GenoMycAnalyzer: a web-based tool for species and drug resistance prediction for Mycobacterium genomes.

BACKGROUND: Drug-resistant tuberculosis (TB) is a major threat to global public health. Whole-genome sequencing (WGS) is a useful tool for species identification and drug resistance prediction, and many clinical laboratories are transitioning to WGS as a routine diagnostic tool. However, user-friendly and high-confidence automated bioinformatics tools are needed to rapidly identify M. tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM), detect drug resistance, and further guide treatment options. RESULTS: We developed GenoMycAnalyzer, a web-based software that integrates functions for identifying MTBC and NTM species, lineage and spoligotype prediction, variant calling, annotation, drug-resistance determination, and data visualization. The accuracy of GenoMycAnalyzer for genotypic drug susceptibility testing (gDST) was evaluated using 5,473 MTBC isolates that underwent phenotypic DST (pDST). The GenoMycAnalyzer database was built to predict the gDST for 15 antituberculosis drugs using the World Health Organization mutational catalogue. Compared to pDST, the sensitivity of drug susceptibilities by the GenoMycAnalyzer for first-line drugs ranged from 95.9% for rifampicin (95% CI 94.8-96.7%) to 79.6% for pyrazinamide (95% CI 76.9-82.2%), whereas those for second-line drugs ranged from 98.2% for levofloxacin (95% CI 90.1-100.0%) to 74.9% for capreomycin (95% CI 69.3-80.0%). Notably, the integration of large deletions of the four resistance-conferring genes increased gDST sensitivity. The specificity of drug susceptibilities by the GenoMycAnalyzer ranged from 98.7% for amikacin (95% CI 97.8-99.3%) to 79.5% for ethionamide (95% CI 76.4-82.3%). The incorporated Kraken2 software identified 1,284 mycobacterial species with an accuracy of 98.8%. GenoMycAnalyzer also perfectly predicted lineages for 1,935 MTBC and spoligotypes for 54 MTBC. CONCLUSIONS: GenoMycAnalyzer offers both web-based and graphical user interfaces, which can help biologists with limited access to high-performance computing systems or limited bioinformatics skills. By streamlining the interpretation of WGS data, the GenoMycAnalyzer has the potential to significantly impact TB management and contribute to global efforts to combat this infectious disease. GenoMycAnalyzer is available at http://www.mycochase.org .

Carbapenem non-susceptibility overcalling by BD phoenix NMIC-500 panel.

We aimed to assess the accuracy of BD Phoenix for determining carbapenem susceptibility because we observed a decline in carbapenem susceptibility rate from the biannual cumulative data, after we transitioned to the BD Phoenix form Vitek 2 system. Between October 2021 and May 2022, we collected 82 non-duplicated Enterobacterales showing non-susceptible to at least one of the three carbapenems by BD Phoenix. We performed the broth microdilution (BMD) and disk diffusion (DD) according to the CLSI guideline. Compared to BMD, the categorical agreements for ertapenem (ERT), imipenem (IPM) and meropenem (MEPM) was 58.8%, 56.8% and 91.5% for BD Phoenix and it was 85.4%, 89.0%, and 97.6%, respectively, for DD (p value; 0.0001 for ERT and IPM, p value; 0.17 for MEPM). The major errors/minor errors for ERT, IPM, and MEPM were 14.0%/31.7%, 2.94%/40.7%, and 2.56%/6.10%, respectively for BD Phoenix, compared to 0%/14.6%, 0%/9.8%, and 0%/2.5%, for DD. While errors in the BD Phoenix showed tendency towards resistance, those in DD displayed no tendency towards either resistance or susceptibility. With DD, 21 out of the 27 isolates showing susceptible/intermediate/susceptible pattern (ERT/IPM/MEPM) and 13 out of the 16 isolates showing intermediate/susceptible/susceptible pattern (ERT/IPM/MEPM), were correctly categorized by DD. However, for 22 isolates showing resistant/susceptible/susceptible pattern (ERT/IPM/MEPM), only 13 isolates were correctly categorized by DD. In conclusion, to mitigate the risk of overcalling carbapenem non-susceptibility with BD Phoenix, it will be helpful to perform a complementary test using DD and to provide comments on the DD results to clinicians.

Prevalence and Molecular Characterization of Vancomycin Variable Enterococcus faecium Isolated From Clinical Specimens.

