods: We retrospectively reviewed the hs-TnI values of patients who presented to our ED with chest discomfort between June 2019 and June 2020. We evaluated the diagnostic accuracy of AMI with the Beckman Coulter Access hs-TnI assay by comparing the 99th percentile upper reference limits (URLs) based on the manufacturer's claims, the newly designated URLs in the Korean population, and an algorithmic approach. Results: A total of 1296 patients who underwent hs-TnI testing in the ED were reviewed and 155 (12.0%) were diagnosed with AMI. With a single measurement, a baseline hs-TnI cut-off of 18.4 ng/L showed the best performance for the whole population with a sensitivity of 78.7%, specificity of 95.7%, negative predictive value (NPV) of 97.1%, and positive predictive value (PPV) of 71.3%. An algorithm using baseline and 2-3 h hs-TnI values showed an 100% sensitivity, 97.7% specificity, an NPV of 100%, and a PPV of 90.1%. This algorithm used a cut-off of <4 ng/L for a single measurement 3 h after symptom onset or an initial level of <5 ng/L and a change of <5 ng/L to rule a patient out, and a cut-off of ≥50 ng/L for a single measurement or a change of ≥20 ng/L to rule a patient in. Conclusions: The algorithmic approach using serial measurements could help differentiate AMI patients from patients who could be safely discharged from the ED, ensuring that patients were triaged accurately and did not undergo unnecessary testing. The cut-off values from previous studies in different countries were effective in the Korean population.

Sample size and rejection limits for detecting reagent lot variability: analysis of the applicability of the Clinical and Laboratory Standards Institute (CLSI) EP26-A protocol to real-world clinical chemistry data.

Objectives: To maintain the consistency of laboratory test results, between-reagent lot variation should be verified before using new reagent lots in clinical laboratory. Although the Clinical and Laboratory Standards Institute (CLSI) document EP26-A deals with this issue, evaluation of reagent lot-to-lot difference is challenging in reality. We aim to investigate a practical way for determining between-reagent lot variation using real-world data in clinical chemistry. Methods: The CLSI EP26-A protocol was applied to 83 chemistry tests in three clinical labs. Three criteria were used to define the critical difference (CD) of each test as follows: reference change value and total allowable error, which are based on biological variation, and acceptable limits by external quality assurance agencies. The sample size and rejection limits that could detect CD between-reagent lots were determined. Results: For more than half of chemistry tests, reagent lot-to-lot differences could be evaluated using only one patient sample per decision level. In many cases, the rejection limit that could detect reagent lot-to-lot difference with ≥90% probability was 0.6 times CD. However, the sample size and rejection limits vary depending on how the CD is defined. In some cases, impractical sample size or rejection limits were obtained. In some cases, information on sample size and rejection limit that met intended statistical power was not found in EP26-A. Conclusions: The CLSI EP26-A did not provide all necessary answers. Alternative practical approaches are suggested when CLSI EP26-A does not provide guidance.

Performance of Norudia Glycated Albumin Assay on Multiple Analytical Platforms and Comparison to Lucica Assay.

BACKGROUND: The Norudia glycated albumin (GA) assay was evaluated for analytical performance and assay applicability on multiple analytical platforms. METHODS: The evaluation included precision, linearity, reference interval, and comparison with Lucica GA assay. A multicenter study was conducted to compare the results of Norudia GA assay on five kinds of widely used automated clinical chemistry analyzers. RESULTS: Within-laboratory imprecisions for GA% presented 1.3 - 3.3% and 0.8 - 2.6% for low- and high-level control materials, respectively, on different analyzers. GA assay was linear from 20.0 to 680.0 µmol/L of GA. The claimed reference range (12 - 16 GA%) was verified. Norudia GA showed a good GA% correlation with Lucica GA (correlation coefficient 0.999). GA% from each analyzer showed good correlation with the consensus mean of the results of five analyzers (correlation coefficient 0.997 - 0.999). CONCLUSIONS: The Norudia GA assay can successfully be implemented in all the tested platforms, with good GA% correlation.

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.

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.

