Journal of Clinical Microbiology最新文献

{"title":"Clinical significance and antifungal susceptibility profile of 103 clinical isolates of <i>Scedosporium</i> species complex and <i>Lomentospora prolificans</i> obtained from NIH patients.","authors":"Mary M Czech, Jennifer Cuellar-Rodriguez, Kyung J Kwon-Chung, Frida Stock, Chioma I Aneke, Kenneth N Olivier, Kevin P Fennelly, Juan Gea-Banacloche, Christa S Zerbe, Alexandra F Freeman, Steven M Holland, Michail S Lionakis, Amir Seyedmousavi","doi":"10.1128/jcm.01550-24","DOIUrl":"https://doi.org/10.1128/jcm.01550-24","url":null,"abstract":"<p><p>Reduced susceptibility to antifungals is common among members of genera <i>Scedosporium</i> and <i>Lomentospora</i>, with optimal treatments still not fully defined. <i>In vitro</i> antifungal susceptibility results and clinical data do not comprehensively account for the advent of new <i>Scedosporium</i> species identified by molecular phylogenetics. Using Clinical and Laboratory Standards Institute (CLSI) methodology, we tested a total of 103 clinical isolates obtained from patients at the NIH Clinical Center. The most frequent species were <i>Scedosporium apiospermum</i> (63%) and <i>Scedosporium boydii</i> (11%), followed by <i>Lomentospora prolificans</i> (7%). The novel antifungal olorofim showed the lowest MICs against all <i>Scedosporium</i> spp. and <i>L. prolificans</i>, followed by micafungin. Among the triazoles, voriconazole showed lower MICs against <i>Scedosporium</i> spp. Amphotericin B and posaconazole demonstrated species-specific and inter-species variable activity. Itraconazole, isavuconazole, and terbinafine had higher MIC values against <i>Scedosporium</i> spp. and <i>L. prolificans</i>. Clinical data were retrospectively reviewed for 90 isolates, of which nine patients (28 isolates) had active disease/infection and received antifungal treatment that included voriconazole or posaconazole. Five of these patients (56%) died, while three patients (33%) with chronic granulomatous disease were cured following hematopoietic cell transplantation. In 24 patients (62 isolates), the presence of the fungus was considered airway colonization. In conclusion, our data support the existence of species-specific and inter-species differences in the antifungal susceptibility patterns among members of genera <i>Scedosporium</i> and <i>L. prolificans</i>. The novel investigational antifungal olorofim may be a promising therapy. Our clinical data suggest that host status and administration of antifungal therapy most effective for each <i>Scedosporium</i> species complex are important determinants of outcomes.IMPORTANCEUnderstanding the epidemiology and clinical spectrum of infections caused by <i>Scedosporium</i> species complex and <i>Lomentospora prolificans</i> is integral to improving outcomes, particularly in severely ill and immunocompromised patients. <i>In vitro</i> antifungal susceptibility testing can provide an estimate of antifungal activity against fungal pathogens. Our study showed that species-specific and inter-species differences exist in the distribution of antifungal susceptibility patterns between <i>Scedosporium</i> and <i>L. prolificans</i>. Our clinical data also highlight that host status, along with effective antifungal therapy, plays a crucial role in determining treatment outcomes.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0155024"},"PeriodicalIF":6.1,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143572347","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":"Standard E TB-Feron ELISA and Standard F TB-Feron FIA positivity rates and agreement with QuantiFERON-TB Gold Plus among TB high-risk population in Bandung, Indonesia.","authors":"Dewi Kartika Turbawaty, Syifa Nur Maulida, Darin Rizka Anadhea, Mulyanusa Amarullah Ritonga, Basti Andriyoko, Rudi Wisaksana, Agnes Rengga Indrati, Nanny Natalia Mulyani Soetedjo, Laniyati Hamijoyo, Raspati Cundarani Koesoemadinata, Bachti Alisjahbana, Ida Parwati","doi":"10.1128/jcm.01486-24","DOIUrl":"https://doi.org/10.1128/jcm.01486-24","url":null,"abstract":"<p><p>Tuberculosis (TB) remains a global public health problem. The determination of tuberculosis infection (TBI) using interferon-gamma release assay has now been used widely. We aim to evaluate the positivity rates of Standard E TB-Feron enzyme-linked immunosorbent assay (TB-Feron ELISA) and Standard F TB-Feron fluorescent immunoassay (TB-Feron FIA) and their agreement with