Vancomycin variable Enterococcus (VVE) bacteria are phenotypically susceptible to vancomycin, but they harbor the vanA gene. We aimed to ascertain the prevalence of VVE among clinically isolated vancomycin-susceptible Enterococcus faecium (VSE) isolates, as well as elucidate the molecular characteristics of the vanA gene cluster within these isolates. Notably, we investigated the prevalence and structure of the vanA gene cluster of VVE. Between June 2021 and May 2022, we collected consecutive, non-duplicated vancomycin-susceptible Enterococcus faecium (VSE) samples. Real-time PCR was performed to detect the presence of vanA, vanB, and vanC. Overlapping PCR with sequencing and whole-genome sequencing were performed for structural analysis. Sequence types (STs) were determined by multilocus sequence typing. Exposure testing was performed to assess the ability of the isolates to acquire vancomycin resistance. Among 282 VSE isolates tested, 20 isolates (7.1%) were VVE. Among them, 17 isolates had partial deletions in the IS1216 or IS1542 sequences in vanS (N=10), vanR (N=5), or vanH (N=2). All VVE isolates belonged to the CC17 complex and comprised five STs, namely ST17 (40.0%), ST1421 (25.0%), ST80 (25.0%), ST787 (5.0%), and ST981 (5.0%). Most isolates were related to three hospital-associated clones (ST17, ST1421, and ST80). After vancomycin exposure, 18 of the 20 VVEs acquired vancomycin resistance. Considering the high reversion rate, detecting VVE by screening VSE for vanA is critical for appropriate treatment and infection control.

Dextrose-containing fluids causing false-positive serum galactomannan: a case-control study and interrupted time series analysis.

OBJECTIVES: This study aimed to identify the cause of false-positive serum Aspergillus antigen galactomannan (GM) results in our centre. METHODS: We performed a case-control study aiming to elucidate the factors associated with false-positive GM results. Independent risk factors for false-positive GM were evaluated through a multivariable regression analysis. An interrupted time series analysis was used to evaluate the effectiveness of an intervention removing the identified factors. RESULTS: Among 568 patients tested, GM was positive in 130 patients of whom 97 had false-positive GM (cases). These were compared with 427 patients with true-negative GM (controls). Administration of dextrose-containing fluids within 6 days before GM testing was an independent predictor for false-positive GM results (adjusted odds ratio [aOR], 18.60; 95% CI, 8.95-38.66. An analysis of GM presence in different dextrose-containing fluids revealed positivity in 34.8% (8 of 23) (manufacturer A) and 33.3% (5 of 15) (manufacturer B) of the samples. Investigation of the manufacturing process revealed that the saccharification process employed enzymes derived from Aspergillus niger. After identifying the root cause of false positivity, GM-containing dextrose fluid use was restricted. Interrupted time series analysis showed an immediate reduction of GM false-positivity (-6.5% per week, p = 0.045) and a declining trend (-0.33% per week, p = 0.005) postintervention. CONCLUSIONS: Administering dextrose-containing fluids was the primary factor causing false-positive serum Aspergillus antigen GM assay results. Our investigation led to a modification of the manufacturing process of the dextrose-containing fluids.

Clinical Implementation of ß-Tubulin Gene-Based Aspergillus Polymerase Chain Reaction for Enhanced Aspergillus Diagnosis in Patients with Hematologic Diseases: A Prospective Observational Study.

The ß-tubulin (benA) gene is a promising target for the identification of Aspergillus species. Assessment of the clinical implementation and performance of benA gene-based Aspergillus polymerase chain reaction (PCR) remains warranted. In this study, we assessed the analytical performance of the BenA probe PCR in comparison with the Aspergenius kit. We prospectively collected bronchoalveolar lavage (BAL) fluid via diagnostic bronchoscopy from adult patients with hematologic diseases. BenA gene-based multiplex real-time PCR and sequential melting temperature analysis were performed to detect the azole resistance of Aspergillus fumigatus. In total, 76 BAL fluids in 75 patients suspicious of invasive pulmonary aspergillosis (IPA) were collected. Before the application of PCR, the prevalence of proven and probable IPA was 32.9%. However, after implementing the benA gene-based PCR, 15.8% (12 out of 76) of potential IPA cases were reclassified as probable IPA. The analytical performance of the BenA probe PCR in BAL samples was comparable to that of the Aspergenius kit. The diagnostic performance was as follows: sensitivity, 52.0%; specificity, 64.7%; positive predictive value, 41.9%; negative predictive value, 73.3%; positive likelihood ratio, 1.473; and negative likelihood ratio, 0.741. Moreover, benA gene-based Aspergillus PCR discriminated all major sections of Aspergillus, including cryptic species such as Aspergillus tubingensis. Sequential melting temperature analysis successfully detected 2 isolates (15.4%) of A. fumigatus carrying resistant mutations. BenA gene-based Aspergillus PCR with melting temperature analysis enhances diagnostic accuracy and detects not only cryptic species but also resistant mutations of A. fumigatus. It shows promise for clinical applications in the diagnosis of IPA.

