Journal of Clinical Microbiology最新文献

{"title":"Hematology thin smears perform equally to parasitology thick and thin blood smears for the diagnosis of <i>Plasmodium</i> and <i>Babesia</i> infections in a low prevalence setting.","authors":"Janmesh Patel, Jill Schuett, Derrick J Chen","doi":"10.1128/jcm.01601-24","DOIUrl":"https://doi.org/10.1128/jcm.01601-24","url":null,"abstract":"<p><p>Malaria and babesiosis are significant parasitic infections, requiring timely diagnosis to avoid severe complications. This study retrospectively compared hematology thin smears (HS) with parasitology thick and thin blood smears (PS), the gold standard for diagnosis, to evaluate HS's performance in detecting <i>Plasmodium</i> and <i>Babesia</i> infections. Of 529 cases with paired HS and PS testing, HS demonstrated 93.3% sensitivity and 99.8% specificity, with 97.7% positive and 99.4% negative predictive values. When only considering new diagnoses, HS and PS were 100% concordant. No significant difference was found in percent parasitemia between HS and PS, highlighting HS as a reliable diagnostic tool in settings where PS or other diagnostic modalities may not be readily available.IMPORTANCEThis study demonstrates that hematology thin smears-often available in laboratories that may not have other means of diagnosing blood parasite infections such as parasitology thick and thin smears, rapid diagnostics tests, or polymerase chain reaction-are an accurate and reliable way to diagnose <i>Plasmodium</i> and <i>Babesia</i> infections in a low prevalence setting.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0160124"},"PeriodicalIF":6.1,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700633","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":"Correction for Lamberink et al., \"Multicenter validation of a galactomannan chemiluminescence immunoassay for the diagnosis of pulmonary aspergillosis on serum of patients with hematological disease\".","authors":"Hanne Lamberink, Sammy Huygens, Robina Aerts, Katrien Lagrou, Karin van Dijk, Diana Langerak, Ine Moors, Jerina Boelens, Marijke Reynders, Johan Maertens, Alexander Schauwvlieghe, Mireille van Westreenen, Ga-Lai M Chong, Paul E Verweij, Jochem B Buil, Bart J A Rijnders","doi":"10.1128/jcm.00394-25","DOIUrl":"https://doi.org/10.1128/jcm.00394-25","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0039425"},"PeriodicalIF":6.1,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700553","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":"Impact of media brand on cefiderocol disk diffusion results.","authors":"M G DeMarco, A M Field, L E Donohue, H L Cox, T S Kidd, K E Barry, A J Mathers","doi":"10.1128/jcm.01648-24","DOIUrl":"https://doi.org/10.1128/jcm.01648-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Cefiderocol is a siderophore cephalosporin that utilizes iron transport systems to cross cell membranes. This unique strategy complicates antimicrobial susceptibility testing (AST) due to variable iron content in media. While guidance for using iron-depleted media exists for broth microdilution (BMD), disk diffusion (DD) with commercial media is a common AST method in the clinical laboratory. We investigated cefiderocol DD result variability using multiple Mueller-Hinton agar (MHA) brands. DD results using Remel (Thermo Fisher Scientific, San Diego, CA), Hardy (Hardy Diagnostics, Springboro, OH), and BBL (Becton Dickinson, East Rutherford, NJ) MHA were compared to those of BMD using iron-depleted cation-adjusted Mueller-Hinton broth. BMD reproducibility, BMD trailing endpoints, and DD intra- and inter-brand variability in zones of inhibition were investigated. Forty-seven multidrug-resistant clinical isolates and three Antibiotic Resistance Bank isolates composed of &lt;i&gt;Pseudomonas aeruginosa&lt;/i&gt;, carbapenemase (CP-) and non-carbapenemase-producing (non-CP-) carbapenem-resistant Enterobacterales (CRE), &lt;i&gt;Acinetobacter baumannii&lt;/i&gt; complex, &lt;i&gt;Stenotrophomonas maltophilia&lt;/i&gt;, and &lt;i&gt;Burkholderia cepacia&lt;/i&gt; complex were tested. Categorical agreement (CA) ≥ 90% was only demonstrated using CLSI breakpoints with BBL agar. Intra- and inter-brand variability in DD were highest for &lt;i&gt;P. aeruginosa&lt;/i&gt; and CRE, with 25% (5/20) and 16.7% (3/18) exhibiting discrepant AST interpretations, respectively. Isolates not susceptible to cefiderocol via BMD were commonly associated with AST interpretation errors and lower CA. Using commercial MHA for DD resulted in frequent AST interpretation discrepancies, particularly for isolates that were not susceptible to cefiderocol by BMD. Methods and quality control may need to be revisited to ensure the reliability of DD for cefiderocol AST.