Journal of Clinical Microbiology最新文献

{"title":"Predictive performance of urinalysis for urine culture results according to causative microorganisms: an integrated analysis with artificial intelligence","authors":"Min Hyuk ChoiDokyun KimHye Gyung BaeAe-Ran KimMikyeong LeeKyungwon LeeKyoung-Ryul LeeSeok Hoon Jeong1Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea2Seoul Clinical Laboratories, Yongin-si, South KoreaErin McElvania","doi":"10.1128/jcm.01175-24","DOIUrl":"https://doi.org/10.1128/jcm.01175-24","url":null,"abstract":"Journal of Clinical Microbiology, Ahead of Print. <br/>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142176574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Brief Case: Tricky Trichosporon asahii in the urinary tract","authors":"Michaela J. EickhoffRebekah E. Dumm1Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USAAlexander J. McAdam","doi":"10.1128/jcm.00557-24","DOIUrl":"https://doi.org/10.1128/jcm.00557-24","url":null,"abstract":"Journal of Clinical Microbiology, Volume 62, Issue 9, September 2024. <br/>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142176622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Photo Quiz: Treatment-resistant rash in cardiac transplant patient","authors":"Nicole WinkelmannMark MochelChristopher DoernSara LambColin ThibodeauMelissa GodwinAlexandra L. Bryson1Department of Pathology, Virginia Commonwealth University Health Center, Richmond, Virginia, USA2Department of Dermatology, Virginia Commonwealth University Health Center, Richmond, Virginia, USABobbi S. Pritt","doi":"10.1128/jcm.01618-23","DOIUrl":"https://doi.org/10.1128/jcm.01618-23","url":null,"abstract":"Journal of Clinical Microbiology, Volume 62, Issue 9, September 2024. <br/>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142176575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reduced sensitivity of a multiplex commercial respiratory panel for detection of Mycoplasma pneumoniae is due to specimen type","authors":"Amy L. LeberSophonie J. OyeniranHuanyu Wang1Division of Infectious Diseases, Department of Pediatrics, Nationwide Children’s Hospital and The Ohio State University, Columbus, Ohio, USA2Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA3Department of Pathology, The Ohio State University, Columbus, Ohio, USAErik Munson","doi":"10.1128/jcm.01139-24","DOIUrl":"https://doi.org/10.1128/jcm.01139-24","url":null,"abstract":"Journal of Clinical Microbiology, Ahead of Print. <br/>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142176576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Defining our worth","authors":"Susan E. Sharp1Copan Diagnostics, Inc., Carlsbad, California, USAErin McElvania","doi":"10.1128/jcm.00880-24","DOIUrl":"https://doi.org/10.1128/jcm.00880-24","url":null,"abstract":"Journal of Clinical Microbiology, Ahead of Print. <br/>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142176577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nanopore-based targeted sequencing test for direct tuberculosis identification, genotyping, and detection of drug resistance mutations: a side-by-side comparison of targeted next-generation sequencing technologies.","authors":"Andrea Maurizio Cabibbe, Kiarash Moghaddasi, Virginia Batignani, Godstime Stephen Kojo Morgan, Federico Di Marco, Daniela Maria Cirillo","doi":"10.1128/jcm.00815-24","DOIUrl":"https://doi.org/10.1128/jcm.00815-24","url":null,"abstract":"<p><p>We investigated the performance of the targeted next-generation sequencing (tNGS)-based Oxford Nanopore Diagnostics AmPORE TB assay, recently approved by the World Health Organization (WHO) as tuberculosis (TB) diagnostic test for the detection of drug resistance on respiratory specimens. A total of 104 DNA samples from Xpert MTB/RIF-positive TB sputum specimens were tested using the AmPORE TB kit, with the GenoScreen Deeplex Myc-TB as a comparative tNGS assay. For AmPORE TB, DNA samples were divided into five sequencing runs on the MinION device. Data analysis was performed using proprietary software. The WHO catalog of mutations was used for drug resistance interpretation. The assay achieved a high validity rate of 98% (102/104 DNA samples), homogeneous mean reads coverage across TB-positive specimens, and 100% positive and negative agreements for detecting mutations associated with resistance to rifampicin, pyrazinamide, fluoroquinolones, ethambutol, and capreomycin compared with Deeplex Myc-TB. The main discrepancies for the remaining drugs were attributable to the different assay panel designs. The AmPORE TB turnaround time was approximately 5-6 hours from extracted DNA to tNGS reporting for batches of 22 DNA samples. The AmPORE TB assay drastically reduced the time to tNGS reporting from days to hours and showed good performance for drug-resistant TB profiling compared with Deeplex Myc-TB.