Culture-independent diagnostic approaches for invasive aspergillosis in solid organ transplant recipients.

Prompt and accurate diagnosis of invasive aspergillosis (IA) is crucial for immunocompromised patients, including those who have received a solid organ transplant (SOT). Despite their low sensitivity, microscopic detection and conventional culture are considered the 'gold standard' methods. In conjunction with conventional culture, culture-independent assays such as serum galactomannan testing and Aspergillus polymerase chain reaction (PCR) have been incorporated into the diagnostic process for IA. The recently revised consensus definitions from the European Organization for Research and Treatment of Cancer and the Mycosis Study Group have adjusted the threshold for positive galactomannan testing based on the sample type, and have excluded 1,3-ß-D-glucan testing as a mycological criterion. Following extensive standardization efforts, positive Aspergillus PCR tests using serum, plasma, or bronchoalveolar lavage fluid have been added. However, there are limited studies evaluating the clinical utility of these culture-independent assays for the early diagnosis of IA in SOT recipients. Therefore, further research is required to determine whether these assays could aid in the early diagnosis of IA in SOT recipients, particularly in relation to the organ transplanted. In this review, we examine the culture-independent diagnostic methods for IA in SOT recipients, as well as the clinical utility of these assays.

Evaluation of the BioFire® FilmArray® Pneumonia Panel with Conventional Bacterial Culture in Conjunction with Leukocyte Esterase Test.

We evaluated the performance of the BioFire® FilmArray® Pneumonia panel (PN-panel) in detecting bacterial pathogens by comparing it to cultures and to the usefulness of the leukocyte esterase (LE) urine strip test. Between January and June 2022, a total of 67 sputum specimens were obtained from community-acquired pneumonia patients. The PN-panel and LE test were performed simultaneously with conventional cultures. The pathogen detection rates of the PN-panel and culture were 40/67 (59.7%) and 25/67 (37.3%), respectively. The concordance rate between the PN-panel and culture was high (76.9%) when the bacterial burden was high (107 copies/mL), but it was low (8.6%) when it was 104-6 copies/mL, irrespective of the sputum quality. According to the LE positivity, the overall culture positive rate and PN-panel positive rate were significantly higher among the LE-positive specimens (23/45, 31/45) than among the LE-negative specimens (2/21, 8/21). Moreover, the difference in concordance rate between the PN-panel test and culture was significant according to the LE positivity, but not the Gram stain grading. In conclusion, the PN-panel showed high concordance when the bacterial burden was high (107 copies/mL) and ancillary use of LE test will be helpful in interpreting the PN-panel results, especially when the copy number of bacterial pathogens is low.

A fatal case of pneumonia caused by Thermothelomycesthermophila.

Thermothelomyces thermophila (formerly Myceliophthora thermophila) is usually found in soil and specifically compost as an environmental dematiaceous fungus. Here, we report the first case of invasive pulmonary infection caused by T. thermophila in a pediatric patient with acute lymphoblastic leukemia. T. thermophila was serially cultured from bronchoalveolar lavage (BAL) fluid and sputum samples obtained from this patient with respiratory symptoms. The patient received antifungal treatment with liposomal amphotericin B (160 mg daily) and itraconazole (200 mg daily) combination therapy, but she died. By the antifungal susceptibility testing, low minimum inhibitory concentrations (MIC) were observed for itraconazole (MIC 0.06 µg/mL), voriconazole (MIC 0.12 µg/mL), and posaconazole (MIC 0.03 µg/mL) but high MIC was observed with amphotericin B (MIC 4.0 µg/mL). Since T. thermophila is usually found in the environment, it can be considered as a contaminant and may cause difficulties in diagnosis. Therefore, it is necessary to confirm the potential of pathogen through repeated culture and to conduct an antifungal susceptibility testing to find a suitable antifungal agent.