QuantiFERON-TB Gold Plus (QFT-Plus) among TB high-risk populations in Bandung City, Indonesia. We conducted a cross-sectional study, including people with a high risk of acquiring TB. We screened subjects for TB symptoms and offered chest X-ray (CXR). Anyone with cough or CXR suggestive of TB was asked to give sputum samples for GeneXpert MTB/RIF Ultra test. The positivity rates and corresponding 95% confidence intervals (CI) were calculated among patients with bacteriologically confirmed TB and among patients with no evidence of TB, no history of TB, and no known contact with TB patient (low risk of TBI). The agreement with QFT-Plus was calculated using Cohen's κ score. We enrolled 527 subjects, and the proportion of positive results among bacteriologically confirmed TB patients were 8 (53.3%; 95% CI 26.6-78.7), 9 (60.0%, 95% CI 32.3-83.7), and 10 (66.7%, 95% CI 38.4-88.8) by TB-Feron FIA, TB-Feron ELISA and QFT-Plus. The agreement between TB-Feron FIA and QFT-Plus among all subjects was similar to that of TB-Feron ELISA and QFT-Plus (84.1%, κ = 0.66, 95% CI 0.59-0.72). TB-Feron FIA and TB-Feron ELISA showed an acceptable clinical performance compared with QFT-Plus. These tests are useful alternatives for detecting TB infection.IMPORTANCEThis study evaluates the performance of two alternative interferon-gamma release assays, Standard E TB-Feron enzyme-linked immunosorbent assay and Standard F TB-Feron fluorescent immunoassay, for diagnosing tuberculosis infection (TBI) among high-risk populations in Bandung, Indonesia. Both assays demonstrated comparable clinical performance to the widely used QuantiFERON-TB Gold Plus (QFT-Plus). Given the global burden of tuberculosis, particularly in resource-limited settings, these findings suggest that the TB-Feron assays could serve as reliable alternatives to QFT-Plus for TBI detection. This research highlights the potential for these assays to improve tuberculosis diagnosis, offering a more accessible and efficient screening tool, especially for high-risk populations, and supporting broader tuberculosis surveillance.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0148624"},"PeriodicalIF":6.1,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143572815","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":"Direct thin-layer agar for bedaquiline-susceptibility testing of <i>Mycobacterium tuberculosis</i> at BSL2 level yields high accuracy in 15 days from sputum processing.","authors":"I Cuella-Martin, D Runyambo, S De Bock, M Diels, H Niyompano, F Hakizayezu, J Keysers, W B De Rijk, Y M Habimana, N Gahamanyi, E Ardizzoni, C M Muvunyi, B C de Jong, J C S Ngabonziza, L Rigouts","doi":"10.1128/jcm.01806-24","DOIUrl":"https://doi.org/10.1128/jcm.01806-24","url":null,"abstract":"<p><p>This study evaluated thin-layer agar (TLA) as a faster alternative for both indirect minimum inhibitory concentration (MIC) determination of bedaquiline (BDQ) from culture isolates and direct drug-susceptibility testing (DST) from sputum samples. Indirect BDQ-MIC results from TLA were compared to the established 7H11 solid DST. Direct-TLA-DST performance was assessed using 143 baseline sputum samples from rifampicin-resistant TB cases. Direct-TLA tested susceptibility to rifampicin, isoniazid, levofloxacin, and BDQ, with results compared to Löwenstein-Jensen (LJ) and MGIT. For indirect BDQ-MIC determination, TLA accurately identified H37Rv MICs within the WHO control range (0.015-0.12μg/mL). Optimal results were obtained with standard incubation and day 7 reading of the plates. TLA correctly classified all wild-type clinical strains as BDQ-susceptible and detected 9 out of 10 BDQ-resistant strains with elevated MICs. Direct-TLA-DST detected MTB in 53.8% of samples, compared to 55.9% on LJ and 69.4% in MGIT. Uninterpretable results due to contamination or medium drying were low (4.9%). The median time to result was 15 days for smear-positive and 22 days for smear-negative samples, faster than WHO-endorsed methods. Sensitivity was 100% for rifampicin and 87.8% for isoniazid, with a specificity of 100% for all drugs except isoniazid (96.2%). No BDQ nor levofloxacin resistance was detected, thus direct TLA sensitivity could not be assessed. In conclusion, direct-TLA-DST offers a reliable and faster alternative to conventional DST methods for BDQ and other anti-TB drugs. Essentially, this technique can be operated at BioSafety Level 2, allowing decentralization of pDST for managing drug-resistant TB in settings with limited laboratory infrastructure.