</p><p><strong>Importance: </strong>Targeted next-generation sequencing (tNGS) of <i>Mycobacterium tuberculosis</i> provides comprehensive resistance predictions matched to new multidrug-resistant/rifampicin-resistant tuberculosis regimens and received World Health Organization approval for clinical use in respiratory samples in 2024. The advanced version of the Oxford Nanopore Diagnostics AmPORE TB tNGS kit was evaluated in this study for the first time and demonstrated good performance, flexibility, and faster turnaround time compared with the existing solutions.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142140186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An immunoassay based on bioluminescent sensors for rapid detection of African swine fever virus antibodies.","authors":"Zhonghui Zhang, Jinming Wang, Qingli Niu, Guiquan Guan, Hong Yin, Jifei Yang","doi":"10.1128/jcm.00463-24","DOIUrl":"https://doi.org/10.1128/jcm.00463-24","url":null,"abstract":"<p><p>Serological assays for antibody detection have contributed significantly to the diagnosis and control of infectious diseases. African swine fever is the most devastating infectious disease of domestic pigs and wild boars, severely threatening the global pig industry in recent years. Here, we developed a rapid, simple, and sensitive immunoassay based on the split-luciferase system to detect IgG antibodies against African swine fever virus (ASFV). In this assay, the p30 protein of ASFV was genetically coupled to the LgBiT and SmBiT subunits of nanoluciferase, which were used as fusion probes for specific antibodies. Target engagement of the probes results in the reconstitution of a functional nanoluciferase, which further catalyzes bioluminescent reactions. Different orientations of the LgBiT and SmBiT-p30 fusion sensors were designed and investigated, and N-LgBiT/p30 and N-SmBiT/p30 were identified as a promising sensor pair for reforming active nanoluciferase in the presence of specific antibodies. After optimization, this split-luciferase complementation assay showed high sensitivity and specificity for the detection of ASFV antibodies. The analytical sensitivity of the assay was 16 times greater than that of the blocking enzyme-linked immunosorbent assay (ELISA) by the detection of serial dilutions of serum, and no cross-reaction was observed with other swine pathogens. As demonstrated in clinical samples, its performance is highly consistent with that of a commercial ELISA kit, with a concordance rate of 98.19%. This assay is simple and easy to perform, providing a more flexible and efficient approach for the measurement of ASFV antibodies in clinical applications.</p><p><strong>Importance: </strong>The study is about a homogeneous split-luciferase assay for antibody detection. Split nanoluciferase biosensors for the detection of ASFV antibodies were designed. This sensor platform enables the sensitive and specific detection of antibodies. The split-luciferase assay is simple, rapid, and easy to use.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Performance of MALDI-TOF MS, real-time PCR, antigen detection, and automated biochemical testing for the identification of <i>Burkholderia pseudomallei</i>.","authors":"Stuart Campbell, Brooke Taylor, Dimitrios Menouhos, Jann Hennessy, Mark Mayo, Robert Baird, Bart J Currie, Ella M Meumann","doi":"10.1128/jcm.00961-24","DOIUrl":"https://doi.org/10.1128/jcm.00961-24","url":null,"abstract":"<p><p><i>Burkholderia pseudomallei</i> is the causative agent of melioidosis, a disease highly endemic to Southeast Asia and northern Australia, though the area of endemicity is expanding. Cases may occur in returning travelers or, rarely, from imported contaminated products. Identification of <i>B. pseudomallei</i> is challenging for