Importance of Susceptibility Rate of 'the First' Isolate: Evidence of Real-World Data.

Background and objectives: For proper antimicrobial therapy, cumulative antibiograms should be representative of geographic region and be accurate. Clinical and Laboratory Standards Institute (CLSI) guidelines recommend that only the first isolates (FI) of a species per patient are used when reporting cumulative antibiograms. However, >50% of hospitals in the United States report antibiograms of all isolates. We compared antibiograms from the FI with those from total isolates (TI). Materials and Methods: Antimicrobial data of all isolates identified in the Microbiology unit of Ilsan Paik Hospital in 2019 were retrospectively acquired from the hospital information system. The susceptibility rates to antimicrobials of Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, Enterococcus faecium, and Enterococcus faecalis were analyzed by FI and TI, respectively. Isolate counts and susceptibility rates of each species for the reported antimicrobials were compared. Results: The numbers of isolates by FI/TI were as follows: 1824/2692 E. coli, 480/1611 A. baumannii, and 662/1306 K. pneumoniae, and 407/953 P. aeruginosa for gram-negative bacteria and 649/1364 S. aureus, 211/313 E. faecium, and 323/394 E. faecalis for gram-positive bacteria. All antimicrobial agents showed higher susceptibility rates when calculated as FI than as TI in gram-negative bacteria except colistin: 3.7% for E. coli, 14.5% for A. baumannii, 8.3% for K. pneumoniae, and 7.9% for P. aeruginosa. In S. aureus, 8/11 antimicrobial agents revealed higher susceptibility rates for FI than for TI. E. faecalis and E. faecium showed lower susceptibility rates for 7/10 antimicrobial agents for FI than for TI. The oxacillin susceptibility rates of S. aureus were 36.6%/30.2% with FI/TI and vancomycin susceptibility rates for E. faecium were 54.1% and 49.5%, respectively. Conclusions: When comparing cumulative antibiograms by FI with TI using real-world data, there is a large gap for critical species requiring hospital infection control. Although FI calculation is difficult, antibiograms must be calculated as FI for proper preemptive antimicrobial therapy because FI provides proper antimicrobial susceptibility data.

Improvement of blood culture contamination rate, blood volume, and true positive rate after introducing a dedicated phlebotomy team.

The introduction of dedicated phlebotomy teams certified for blood collection has been reported to be highly cost-effective by reducing contamination rates. However, data on their effects on blood volume and true positive rate are limited. Therefore, we investigated the effect of replacing interns with a phlebotomy team on blood culture results. We performed a 24-month retrospective, quasi-experimental study before and after the introduction of a phlebotomy team dedicated to collecting blood cultures in a 2700-bed tertiary-care hospital. The microbiology laboratory database was used to identify adult patients with positive blood culture results. During the study period, there were no changes in blood collection method, blood culture tubes, and the application of antiseptic measures. Blood volume was measured by the BACTEC™ FX system based on red blood cell metabolism. A total of 162,207 blood cultures from 23,563 patients were analyzed, comprising 78,673 blood cultures during the intern period and 83,534 during the phlebotomy team period. Blood volume increased from a mean of 2.1 ml in the intern period to a mean of 5.6 ml in the phlebotomy team period (p < 0.001). Introduction of the phlebotomy team also reduced contamination rate (0.27% vs. 0.45%, p < 0.001) and led to a higher true positive rate (5.87% vs. 5.01%, p < 0.05). The increased true positive rate associated with the phlebotomy team involved both gram-positive and gram-negative bacteria. The introduction of a dedicated phlebotomy team can increase blood volumes, reduce blood culture contamination rate, and increase true positive rate.

Emergence of NDM-4-producing Klebsiella pneumoniae in a Korean hospital due to a patient hospitalized in Vietnam and case review.