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;The novel mechanism of action of cefiderocol overcomes a variety of resistance mechanisms associated with gram-negative bacteria and positions the agent as an attractive option for treating infections involving multidrug-resistant pathogens. The availability of accurate, timely antimicrobial susceptibility testing methods for cefiderocol in clinical microbiology laboratories is critical as cefiderocol-resistant isolates have been described and may contribute to treatment failure. Iron-depleted broth microdilution testing may not be feasible for use in many clinical laboratories. While disk diffusion is an appealing, practical method to implement, our data demonstrate reproducibility issues across agar brands, most notably for organisms that do not test susceptible to cefiderocol when using broth microdilution. Discrepancy errors and misclassifications of resistant isolates as susceptible, and susceptible isolates as resistant, may mislead clinicians and compromise the treatment efficacy. More work is needed to standardize practical yet repro","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0164824"},"PeriodicalIF":6.1,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700640","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 sequencing for precise detection of <i>Mycobacterium tuberculosis</i> and drug resistance: a retrospective multicenter study in China.","authors":"Shanshan Yu, Ning Liu, Zhouhua Xie, Yi Zeng, Hua Wang, Qian Wang, Peibo Li, Haoran Li, Jinhao Sun, Qingdong Zhu, Weiwei Gao, Hongcang Gu, Fuyou Liu, Peisong Xu, Yunfei Wang, Liang Li, Yu Pang","doi":"10.1128/jcm.01813-24","DOIUrl":"https://doi.org/10.1128/jcm.01813-24","url":null,"abstract":"<p><p>Tuberculosis (TB) management in endemic regions often grapples with resource constraints, including the scarcity of <i>Mycobacterium tuberculosis</i> (<i>M.tb</i>) culture laboratories. The emergence of <i>M.tb</i> strains with complex drug resistance profiles necessitates rapid and comprehensive drug susceptibility testing (DST) to guide patient treatment. However, traditional phenotypic DST (pDST) for <i>M.tb</i> is costly and time-consuming. In this study, we retrospectively enrolled 829 participants from six specialized TB treatment hospitals in China from September 2022 to July 2023. The diagnostic performance of TBseq test, a targeted-nanopore sequencing assay, was compared head-to-head with <i>M.tb</i> culture, acid-fast bacillus smear, quantitative polymerase chain reaction, and Xpert MTB/RIF Ultra by using clinical diagnosis as the reference standard. Subsequently, pDST for seven anti-TB drugs (rifampicin, isoniazid, ethambutol, streptomycin, levofloxacin, amikacin, and capreomycin) was performed. The resistance predictions provided by the TBseq test were compared with pDST results, which were used as a reference standard. The performance estimates of TBseq test were quantified through sensitivity, specificity, positive predictive value, negative predictive value, and the area under the receiver operating characteristic curve (AUC), providing a comprehensive assessment of its diagnostic accuracy. We found that TBseq test demonstrated significantly superior diagnostic performance for TB compared to other methods, achieving a sensitivity of 90.9% (95% CI: 88.9%-93.0%), specificity of 93.0% (95% CI: 97.2%-99.5%), and an AUC of 0.92 (95% CI: 0.876-0.963). TBseq test also exhibited robust predictive capabilities for drug resistance to the seven