Identification of the rare yeast Cutaneotrichosporon (Trichosporon) debeurmannianum from diabetic foot infection.

BACKGROUND: Diabetic foot infection is the most common complications of diabetes mellitus. Although most of the diabetic foot infections has been known to be caused by aerobic and anaerobic bacteria, mycotic diabetic foot infection caused by Candida species has also been reported recently. Here, we present the first case of diabetic foot infection caused by Cutaneotrichosporon debeurmannianum (previously known as Trichosporon debeurmannianum). METHODS: A 68-year-old diabetic male patient was admitted for management of the necrosis of the big toe. Wound swab culture was performed three times, and each time after 5 days of incubation, beige-colored, wrinkled, and rough colonies were observed on chocolate agar plate. RESULTS: The isolate was identified as C. debeurmannianum with the matrix-assisted laser desorption ionization-time of flight mass spectrometry system (MicroIDSys, ASTA corp.). For confirmation, the sequencing for ITS1/ITS2 and D1/D2 ribosomal DNA was also performed, and the isolate was confirmed as C. debeurmannianum with 100% identity. The isolate exhibited low minimum inhibitory concentrations (MICs) for azoles and high MICs for all echinocandins. CONCLUSION: Considering that usual incubation time for bacterial culture of open wound specimens is only 48 h, it is important to include the request for fungus culture to detect pathogen in diabetic foot lesion.

Development and testing of the career decision-making self-efficacy scale for nursing students: a methodological study.

BACKGROUND: The conventional Career Decision-Making Self-Efficacy Scale does not reflect the situation in Korea due to different sociocultural attributes and fails to account for the unique nursing profession and changes in healthcare. We aimed to develop and psychometrically test the Career Decision-Making Self-Efficacy Scale for Nursing Students. METHODS: A methodological study using a newly developed questionnaire tool and investigation of the validity and reliability of the preliminary instrument. Data were collected from 400 nursing students through an online survey conducted in May 2021. We identified 56 preliminary items through a literature review and focus group interviews. Of them, 40 were completed with a content validity index > .80. Content, construct, and criterion-related validity; internal consistency reliability; and test-retest reliability were used in the analysis. RESULTS: Exploratory factor analysis revealed three factors including 21 items: adapting to work (20.5%), understanding the major (20.2%), and goal setting (16.4%), explaining 57.1% of the total variance. As a result of confirmatory factor analysis, 17 items in the three-factor structure were validated. Reliability, as verified by the test-retest interclass correlation coefficient, was .86 and Cronbach's α was .92. The final Career Decision-Making Self-Efficacy Scale for Nursing Students consists of 17 items: adapting to work (7 items); understanding the major (4 items); and goal setting (6 items). CONCLUSION: The scale developed to measure the career decision-making self-efficacy of nursing students showed sufficient validity and reliability.

Bile duct anastomosis does not promote bacterial contamination of autologous blood salvaged during living donor liver transplantation.

Bile duct surgeries are conventionally considered to promote bacterial contamination of the surgical field. However, liver transplantation recipients' bile produced by the newly implanted liver graft from healthy living donors may be sterile. We tested bacterial contamination of autologous blood salvaged before and after bile duct anastomosis (BDA) during living donor liver transplantation (LDLT). In 29 patients undergoing LDLT, bacterial culture was performed for four blood samples and one bile sample: two from autologous blood salvaged before BDA (one was nonleukoreduced and another was leukoreduced), two from autologous blood salvaged after BDA (one was nonleukoreduced and another was leukoreduced), and one from bile produced in the newly implanted liver graft. The primary outcome was bacterial contamination. The risk of bacterial contamination was not significantly different between nonleukoreduced autologous blood salvaged before BDA and nonleukoreduced autologous blood salvaged after BDA (44.8% and 31.0%; odds ratio 0.33, 95% confidence interval 0.03-1.86; p = 0.228). No bacteria were found after leukoreduction in all 58 autologous blood samples. All bile samples were negative for bacteria. None of the 29 patients, including 13 patients who received salvaged autologous blood positive for bacteria, developed postoperative bacteremia. We found that bile from the newly implanted liver graft is sterile in LDLT and BDA does not increase the risk of bacterial contamination of salvaged blood, supporting the use of blood salvage during LDLT even after BDA. Leukoreduction converted all autologous blood samples positive for bacteria to negative. The clinical benefit of leukoreduction for salvaged autologous blood on post-LDLT bacteremia needs further research.