NDM-4-producing Klebsiella pneumoniae (NDM-4-KP) was detected from the patient who had previously been injured and hospitalized for 5 days in Vietnam in a neurosurgical intensive care unit (NSICU) of a Korean tertiary-care hospital in December 2016. He admitted with ventilator-associated pneumonia and NDM-4-KP was isolated, which was subsequently detected in two other NSICU patients. All NDM-4-KP isolates from patient and environmental surveillance cultures were sequence type 11. Colonization of three patients persisted for 5-12 months. Dedicated environmental cleaning was added to single room isolation of NDM-4-KP patients and universal chlorhexidine bathing, and no further transmission of NDM-4-KP occurred. This is the first report of NDM-4-KP in a Korean hospital where a patient with a history of hospitalization abroad was the index case initiating an outbreak involving three patients. The spread of newly introduced CPE was controlled using a bundle of infection control.

Status of Pre-analytical Quality Management of Laboratory Tests at Primary Clinics in Korea.

Background: The quality of laboratory test results is crucial for accurate clinical diagnosis and treatment. Pre-analytical errors account for approximately 60%-70% of all laboratory test errors. Laboratory test results may be largely impacted by pre-analytical phase management. However, primary care clinics currently do not have pre-analytical quality management audit systems. We aimed to understand the current status of pre-analytical quality management in laboratory medicine in Korean primary care clinics. Methods: Questionnaires were designed to focus on essential components of the pre-analytical process of primary care clinics. An online survey platform was used to administer the survey to internal medicine or family medicine physicians in primary care clinics. Results: A total of 141 physicians provided a complete response to the questionnaire. In 65.2% of the clinics, patient information was hand-labeled rather than barcoded on the specimen bottles; 14.2% of clinics displayed only one piece of patient information (name or identification number), and 19.9% of clinics displayed two pieces of information. Centrifuges were not available in 29.1% of the clinics. Institutions carrying out the National Health Screening Program (NHSP) used more barcode system and had more centrifuges than institutions that did not carrying out the NHSP. Conclusions: Pre-analytical quality management is inadequate in many primary clinics. We suggest implementation of a mandatory management system, allowing for a pre-analytical quality management to be carried out in primary care clinics.

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.

Interpreting changes in consecutive laboratory results: clinician's perspectives on clinically significant change.

BACKGROUND: Clinical laboratory tests are inevitably affected by various factors. Therefore, when comparing consecutive test results, it is crucial to consider the inherent uncertainty of the test. Clinical laboratories use reference change value (RCV) to determine a significant change between 2 results. Whereas the criteria for the interpretation of consecutive results by clinicians are not well known. We investigated the clinician's interpretation of a clinically significant change in consecutive laboratory test results and compared them to RCV. METHODS: We performed a questionnaire survey on clinicians, which comprised 2 scenarios with 22 laboratory test items suggesting initial test results. Clinicians were asked to choose a result showing clinically significant change. RCV of the analytes from EFLM database were collected. RESULTS: We received 290 valid questionnaire responses. Clinicians' opinions on clinically significant change was inconsistent between clinicians and scenarios, and was generally larger than RCV. Clinicians commented that they were not familiar with the variability of the laboratory tests. CONCLUSIONS: Clinicians' opinions on clinically significant changes were more prominent than RCV. Meanwhile, they tended to neglect the analytical and biological variation. Laboratories should properly guide clinicians on the RCV of tests for better decision-making on patients' clinical states.

Quantitative Computed Tomography Parameters in Coronavirus Disease 2019 Patients and Prediction of Respiratory Outcomes Using a Decision Tree.

Background: Chest computed tomography (CT) scans play an important role in the diagnosis of coronavirus disease 2019 (COVID-19). This study aimed to describe the quantitative CT parameters in COVID-19 patients according to disease severity and build decision trees for predicting respiratory outcomes using the quantitative CT parameters. Methods: Patients hospitalized for COVID-19 were classified based on the level of disease severity: (1) no pneumonia or hypoxia, (2) pneumonia without hypoxia, (3) hypoxia without respiratory failure, and (4) respiratory failure. High attenuation area (HAA) was defined as the quantified percentage of imaged lung volume with attenuation values between -600 and -250 Hounsfield units (HU). Decision tree models were built with clinical variables and initial laboratory values (model 1) and including quantitative CT parameters in addition to them (model 2). Results: A total of 387 patients were analyzed. The mean age was 57.8 years, and 50.3% were women. HAA increased as the severity of respiratory outcome increased. HAA showed a moderate correlation with lactate dehydrogenases (LDH) and C-reactive protein (CRP). In the decision tree of model 1, the CRP, fibrinogen, LDH, and gene Ct value were chosen as classifiers whereas LDH, HAA, fibrinogen, vaccination status, and neutrophil (%) were chosen in model 2. For predicting respiratory failure, the decision tree built with quantitative CT parameters showed a greater accuracy than the model without CT parameters. Conclusions: The decision tree could provide higher accuracy for predicting respiratory failure when quantitative CT parameters were considered in addition to clinical characteristics, PCR Ct value, and blood biomarkers.