anti-TB drugs, with sensitivity and specificity consistently above 90% for all drugs. The AUC values ranged from 0.919 to 0.998, indicative of high diagnostic accuracy in forecasting drug resistance.IMPORTANCEOur results show that TBseq test offers excellent identification performance for tuberculosis (TB), significantly outperforming <i>Mycobacterium tuberculosis</i> (<i>M.tb)</i> culture, acid-fast bacillus (AFB) smear, qPCR, and Xpert MTB/RIF. Its diagnostic accuracy for anti-TB drug resistance is also superior, with sensitivity and specificity above 90% for all drugs tested. This method can be integrated into routine clinical diagnostic workflows, enabling early diagnosis and reporting of drug resistance simultaneously.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0181324"},"PeriodicalIF":6.1,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657367","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":"External quality assessment of molecular detection and variant typing of SARS-CoV-2 in European expert laboratories in 2023.","authors":"Kim C Heimsch, Kamelia R Stanoeva, Ramona Mögling, Annette Kraus, Eeva K Broberg, Jan Felix Drexler, Chantal B E M Reusken, Adam Meijer, Christian Drosten, Victor M Corman","doi":"10.1128/jcm.01538-24","DOIUrl":"https://doi.org/10.1128/jcm.01538-24","url":null,"abstract":"<p><p>The COVID-19 pandemic highlighted the importance of laboratory preparedness. Regular monitoring of diagnostic tools via external quality assessments (EQAs) is key to maintaining robust public health response service. We hereby conducted a third SARS-CoV-2 EQA assessing the diagnostic capabilities of European expert public health laboratories. A 10 samples panel containing Alpha (used in previous EQA), BA.4, BA.5, and BQ.1.18 variants along with human seasonal coronaviruses and negative controls was produced and validated. Participants were invited by the European Centre for Disease Prevention and Control (ECDC) and asked to submit results and assay details via electronic forms. Thirty-eight laboratories from 31 European countries participated. Most (<i>n</i> = 32, 84%) identified all panel samples correctly and used in-house (11, 29%), commercial assays (22, 58%), or both (5, 13%). Compared to previous EQAs, correct detection of the SARS-CoV-2 samples in the panels increased: 8 (12%) in 2020, 45 (75%) in 2021, and 34 (90%) laboratories in 2023, respectively. The number of participants decreased to an average of one laboratory per country (range 1-3) compared to two (1-7) laboratories in both previous EQAs. The usage of commercial assays gradually increased in contrast to the usage of in-house or both approaches. The capacity for SARS-CoV-2 molecular diagnostics has markedly improved in Europe as evidenced by three consecutive EQAs carried out by expert public health laboratories. Routine monitoring of diagnostic and surveillance assays via EQAs remains key to maintaining rapid public health laboratory response systems.IMPORTANCEExternal quality assessments (EQAs) are crucial to ensure the reliability and consistency of diagnostic laboratories. They provide an objective framework for evaluating the performance of testing systems, enabling laboratories to identify weaknesses and implement improvements promptly. In the context of SARS-CoV-2, EQAs have become even more critical due to the high demand for accurate molecular diagnostics and the emergence of new variants. Accurate detection and typing of variants are especially essential for monitoring viral evolution. EQAs help standardize methodologies, ensuring that results across laboratories remain comparable and trustworthy. Moreover, they play a pivotal role in minimizing errors such as false positives or negatives. In this rapidly evolving landscape, regular EQAs are indispensable for maintaining high-quality standards in molecular diagnostics and variant surveillance. We demonstrate here that regular EQAs improve the molecular detection of SARS-CoV-2 in European laboratories.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0153824"},"PeriodicalIF":6.