laboratories that do not see this organism frequently, and misidentifications by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and automated biochemical testing have been reported. The <i>in vitro</i> diagnostic database for use with the Vitek MS has recently been updated to include <i>B. pseudomallei</i> and we aimed to validate the performance for identification in comparison to automated biochemical testing with the Vitek 2 GN card, quantitative real-time polymerase chain reaction (qPCR) targeting the type III secretion system, and capsular polysaccharide antigen detection using a lateral flow immunoassay (LFA). We tested a \"derivation\" cohort including geographically diverse <i>B. pseudomallei</i> and a range of closely related <i>Burkholderia</i> species, and a prospective \"validation\" cohort of <i>B. pseudomallei</i> and <i>B. cepacia</i> complex clinical isolates. MALDI-TOF MS had a sensitivity of 1.0 and specificity of 1.0 for the identification and differentiation of <i>B. pseudomallei</i> from related <i>Burkholderia</i> species when a certainty cutoff of 99.9% was used. In contrast, automated biochemical testing for <i>B. pseudomallei</i> identification had a sensitivity of 0.83 and specificity of 0.88. Both qPCR and LFA correctly identified all <i>B. pseudomallei</i> isolates with no false positives. Due to the high level of accuracy, we have now incorporated MALDI-TOF MS into our laboratory's <i>B. pseudomallei</i> identification workflow.IMPORTANCE<i>Burkholderia pseudomallei</i> causes melioidosis, a disease associated with high morbidity and mortality that disproportionately affects rural areas in Southeast Asia and northern Australia. The known area of endemicity is expanding and now includes the continental United States. Laboratory identification can be challenging which may result in missed or delayed diagnoses and poor patient outcomes. In this study, we compared mass spectrometry using an updated spectral database with multiple other methods for <i>B. pseudomallei</i> identification and found mass spectrometry highly accurate. We have therefore incorporated this fast and cost-effective method into our laboratory's workflow for <i>B. pseudomallei</i> identification.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analytical and clinical validation of direct detection of antimicrobial resistance markers by plasma microbial cell-free DNA sequencing.","authors":"Fred C Christians, Jamilla Akhund-Zade, Kristin Jarman, Shivkumar Venkatasubrahmanyam, Nicholas Noll, Timothy A Blauwkamp, Sivan Bercovici, Aga Zielinska, Amy L Carr, Arryn Craney, Matthew Pike, John Joseph Farrell, Sanjeet Dadwal, James B Wood, Efrat Matkovich, Staci McAdams, Frederick S Nolte","doi":"10.1128/jcm.00425-24","DOIUrl":"https://doi.org/10.1128/jcm.00425-24","url":null,"abstract":"<p><p>Sequencing of plasma microbial cell-free DNA (mcfDNA) has gained increased acceptance as a valuable adjunct to standard-of-care testing for diagnosis of infections throughout the body. Here, we report the analytical and clinical validation of a novel application of mcfDNA sequencing, the non-invasive detection of seven common antimicrobial resistance (AMR) genetic markers in 18 important pathogens. The AMR markers include SCC<i>mec</i>, <i>mecA, mecC</i>, <i>vanA, vanB</i>, <i>bla</i>_CTX-M, and <i>bla</i>_KPC. The AMR markers were computationally linked to the pathogens detected. Analytical validation showed high reproducibility (100%), inclusivity (54 to 100%), and exclusivity (100%). Clinical accuracy was assessed with 114 unique plasma samples from patients at seven study sites with concordant culture results for target bacteria from a variety of specimen types and correlated with available phenotypic antimicrobial susceptibility test results and genotypic results. The positive percent agreement (PPA), negative percent agreement (NPA), and diagnostic yield (DY) were estimated for each AMR marker. DY was defined as the percentage of tests that yielded an actionable result of either detected or not detected. The results for the combination of SCC<i>mec</i> and <i>mecA</i> for staphylococci were PPA 19/20 (95.0%), NPA 21/22 (95.4%), DY 42/60 (70.0%); <i>vanA</i> for enterococci were PPA 3/3 (100%), NPA 2/2 (100%), DY 5/6 (83.3%); <i>bla</i>_CTX-M for gram-negative bacilli were PPA 5/6 (83.3%), NPA 29/29 (100%), DY 35/49 (71.4%); and <i>bla</i>_KPC for gram-negative bacilli were PPA 0/2 (0%), NPA: 23/23 (100%), DY 25/44 (56.8%). The addition of AMR capability to plasma mcfDNA sequencing should provide clinicians with an effective new culture-independent tool for optimization of therapy.