Rapid species identification of pathogenic bacteria from a minute quantity exploiting three-dimensional quantitative phase imaging and artificial neural network.

The healthcare industry is in dire need of rapid microbial identification techniques for treating microbial infections. Microbial infections are a major healthcare issue worldwide, as these widespread diseases often develop into deadly symptoms. While studies have shown that an early appropriate antibiotic treatment significantly reduces the mortality of an infection, this effective treatment is difficult to practice. The main obstacle to early appropriate antibiotic treatments is the long turnaround time of the routine microbial identification, which includes time-consuming sample growth. Here, we propose a microscopy-based framework that identifies the pathogen from single to few cells. Our framework obtains and exploits the morphology of the limited sample by incorporating three-dimensional quantitative phase imaging and an artificial neural network. We demonstrate the identification of 19 bacterial species that cause bloodstream infections, achieving an accuracy of 82.5% from an individual bacterial cell or cluster. This performance, comparable to that of the gold standard mass spectroscopy under a sufficient amount of sample, underpins the effectiveness of our framework in clinical applications. Furthermore, our accuracy increases with multiple measurements, reaching 99.9% with seven different measurements of cells or clusters. We believe that our framework can serve as a beneficial advisory tool for clinicians during the initial treatment of infections.

Comparison of BD MAX Check-Points CPO assay with Cepheid Xpert Carba-R assay for the detection of carbapenemase-producing Enterobacteriaceae directly from rectal swabs.

We compared the performance of 2 automated systems for detection of carbapenemase-producing Enterobacteriaceae, BD MAX Check-Points CPO (CPO assay) and Xpert Carba-R assay, with culture confirmed by polymerase chain reaction as the reference method. Using 867 samples from 627 patients, the overall sensitivity, specificity, total positive predictive value, and negative predictive value of the CPO assay were 95.7%, 96.5%, 60.8% and 99.8% and for the Xpert assay were 97.9%, 99.8%, 95.8%, and 99.9%, respectively. The cycle threshold values (Ct value) of the false-positive CPO assay results were significantly higher than those of true-positive cases (P < 0.001). By applying a modified cut-off Ct value of 37.3 for klebsiella pneumoniae carbapenemases (KPC), the positive predictive value for KPC was improved from 52.9% to 89.5%. The CPO assay will be useful when handling many specimens, as tests are conducted in batches. However, positive cases showing high Ct values should be confirmed by another assay to rule out false positivity.

Clinical Utility of Next-Generation Flow-Based Minimal Residual Disease Assessment in Patients with Multiple Myeloma.

Background: Minimal residual disease (MRD) is an important prognostic factor for evaluating a deeper treatment response in patients with multiple myeloma (MM). We evaluated the clinical utility of next-generation flow (NGF)-based MRD assessment in a heterogeneous MM patient population. Methods: Patients with suspected morphological remission after or during MM treatment were prospectively enrolled. In total, 108 bone marrow samples from 90 patients were analyzed using NGF-based MRD assessment according to the EuroFlow protocol, and progression-free survival (PFS) was evaluated according to the International Myeloma Working Group response status, cytogenetic risk, and MRD status. Results: The overall MRD-positive rate was 31.5% (34/108 samples), and MRD-positive patients showed a lower PFS than MRD-negative patients (P=0.005). MRD-positive patients showed inferior PFS than MRD-negative in patients with stringent complete remission (sCR)/complete remission (P=0.014) and high-risk cytogenetic abnormalities (P=0.016). MRD was assessed twice in 18 patients with a median interval of 12 months. Sustained MRD negativity was only observed in patients with sustained sCR, and their PFS was superior to that of patients who were not MRD-negative (P=0.035). Conclusions: Clinical application of NGF-based MRD assessment can provide valuable information for predicting disease progression in patients with MM in remission, including those with high-risk cytogenetic abnormalities.

Career education needs of Korean nursing students and professionals: A cross-sectional survey.