First report of Yokenella regensburgei isolated from external auditory canal after diving in valley.

Yokenella regensburgei is a Gram-negative, oxidase-negative motile rod which is rarely isolated from human caused a few opportunistic infections in immunocompromised patients so far. We report the first case of otitis media combined with externa caused by Y. regensburgei in an immunocompetent patient. A 56-year-old male patient visited the outpatient clinic of the Otolaryngology Department due to otorrhea of the right ear started after diving in mountain valley in Korea 3 days ago. He was immunocompetent adult and clinical examination revealed swelling and debris accumulation in the right external auditory canal with an intact, erythematous tympanic membrane, and clear, odorless otorrhea. Microbiological culture of otorrhea revealed Y. regensburgei by matrix-assisted laser desorption/ionization time-of-flight and PCR-based 16S rRNA gene sequencing. His otorrhea persisted, and a pinpoint perforation occurred in the inferior anterior portion of the tympanic membrane. 50% acetic acid irrigation and 500 mg of oral ciprofloxacin were prescribed, and his infection was cured after 4 weeks. This is the first case of otitis media combined with externa caused by Yokenella regensburgei in an immunocompetent patient. Given that Yokenella species infections are rare, especially in immunocompetent patients, this case highlights the importance of history taking and communication between clinicians and laboratory physicians. Molecular identification methods assist in identifying rare pathogens.

Performance Assessment of Xpert MTB/RIF Assay for Detecting Pulmonary Tuberculosis and Rifampin Resistance in a Tertiary Care Hospital in Korea.

In this study, we aimed to assess the performance of the Xpert MTB/RIF assay for the detection of pulmonary tuberculosis compared to the acid-fast bacilli (AFB) smear and culture analysis, and the incidence of rifampin resistance using the drug susceptibility test. The specimens referred for AFB smear and culture analysis and Xpert MTB/RIF assay from April 2015 to March 2018 were retrospectively reviewed. The sensitivity, specificity, and mean cycle threshold (Ct) values obtained in Xpert MTB/RIF assay and for rifampin resistance were analyzed. The results of Xpert MTB/RIF assay for pulmonary tuberculosis were evaluated based on the AFB smear grade. Among 3,840 specimens, 491 were positive in Xpert MTB/RIF assay and 626 in culture analysis. The sensitivity and specificity of Xpert MTB/RIF assay were 75.6% and 99.4%, respectively. The sensitivity of Xpert MTB/RIF assay for smear-positive/culture-positive specimens was 98.6% and that of smear-negative and -trace/culture-positive specimens was 63.1%. The positivity of Xpert MTB/RIF assay for culture-positive specimens was 89.9%, 98.6%, 95.7%, 100.0%, and 100.0% for the smear grades trace, 1+, 2+, 3+, 4+, respectively. The Ct values of 491 specimens significantly decreased as the AFB smear grade increased (P < 0.0001). The Ct values of smear-positive, -trace, and -negative specimens were 21.7 ± 4.2, 26.5 ± 3.9, and 27.4 ± 3.6, respectively. Rifampin resistance evaluated using Xpert MTB/RIF assay and culture analysis exhibited a correlation of 98.3%. The region covered by probe E was the most frequently mutated region (50.0%). Xpert MTB/RIF assay demonstrated reliable performance in detecting pulmonary tuberculosis from smear-positive and culture-positive specimens; however, further improvements are still required to detect smear-negative and culture-positive specimens.

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.