</p><p><strong>Importance: </strong>This paper addresses the critical need for faster direct drug-susceptibility testing (DST) on sputum, especially for bedaquiline (BDQ), which is a key drug in treating drug-resistant TB. Currently, there is a lack of rapid, reliable methods for direct BDQ testing from sputum samples, limiting timely and accurate treatment decisions and monitoring. By demonstrating the potential of thin-layer agar (TLA) for direct BDQ-MIC determination, this study offers a promising solution that could significantly improve patient care.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0180624"},"PeriodicalIF":6.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143542208","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":"A call for the United States to continue investing in science.","authors":"Ira Blader, Felicia Goodrum, Michael J Imperiale, Arturo Casadevall, Cesar Arias, Andreas Baumler, Carey-Ann Burnham, Christina Cuomo, Corrella Detweiler, Graeme Forrest, Jack Gilbert, Susan Lovett, Stanley Maloy, Alexander McAdam, Irene Newton, Gemma Reguera, George A O'Toole, Patrick D Schloss, Ashley Shade, Marvin Whiteley","doi":"10.1128/jcm.00348-25","DOIUrl":"https://doi.org/10.1128/jcm.00348-25","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0034825"},"PeriodicalIF":6.1,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143515776","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":"Biographical Feature: Ruth Ella Moore, Ph.D.","authors":"Marian C Johnson-Thompson","doi":"10.1128/jcm.01863-24","DOIUrl":"https://doi.org/10.1128/jcm.01863-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0186324"},"PeriodicalIF":6.1,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143515817","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":"A call for healing and unity.","authors":"Patrick D Schloss","doi":"10.1128/jcm.00338-25","DOIUrl":"https://doi.org/10.1128/jcm.00338-25","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0033825"},"PeriodicalIF":6.1,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143515764","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":"Use of gastrointestinal syndromic multiplex molecular assays and detection of <i>Escherichia coli</i> pathotypes in pediatric wards.","authors":"Etienne Bizot, Stéphane Bonacorsi, Pauline Labé, Yael Pinhas, Aurélie Cointe, Agnès Ferroni, Jérémie F Cohen, Hervé Lécuyer, Julie Toubiana","doi":"10.1128/jcm.01073-24","DOIUrl":"https://doi.org/10.1128/jcm.01073-24","url":null,"abstract":"<p><p><i>Escherichia coli</i> pathotypes are enteric pathogens detected in gastrointestinal multiplex polymerase chain reaction (mPCR), with controversial clinical relevance. Our study aimed to describe clinical features and therapeutic decisions associated with <i>E. coli</i> detections in gastrointestinal mPCR. Children with positive mPCR for enteroaggregative (EAEC)<i>,</i> enteropathogenic (EPEC)<i>,</i> enterotoxigenic (ETEC), Shiga toxin-producing <i>E. coli</i> (STEC), and enteroinvasive <i>E. coli</i> (EIEC)/<i>Shigella</i> identified in two pediatric hospitals over 18 months (2020-2021) were included. We described the frequency of <i>E. coli</i> detection and subsequent modifications in antibiotic strategies. Among the 2,471 mPCRs performed, 338 (14%) tested positive for at least one <i>E. coli</i> pathotype. The patient's mean age was 4.2 years, with 95% experiencing gastrointestinal symptoms. Clinical presentation was generally comparable between <i>E. coli</i> pathotypes. A recent travel abroad was reported in 68/338 (20%) cases and was mainly observed in EIEC/<i>Shigella</i> infections. An <i>E. coli</i> was detected alone in 177/338 (52%) cases and with another virus, bacteria, or parasite in 161 (48%) cases. Multiple enteric pathogens were mainly detected with ETEC (<i>n</i> = 24/26, 92%) and EAEC (<i>n</i> = 82/121, 68%) detections. Antibiotic therapy was prescribed in 136/338 (40%) cases, with initiation based on mPCR results in 69/338 (20%). No antibiotic therapy was discontinued following positive mPCR results. Among the 69 initiations, 31 were deemed inappropriate after retrospective chart review. <i>E. coli</i> detection with mPCR tests may lead to inappropriate antibiotic initiation. Caution is advised when interpreting results from gastrointestinal mPCRs in children, as clinicians may be unaware of their often unclear or irrelevant