BACKGROUND: The career education needs of nursing students and professionals can be met by analyzing the differences between the importance and need levels of their various career education needs, determining priorities, and developing a career education program reflecting these. This approach will enable learner-centered customized career education. OBJECTIVES: To investigate the differences in career education needs between nursing students and professionals, determine their respective priorities, and assess changes in needs between the two survey periods. DESIGN: Descriptive survey study. PARTICIPANTS: The first survey (2017) included 206 nursing students and 40 nursing professionals, while the second survey (2020) included 219 nursing students and 100 nursing professionals. METHODS: Data for the two surveys were collected through face-to-face, postal, and online questionnaire surveys. The research tool to measure career education needs was developed based on an existing tool, top queries on a website for nursing students' career education, literature review, expert opinions, and in-depth interviews with nursing students. RESULTS: The 10 top-ranked items in Jo and Lee's model reflecting the career education needs of nursing students and professionals were as follows: workplace and social etiquette, changes in the healthcare environment and global issues, setting up my career roadmap, interpersonal and communication skills, nursing professionalism and nursing ethics, understanding the latest healthcare policies, my personality type and values, roles and duties of clinical nurses, my aptitude and interest, and nurses' healthcare. Comparing the career education needs of nursing students and professionals between the two survey periods revealed higher scores in the education category of "understanding career" in the second survey. CONCLUSION: Nursing students' career awareness and development will be positively affected by a customized career education program based on the priority items derived from this study; such a program will help them attain nursing professionalism and enhance their occupational identity and job satisfaction.

Comparative Evaluation of Standard E TB-Feron ELISA and QuantiFERON-TB Gold Plus Assays in Patients with Tuberculosis and Healthcare Workers.

Recently, the American Thoracic Society/Infectious Diseases Society of America/Centers for Disease Control and Prevention advised against performing the interferon-γ-release assay (IGRA) test for individuals with a low risk of TB, and also recommended retesting low-risk individuals with an initial positive IGRA result. However, to evaluate both sensitivity and specificity of available tests, we compared the performance of the Standard E TB-Feron (TBF) and QuantiFERON-TB Gold Plus (QFT-Plus) assays in healthcare workers (HCWs) and tuberculosis (TB) patients. We also retrospectively investigated diabetes mellitus (DM) comorbidity among the enrolled TB patients. We prospectively collected samples from 177 HCWs and 48 TB patients. The TBF and QFT-Plus tests were performed and analyzed according to the manufacturers' instructions. We also defined IGRA results between 0.2 and 0.7 IU/mL as 'borderline'. The agreement rate between TBF and QFT-Plus was 92.0% (207/225) with a Cohen's kappa value of 0.77 (95% CI, 0.68-0.87). While the majority (26/31, 83.9%) of borderline TBF results were in HCWs, the majority (14/19, 73.7%) of borderline QFT-Plus results were in TB patients. Discordant results were found in 18 samples, with TBF-positive/QFT-Plus-negative or indeterminate results in 11 HCWs and seven TB patients. After resampling from 10 HCWs (seven borderline-positive and three positive results, all <1.0), six reverted to negative. The prevalence of DM comorbidity was very high (35.4%). In summary, TBF showed substantial agreement with the QFT-Plus assay but had a higher positivity rate in both HCWs and TB patients. The negative conversion rate was high (60%) among HCWs whose initial (TB Ag-nil) result was <1.0.

Quality Improvements in Management of Children with Acute Diarrhea Using a Multiplex-PCR-Based Gastrointestinal Pathogen Panel.

Conventional methods for etiologic diagnoses of acute gastroenteritis (AGE) are time consuming and have low positive yield leading to limited clinical value. This study aimed to investigate quality improvements in patient management, antibiotic stewardship, and in-hospital infection transmission prevention using BioFire® FilmArray® Gastrointestinal Panel (GI Panel) in children with acute diarrhea. This was a prospective study recruiting children < 19 years old with new onset diarrhea during the study period, and a matched historical cohort study of children diagnosed with AGE during the 4 years prior. Patients in the prospective cohort underwent stool testing with GI Panel and conventional methods. A total of 182 patients were included in the prospective cohort, of which 85.7% (n = 156) had community-onset and 14.3% (n = 26) had hospital-onset diarrhea. A higher pathogen positivity rate for community-onset diarrhea was observed by the GI Panel (58.3%, n = 91) compared to conventional studies (42.3%, n = 66) (p = 0.005) and historical cohort (31.4%, n = 49) (p < 0.001). The stool tests reporting time after admission was 25 (interquartile range, IQR 17-46) hours for the GI Panel, and 72 (IQR 48-96) hours for the historical cohort (p < 0.001). A significant reduction in antibiotic use was observed in the prospective cohort compared to historical cohort, 35.3% vs. 71.8%; p < 0.001), respectively. Compared to the GI Panel, norovirus ICT was only able to detect 4/11 (36.4%) patients with hospital-onset and 14/27 (51.8%) patients with community-onset diarrhea. The high positivity rate and rapid reporting time of the GI Panel had clinical benefits for children admitted for acute diarrhea, especially by reducing antibiotic use and enabling early adequate infection precaution and isolation.

