Journal of Clinical Microbiology最新文献

{"title":"2025 American Society for Microbiology Awards and Prize Program: honorees from clinical microbiology.","authors":"Erik Munson","doi":"10.1128/jcm.00001-25","DOIUrl":"https://doi.org/10.1128/jcm.00001-25","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"63 3","pages":"e0000125"},"PeriodicalIF":6.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604836","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":"Field evaluation of nanopore targeted next-generation sequencing to predict drug-resistant tuberculosis from native sputum in South Africa and Zambia.","authors":"Tiana C Schwab, Lavania Joseph, Andrew Moono, Pauline C Göller, Mamello Motsei, Guy Muula, Denise Evans, Stefan Neuenschwander, Gunar Günther, Carolyn Bolton, Peter M Keller, Alban Ramette, Matthias Egger, Shaheed V Omar, Lukas Fenner","doi":"10.1128/jcm.01390-24","DOIUrl":"10.1128/jcm.01390-24","url":null,"abstract":"<p><p>Rapid and comprehensive drug susceptibility testing (DST) is essential for diagnosing and treating drug-resistant tuberculosis effectively, and next-generation sequencing can be an effective genotypic DST method. We implemented and evaluated the performance of a nanopore targeted sequencing assay, called the Tuberculosis Drug Resistance Test (TBDR, Oxford Nanopore Diagnostics, Ltd., United Kingdom), which predicts drug resistance to 16 TB drugs, at a South African reference laboratory and a district diagnostic laboratory in Zambia. We compared the sequencing success rates between unprocessed and decontaminated sputum samples and determined the diagnostic accuracy against local DST (Xpert MTB/RIF Ultra, Xpert MTB/XDR, and BD BACTEC MGIT phenotypic DST). We prospectively sequenced 236 samples and have 148 samples with sequencing results from unprocessed and decontaminated sputum. We obtained successful sequencing results from 66.4% (94/148) unprocessed sputum samples and 75% (111/148) decontaminated samples. Sequencing success rates at the two sites differed, with 50.7% (36/71) successful sequencing results from unprocessed sputum in Zambia and 75.3% (58/77) in South Africa. Samples with \"low\" bacterial load, measured by Xpert MTB/RIF Ultra, tended to produce fewer successful sequencing results. TBDR sequencing predicted resistances in 48 samples, detecting resistance for rifampicin (<i>n</i> = 41) and isoniazid (<i>n</i> = 20), as well as 10 second-line drugs (<i>n</i> = 15). Sensitivity was variable compared to phenotypic DST, ranging from 33 (ethionamide) to 94% (rifampicin), while specificity remained above 90% for all drugs, except clofazimine. The TBDR assay can provide rapid, comprehensive genotypic DST. Technical and operational challenges need to be addressed for its broader implementation in high tuberculosis-burden settings.IMPORTANCEThis study illustrates the use of the Tuberculosis Drug Resistance Test (TBDR, Oxford Nanopore Diagnostics, Ltd., United Kingdom) as a rapid drug susceptibility testing (DST) approach for diagnosing drug-resistant TB in the high TB-burden countries of South Africa and Zambia. The TBDR assay predicts resistance to 16 TB drugs, including first- and second-line treatments. By implementing the TBDR assay in a national reference laboratory in South Africa and a district diagnostic laboratory in Zambia, we demonstrate how this technology can provide faster diagnostic results (days) compared to traditional phenotypic DST methods (~2 months), with adequate sensitivity. Missed resistances compared to phenotypic DST indicate that technical improvements are needed. Successful sequencing from unprocessed and decontaminated sputum samples at different sites suggests feasibility in diverse settings, though operational challenges remain. Implementing this rapid, comprehensive DST approach could enhance drug-resistant tuberculosis diagnosis and treatment, ultimately improving patient outcomes and helping to combat tub","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0139024"},"PeriodicalIF":6.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11898686/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143399425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"2025 American Society for Microbiology Awards and Prize Program: honorees from clinical microbiology.","authors":"Erik Munson","doi":"10.1128/jcm.00001-25","DOIUrl":"10.1128/jcm.00001-25","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"63 3","pages":"e0000125"},"PeriodicalIF":6.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11898749/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Brief Case: Cutaneous ulceration associated with acalabrutinib treatment.","authors":"Victor Luzarraga, Céline Nourrisson, Florence Anglade, Carole Chevenet, Philippe Poirier, Maxime Moniot","doi":"10.1128/jcm.01583-24","DOIUrl":"10.1128/jcm.01583-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"63 3","pages":"e0158324"},"PeriodicalIF":6.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11898747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Photo Quiz: Hematuria in a pediatric patient.","authors":"Víctor Antón Berenguer, Sara Ruiz González, Francisco Jesús Merino Fernández, José Miguel Rubio Muñoz, Sara Gómez de Frutos, María Delmans Flores-Chavez","doi":"10.1128/jcm.00241-24","DOIUrl":"10.1128/jcm.00241-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"63 3","pages":"e0024124"},"PeriodicalIF":6.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11898658/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Erratum for Snyder et al., \"Performance of the LifeScale automated rapid phenotypic antimicrobial susceptibility testing on Gram-negative rods directly from positive blood cultures\".","authors":"James W Snyder, Nadia Chaudhry, Wesley Hoffmann","doi":"10.1128/jcm.00156-25","DOIUrl":"10.1128/jcm.00156-25","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0015625"},"PeriodicalIF":6.