</p><p><strong>Importance: </strong>This manuscript is ideally suited for the Innovative Diagnostic Methods sections as it reports the analytical and clinical validation of a novel application of plasma microbial cell-free DNA sequencing for direct detection of seven selected antimicrobial resistance markers in 18 target pathogens. Clearly, it has potential clinical utility in optimizing therapy and was incorporated into the Karius test workflow in September 2023. In addition, the workflow could readily be adapted to expand the number of target bacteria and antimicrobial resistance markers as needed.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nationwide upsurge in invasive disease in the context of longitudinal surveillance of carriage and invasive <i>Streptococcus pyogenes</i> 2009-2023, the Netherlands: a molecular epidemiological study.","authors":"Lidewij W Rümke, Matthew A Davies, Stefan M T Vestjens, Boas C L van der Putten, Wendy C M Bril-Keijzers, Marlies A van Houten, Nynke Y Rots, Alienke J Wijmenga-Monsuur, Arie van der Ende, Brechje de Gier, Bart J M Vlaminckx, Nina M van Sorge","doi":"10.1128/jcm.00766-24","DOIUrl":"https://doi.org/10.1128/jcm.00766-24","url":null,"abstract":"<p><p>Since 2022, many countries have reported an upsurge in invasive group A streptococcal (iGAS) infections. We explored whether changes in <i>Streptococcus pyogenes</i> carriage rates or emergence of strains with potentially altered virulence, such as <i>emm</i>1 variants M1_UK and M1_DK, contributed to the 2022/2023 surge in the Netherlands. We determined <i>emm</i> (sub)type distribution for 2,698 invasive and 351 <i>S</i>. <i>pyogenes</i> carriage isolates collected between January 2009 and March 2023. Genetic evolution of <i>emm</i>1 was analyzed by whole-genome sequencing of 497 <i>emm</i>1 isolates. The nationwide iGAS upsurge coincided with a sharp increase of <i>emm</i>1.0 from 18% (18/100) of invasive isolates in Q1 2022 to 58% (388/670) in Q1 2023 (Fisher's exact test, <i>P</i> < 0.0001). M1_UK became dominant among invasive <i>emm</i>1 isolates in 2016 and further expanded from 72% in Q1 2022 to 96% in Q1 2023. Phylogenetic comparison revealed evolution and clonal expansion of four new M1_UK clades in 2022/2023. DNase Spd1 and superantigen SpeC were acquired in 9% (46/497) of <i>emm</i>1 isolates. <i>S. pyogenes</i> carriage rates and <i>emm</i>1 proportions in carriage isolates remained stable during this surge, and the expansion of M1_UK in iGAS was not reflected in carriage isolates. During the 2022/2023 iGAS surge in the Netherlands, expansion of four new M1_UK clades was observed among invasive isolates, but not carriage isolates, suggesting increased virulence and fitness of M1_UK compared to contemporary M1 strains. The emergence of more virulent clades has important implications for public health strategies such as antibiotic prophylaxis for close contacts of iGAS patients.IMPORTANCEThis study describes the molecular epidemiology of invasive group A streptococcal (iGAS) infections in the Netherlands based on >3,000 <i>Streptococcus pyogenes</i> isolates from both asymptomatic carriers and iGAS patients collected before, during, and after the COVID-19 pandemic period (2009-2023) and is the first to assess whether changes in carriage rates or carried <i>emm</i> types contributed to the alarming post-COVID-19 upsurge in iGAS infections. We show that the 2022/2023 iGAS surge coincided with a sharp increase of <i>emm</i>1, particularly the toxicogenic M1_UK variant, in invasive isolates, but not in carriage isolates. These findings suggest that increased virulence and fitness of M1_UK likely contributes to an increased dissemination between hosts. The emergence of a more virulent and fit lineage has important implications for iGAS control interventions such as antibiotic prophylaxis for close contacts of iGAS patients and calls for a reappraisal of iGAS control interventions and guidelines.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}