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624902","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":"Lipid fingerprinting by MALDI Biotyper Sirius instrument fails to differentiate the three subspecies of the <i>Mycobacterium abscessus</i> complex.","authors":"Mitsunori Yoshida, Hanako Fukano, Koji Yahara, Satoshi Nakano, Takeshi Komine, Masato Suzuki, Azumi Fujinaga, Kohei Doke, Yoshihiko Hoshino","doi":"10.1128/jcm.01484-24","DOIUrl":"https://doi.org/10.1128/jcm.01484-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0148424"},"PeriodicalIF":6.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624905","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":"Pneumococcal genotype 23B1 as a driver of increased 23B serotype carriage, penicillin non-susceptibility, and invasive disease in Belgium: a retrospective analysis.","authors":"Lara Dierckx, Juan Pablo Rodriguez-Ruiz, Esra Ekinci, Liesbet van Heirstraeten, Laura Willen, Lize Cuypers, Philippe Beutels, Kirsten Maertens, Stefanie Desmet, Heidi Theeten, Surbhi Malhotra-Kumar","doi":"10.1128/jcm.01696-24","DOIUrl":"https://doi.org/10.1128/jcm.01696-24","url":null,"abstract":"<p><p><i>Streptococcus pneumoniae</i> serotype 23B, a non-vaccine serotype, has shown an increasing prevalence and penicillin non-susceptibility among carriage and invasive pneumococcal disease (IPD) isolates. Recently, a novel penicillin non-susceptible genotype has emerged, named 23B1. In the framework of the Belgian pneumococcal carriage study, we studied the prevalence of 23B₀/23B1 among 586 23B strains (2016-2022) in 172 day care centers from 6- to 30-month-old children and among 130 pediatric 23B IPD isolates (2007-2021). Pneumococci were whole genome sequenced to determine the capsular polysaccharide genotype and sequence type (ST). Antimicrobial susceptibility testing determined penicillin and amoxicillin MICs, as well as resistance to co-trimoxazole and levofloxacin. 23B carriage was stable during 2016 ̶ 2022 except in the 2020-2021 winter season when it increased. The proportion of genotype 23B1 compared to 23B₀ decreased from 2016 ̶ to 2022 but remained consistently higher than 23B₀. In 2020-2021, an increase in the proportion of 23B1 was reflected in an overall increase in 23B carriage. All increases in 23B IPD cases were almost entirely driven by 23B1. The median penicillin MICs were significantly different for 23B₀ (0.03 mg/L) and 23B1 (0.25 mg/L). In 2021, increased intermediate levofloxacin susceptibility was noted in 23B. 23B1-associated ST2372 was the most prevalent ST in carriage and IPD during 2013-2022. We show that an increase in 23B carriage among children was paralleled in pediatric IPD in Belgium, reiterating the utility of pneumococcal surveillance in the day care population. Serotype 23B is reported worldwide as an important pediatric non-PCV13 serotype with reduced penicillin susceptibility, with 23B1 as the presumed driver for the increased prevalence.IMPORTANCEDuring the COVID-19 pandemic, the 23B serotype of <i>Streptococcus pneumoniae</i> has increased in prevalence in healthy carriage isolates from Belgian day care centers and pediatric (younger than 18 years of age) invasive pneumococcal disease (IPD) isolates. Additionally, an increase in penicillin non-susceptibility was also observed within this serotype. Recently, a genetic variant of 23B, named 23B1, was discovered, which is known to be related to decreased penicillin susceptibility. We showed that increases in 23B prevalence in healthy carriage and IPD cases always coincided with 23B1 expansions, leading to higher penicillin non-susceptibility rates. Increases in 23B in the day care population paralleled pediatric 23B IPD increases, indicating the vital role of day care monitoring of pneumococcal carriage. Countries should stay vigilant for prevalence increases in <i>S. pneumoniae</i> serotype 23B, given the decreased susceptibility to penicillin and co-trimoxazole of the 23B1 variant.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0169624"},"PeriodicalIF":6.