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11898698/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143399422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The impact of FDA-cleared molecular solutions for BK polyomavirus quantitation.","authors":"Bijal A Parikh, Neil W Anderson","doi":"10.1128/jcm.00348-24","DOIUrl":"10.1128/jcm.00348-24","url":null,"abstract":"<p><p>Accurate detection and monitoring of BK polyomavirus (BKV) infection is of critical importance in the post-transplant period, guiding treatment decisions that balance the anti-rejection effects of immune suppression with host-protective effects of immune defense. Historically, test methods for BKV have been independently developed by laboratories to address this unmet need. However, these assays can suffer from inconsistencies in analytical variability, which in turn have hindered the establishment of commutable and clinically actionable viral load thresholds for clinical management. As a result, the interpretation of viral load quantitation has not been standardized across transplant centers for the purpose of monitoring patients at highest risk for infection-related complications. In this review, we describe challenges that have historically limited widespread adoption of BKV quantitative testing. We then detail how developments in the field, including optimized amplicon selection, the introduction of an international standard, and the availability of Food and Drug Administration (FDA)-cleared methods, have played a role in harmonization of quantitative BKV measurements in the clinical management of transplant recipients.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0034824"},"PeriodicalIF":6.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11898770/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143006406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A rapid and simple MALDI-TOF MS lipid profiling method for differentiating <i>Mycobacterium ulcerans</i> from <i>Mycobacterium marinum</i>.","authors":"Takeshi Komine, Hanako Fukano, Mitsunori Yoshida, Yuji Miyamoto, Makoto Nakaya, Azumi Fujinaga, Kohei Doke, Yoshihiko Hoshino","doi":"10.1128/jcm.01400-24","DOIUrl":"10.1128/jcm.01400-24","url":null,"abstract":"<p><p><i>Mycobacterium ulcerans</i>, a slow-growing nontuberculous mycobacterium, causes Buruli ulcer, a neglected tropical disease. Distinguishing <i>M. ulcerans</i> from related species, including <i>Mycobacterium marinum</i>, poses challenges with respect to making accurate identifications. In this study, we developed a rapid and simple identification method based on mycobacterial lipid profiles and used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze the lipid profiles of <i>M. ulcerans</i> (<i>n</i> = 35) and <i>M. marinum</i> (<i>n</i> = 19) isolates. Bacterial colonies pre-cultured on 2% Ogawa egg slants for 2 months were collected, and total lipids were extracted using an MBT Lipid Xtract kit. Spectra were obtained in negative ion mode using a MALDI Biotyper Sirius system, with ClinProTools v3.0 being used to analyze the spectra based on the application of three algorithms (genetic algorithm [GA], supervised neural network [SNN], and quick classifier [QC)]). Cross-validation was performed using a 20% leave-out set randomly selected from the samples. Models generated using GA, SNN, and QC showed cross-validation values of 100%, 100%, and 97.9%, respectively, and all algorithms achieved 100% recognition capability values. Our findings indicate that MALDI-TOF analysis of lipid profiles can accurately differentiate two mycobacterial species (<i>M. ulcerans</i> and <i>M. marinum</i>) that are difficult to distinguish using conventional protein-targeting methods.IMPORTANCEBuruli ulcer, caused by <i>Mycobacterium ulcerans</i>, is a neglected tropical disease. However, distinguishing <i>M. ulcerans</i> from related species, including <i>Mycobacterium marinum</i>, presents certain challenges. In this study, we demonstrate the utility of a rapid yet simple method for differentiating isolates of these mycobacteria based on their lipid profiles using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. This new approach can accurately identify species that are otherwise difficult to distinguish using conventional techniques. This represents a significant diagnostic advance for clinical laboratories, in that it enables a more rapid and precise identification, thereby leading to earlier treatment initiation and more appropriate treatment regimens for infections caused by these bacteria.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0140024"},"PeriodicalIF":6.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11898672/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143046274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of an analytical intervention to assure the accuracy of LIAISON QuantiFERON-TB Gold Plus results.","authors":"Karolina Pusz-Bochenska, Niaz Banaei","doi":"10.1128/jcm.01879-24","DOIUrl":"10.1128/jcm.01879-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0187924"},"PeriodicalIF":6.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11898571/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143052645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Retrieval-augmented generation salvages poor performance from large language models in answering microbiology-specific multiple-choice questions.","authors":"Grace Perkins, Neil W Anderson, Nicholas C Spies","doi":"10.1128/jcm.01624-24","DOIUrl":"10.1128/jcm.01624-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0162424"},"PeriodicalIF":6.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11898693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143391033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}