Clinical performance of ASTA SepsiPrep kit in direct bacterial identification and antimicrobial susceptibility test using MicroIDSys Elite and VITEK-2 system.

BACKGROUND: Rapid and accurate microbial identification and antimicrobial susceptibility testing (AST) are essential for timely use of appropriate antimicrobial agents for bloodstream infection. To shorten the time for isolating colonies from the positive blood culture, various preparation methods for direct identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) system were developed. Here, we evaluated the SepsiPrep kit (ASTA Corp.) for direct identification of microorganisms and AST from positive blood cultures using MicroIDSys Elite MALDI-TOF MS system (ASTA Corp.) and VITEK-2 system (bioMérieux). METHODS: For direct identification, a total of 124 prospective monomicrobial positive blood culture bottles were included. For direct identification, the pellet was prepared by centrifugation and washing twice. For direct AST, the pellet was suspended in 0.45% saline and adjusted to McFarland 0.5. The results from the direct identification and AST using MicroIDSys Elite and VITEK-2 system were compared to those from the conventional method performed with pure colony subcultured on agar plate. RESULTS: Compared to the conventional method using pure colony, correct direct identification rate was 96.5% and 98.5% for 57 gram-positive isolates and 67 gram-negative isolates, respectively. For direct AST, among the 55 gram-positive isolates, the categorical agreement (CA) for staphylococci, streptococci, and enterococci was 96.7%, 98.4%, and 94.1%, respectively. For 66 gram-negative isolates, the CA for Enterobacterales and non-fermentative gram-negative rods was 99.0% and 96.6%, respectively. CONCLUSIONS: The SepsiPrep kit was easy to use combined with MicroIDSys Elite and VITEK-2 system and also, the correct identification and AST rate were very high.

Predominance and clonal spread of CTX-M-15 in cefotaxime-resistant Klebsiella pneumoniae in Korea and their association with plasmid-mediated quinolone resistance determinants.

INTRODUCTION: ß-lactams and fluoroquinolones are extensively used worldwide in the treatment of infections caused by Enterobacterales. In this study, we investigated the prevalence of extended-spectrum ß-lactamases (ESBL), their correlation with plasmid-mediated quinolone resistance determinants (PMQR) and clonal distribution among the cefotaxime-resistant K. pneumoniae isolates. METHODS: In Korea, a total of 429 K. pneumoniae collected in 2015 were studied. Antimicrobial susceptibility test for cefotaxime, ciprofloxacin and levofloxacin was performed by broth microdilution method. By PCR and/or sequencing, mutations in gyrA and parC genes, PMQR genes and ESBL were identified. Multilocus-sequence-type (MLST) was determined for isolates harboring CTX-M-15. RESULTS: Among the 149 K. pneumoniae showing cefotaxime MICs of >1 µg/ml, 142 (95.3%) isolates were ESBL-producers and CTX-M-15 was predominant (99 isolates). Among the 142 ESBL-producers, mutations in gyrA and parC were found in 112 (78.9%) and 93 isolates (65.5%), respectively. PMQR genes were detected in 141 isolates and the non-susceptibility rate to ciprofloxacin and levofloxacin was 95.1% (135/142) and 82.4% (117/142), respectively. The most frequently found PMQR combination was qnrB-aac(6')-Ib-cr-oqxAB, (58/142, 40.8%). By MLST, four major STs/CC: ST48, ST392, ST307 and CC15 accounted for 67% of the CTX-M-15 producers and the prevalence of qnrB was significantly higher in these four major STs/CC than other groups (P = 0.004). Of note, we found the additive effect of PMQR genes; the more PMQR genes, the higher ciprofloxacin MICs. CONCLUSIONS: CTX-M-15 was predominant among the cefotaxime-resistant K. pneumoniae and co-harboring CTX-M-15 and PMQR genes, especially qnrB, seems to contribute the spread of high risk clones.