clinical significance.IMPORTANCE<i>Escherichia coli</i> pathotypes are increasingly detected through the widely used syndromic gastrointestinal multiplex PCR panels. However, their clinical significance and impact on antibiotic therapy in children remain uncertain. This study describes the clinical and microbiological characteristics associated with <i>E. coli</i> detections, as well as the subsequent modifications in antibiotic strategies. It highlights the frequent detection of <i>E. coli</i> pathotypes, often in association with other enteric pathogens, and reveals that nearly half of the antibiotics prescribed following these results were deemed inappropriate. These results underscore the need to enhance clinicians' interpretation of <i>E. coli</i>-positive results and reassess treatment strategies to optimize patient care.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0107324"},"PeriodicalIF":6.1,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143501470","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":"Epidemiology of positive bacterial cultures and the coverage gaps in multiplex PCR diagnostics: a single-center retrospective study.","authors":"Vishwaratn Asthana, Rishi Chanderraj, J Scott VanEpps, Robert P Dickson","doi":"10.1128/jcm.01600-24","DOIUrl":"https://doi.org/10.1128/jcm.01600-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0160024"},"PeriodicalIF":6.1,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143501469","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":"A novel framework for the automated characterization of Gram-stained blood culture slides using a large-scale vision transformer.","authors":"Jack McMahon, Naofumi Tomita, Elizabeth S Tatishev, Adrienne A Workman, Cristina R Costales, Niaz Banaei, Isabella W Martin, Saeed Hassanpour","doi":"10.1128/jcm.01514-24","DOIUrl":"https://doi.org/10.1128/jcm.01514-24","url":null,"abstract":"<p><p>This study introduces a new framework for the artificial intelligence-based characterization of Gram-stained whole-slide images (WSIs). As a test for the diagnosis of bloodstream infections, Gram stains provide critical early data to inform patient treatment in conjunction with data from rapid molecular tests. In this work, we developed a novel transformer-based model for Gram-stained WSI classification, which is more scalable to large data sets than previous convolutional neural network-based methods as it does not require patch-level manual annotations. We also introduce a large Gram stain data set from Dartmouth-Hitchcock Medical Center (Lebanon, New Hampshire, USA) to evaluate our model, exploring the classification of five major categories of Gram-stained WSIs: gram-positive cocci in clusters, gram-positive cocci in pairs/chains, gram-positive rods, gram-negative rods, and slides with no bacteria. Our model achieves a classification accuracy of 0.858 (95% CI: 0.805, 0.905) and an area under the receiver operating characteristic curve (AUC) of 0.952 (95% CI: 0.922, 0.976) using fivefold nested cross-validation on our 475-slide data set, demonstrating the potential of large-scale transformer models for Gram stain classification. Results were measured against the final clinical laboratory Gram stain report after growth of organism in culture. We further demonstrate the generalizability of our trained model by applying it without additional fine-tuning on a second 27-slide external data set from Stanford Health (Palo Alto, California, USA) where it achieves a binary classification accuracy of 0.926 (95% CI: 0.885, 0.960) and an AUC of 0.8651 (95% CI: 0.6337, 0.9917) while distinguishing gram-positive from gram-negative bacteria.</p><p><strong>Importance: </strong>This study introduces a scalable transformer-based deep learning model for automating Gram-stained whole-slide image classification. It surpasses previous methods by eliminating the need for manual annotations and demonstrates high accuracy and generalizability across multiple data sets, enhancing the speed and reliability of Gram stain analysis.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0151424"},"PeriodicalIF":6.1,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143483329","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":"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":" ","pages":"e0000125"},"PeriodicalIF":6.1,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143483328","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}