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604835","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":"Comparison of the Filamentous Fungi Library v4.0 MALDI Biotyper Platform vs MSI-2 performance for identifying filamentous fungi from liquid cultures.","authors":"María F Gonzalez-Lara, Carla M Román-Montes, Paulette Díaz-Lomelí, Winston Hernández-Ceballos, Lizeth Morales-Camilo, Axel Cervantes-Sánchez, Andrea Cordero-Rangel, Jazmín Tejeda-Olán, Alexandro Bonifaz-Trujillo, Alfredo Ponce-de-León, Areli Martínez-Gamboa","doi":"10.1128/jcm.01371-24","DOIUrl":"10.1128/jcm.01371-24","url":null,"abstract":"<p><p>Correct, rapid, and reliable filamentous fungi identification is crucial for timely diagnosis and therapy. We compared the performance of the FFLv4.0 MALDI Biotyper and MSI-2 to identify filamentous fungi from clinical isolates. We analyzed 307 clinical isolates of <i>Aspergillus</i> spp.<i>, Fusarium</i> spp.<i>,</i> and <i>Mucorales</i> and compared them to sequencing as the reference standard. The overall identification rates to genus (<i>Mucorales</i>), section (<i>Aspergillus</i>), and species complex (<i>Fusarium</i>) level were 96% (296/307) for FFLv4.0 and 78.5% (241/307) for MSI-2. By each genus, correct species identification was achieved by FFLv4.0 and MSI-2 as follows: 72.4% (165/228) and 55.3% (126/228) for <i>Aspergillus</i> species, 17.6% (6/34) and 38.2% (13/34) for <i>Fusarium</i> species, and 88.9% (40/45) and 55.5% (25/45) for the <i>Mucorales</i>. The rates of non-identification by FFLv4.0 and MSI-2, respectively, were 4% (9/228) and 18% (41/228) for <i>Aspergillus</i> spp., 0% and 17.6% (6/34) for <i>Fusarium</i> spp. and 4.4% (2/45) and 42.2% (19/45%) for the <i>Mucorales</i>. Misidentification rates by FFLv4.0 and MSI-2, respectively, were 16.2% (37/228) and 6.1% (14/228) for <i>Aspergillus</i> species, 67.6% (23/34) and 14.7% (5/34) for <i>Fusarium</i> spp., and 0% and 2.2% (1/45) for the <i>Mucorales</i>. The FFLv4.0 MALDI Biotyper outperformed MSI-2 in identifying filamentous fungi from liquid culture spectra.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0137124"},"PeriodicalIF":6.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11898572/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143065888","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":"An overview of the laboratory diagnosis of <i>Pneumocystis jirovecii</i> pneumonia.","authors":"Alexis Jaramillo Cartagena, Osaretin Emmanuel Asowata, Dianna Ng, N Esther Babady","doi":"10.1128/jcm.00361-24","DOIUrl":"10.1128/jcm.00361-24","url":null,"abstract":"<p><p><i>Pneumocystis jirovecii</i> (<i>P. jirovecii</i>) is a fungal pathogen associated with significant morbidity in immunocompromised patients, including both HIV- and non-HIV-infected patients. The nonspecific clinical and radiological presentation makes clinical diagnostic challenging, emphasizing the need for accurate laboratory diagnostic tests. However, <i>P. jirovecii</i> does not grow in routine culture media, which presents diagnostic challenges in the laboratory as well. Recent publications from the European Organization for Research and Treatment of Cancer and the Mycoses Study Group Education and Research Consortium continue to rely on direct detection of <i>P. jirovecii</i> organisms in tissues and respiratory samples to define proven <i>P. jirovecii</i> pneumonia (PCP) even as the sensitivity of these methods are lower. Novel, standardized methods are needed to improve the clinical and laboratory diagnosis and management of PCP. This minireview provides an overview of current diagnostic tests for PCP and emerging applications that aim at filling existing diagnostic gaps and providing more accurate and less invasive diagnoses for this significant disease.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0036124"},"PeriodicalIF":6.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11898755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143080214","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 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":"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":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11898657/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}