Lawson Copley, Gina Lee, Mary Villani, Naureen Tareen, Laura M Filkins
{"title":"Performance evaluation of a commercial multiplex pathogen panel for the diagnosis of pediatric joint infections.","authors":"Lawson Copley, Gina Lee, Mary Villani, Naureen Tareen, Laura M Filkins","doi":"10.1128/jcm.00278-25","DOIUrl":"10.1128/jcm.00278-25","url":null,"abstract":"<p><p>This study evaluates the performance of the BIOFIRE Joint Infection (JI) Panel compared to joint fluid culture and/or 16S rRNA PCR, followed by Sanger sequencing (16S PCR/S) for the diagnosis of joint infections in pediatric patients. An on-panel organism was detected by standard-of-care joint (SOCj) studies (joint fluid culture with or without 16S PCR/S, as ordered by the treating physician) in 29/65 samples (44.6%), and the same organism was detected by the BIOFIRE JI panel in all samples. The cumulative positive percent agreement in the detection of on-panel genus or species-level targets by the BIOFIRE JI panel was 100% (36/36), 100% (25/25), and 100% (27/27), and the negative percent agreement was 99.7% (1,974/1,979), 99.2% (1,974/1,990), and 99.7% (1,303/1,307) compared to detection by SOCj, joint fluid culture only, or 16S PCR/S only, respectively. The potential clinical impact of employing the BIOFIRE JI panel was predicted by retrospective adjudication using a study-specific rubric. We predicted that 27.7% (18/65) of BIOFIRE JI panel results could have had a positive impact on patient care. One case (1.5%) was predicted to potentially have a negative impact, and three cases (4.6%) were adjudicated to have an unknown impact. All organisms detected by 16S PCR/S, but not by culture, were also detected by the BIOFIRE JI panel during this study.</p><p><strong>Importance: </strong>The BIOFIRE JI Panel has been limitedly evaluated in pediatric patients. Our study shows a strong agreement between the BIOFIRE JI panel and culture and/or 16S rRNA PCR with Sanger sequencing for the detection of the most common pathogenic causes of joint infection in children. The faster time to results of the BIOFIRE JI panel has the potential to guide optimal treatment faster than conventional methods.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0027825"},"PeriodicalIF":6.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12239719/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144199275","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}
Amary Fall, Julie M Norton, Omar Abdullah, Andrew Pekosz, Eili Klein, Heba H Mostafa
{"title":"Enhanced genomic surveillance of enteroviruses reveals a surge in enterovirus D68 cases, the Johns Hopkins health system, Maryland, 2024.","authors":"Amary Fall, Julie M Norton, Omar Abdullah, Andrew Pekosz, Eili Klein, Heba H Mostafa","doi":"10.1128/jcm.00469-25","DOIUrl":"10.1128/jcm.00469-25","url":null,"abstract":"<p><p>This study reports increased Enterovirus D68 (EV-D68) circulation in 2024, re-establishing its biennial circulation cycle after its interruption during the COVID-19 pandemic. A total of 1,395 respiratory and cerebrospinal fluid (CSF) samples, positive for rhinovirus/enterovirus, collected from January to November 2024 were screened. EV-D68 was the predominant enterovirus detected (72.6% of EV-positive samples), with cases peaking in October, consistent with historical seasonal patterns. Demographically, children under 5 years were predominantly infected with EV-D68 (41.6% of cases). Phylogenetic analysis revealed the co-circulation of two EV-D68 subclades: B3 (71%) and A2 (29%). Subclade B3 was primarily associated with pediatric infections (median age: 5 years), while A2 was more common in adults (median age: 42 years). Comparative genomic analysis of the 2024 B3 genomes, along with genomes from 2018 and 2022, identified the emergence of four amino acid substitutions, including three in nonstructural proteins (3C: I597V; 3D: I950V, T2173A) and one in the structural protein VP2 (T145S). The six positive enterovirus CSF samples diagnosed in 2024 included six different types: EV-D68, E9, E30, E18, CV-A9, and CV-B1. Notably, the 2024 EV-D68 outbreak did not coincide with a reported increase in acute flaccid myelitis (AFM) cases. This study highlights the importance of EV-D68 genomic surveillance for monitoring EV-D68 evolution, given its association with severe respiratory disease and neurological complications. Enhanced surveillance is also critical for the early detection of the emergence of enteroviruses, such as EV-C105, identified in this study.IMPORTANCEEnteroviruses (EVs), a genus within the <i>Picornaviridae</i> family, are small, single-stranded RNA viruses linked to a wide spectrum of diseases, including neurological conditions. Despite their prevalence, they remain understudied. EV-D68 and EV-A71 have raised global public health concerns due to outbreaks of acute flaccid myelitis (AFM) and encephalomyelitis in North America and Europe. EVs exhibit high genetic variability, and viral evolution has been associated with changes in neurovirulence. Notably, EV-D68 epidemics in 2014, 2016, and 2018 coincided with spikes in AFM cases. However, AFM reports from 2019 to 2022 were low, even with a significant increase in EV-D68 infections in 2022. We developed an EV-D68 genomic surveillance workflow to investigate genotype associations with severe disease. Our previous work linked amino acid substitutions in 2018 strains to increased disease severity. This study analyzes EV-D68 evolution in 2024 and documents the return of its biennial circulation pattern following disruption during the COVID-19 pandemic.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0046925"},"PeriodicalIF":6.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12239729/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144258126","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}
Julie M Norton, Gaby Dashler, Eili Klein, Heba H Mostafa
{"title":"The utility of syndromic respiratory pathogen panels: the premise of flexible and customizable approaches.","authors":"Julie M Norton, Gaby Dashler, Eili Klein, Heba H Mostafa","doi":"10.1128/jcm.00313-25","DOIUrl":"10.1128/jcm.00313-25","url":null,"abstract":"<p><p>Extended respiratory panels have been limited to specific patient populations due to cost and inconclusive clinical utility. Customizing syndromic panels offers a way to balance clinical utility and available resources. In this study, we evaluated strategies and assessed the value of flexible, customized respiratory panels. A total of 200 specimens from symptomatic patients (December 2023 to September 2024), negative for SARS-CoV-2/Flu/RSV, were tested with the LIAISON PLEX Respiratory Flex Assay-an extended respiratory panel that offers flexibility in target selection. The study assessed additional diagnoses, correlations with institutional and state-wide pathogen prevalence, and whether customizable panels could optimize diagnostic yield. Sixty-two samples (31%) negative for SARS-CoV-2/Flu/RSV tested positive for other targets, primarily rhinovirus/enterovirus (60%), correlating with local and state prevalence. Weighted estimates for 18,373 symptomatic patients during the study period modeled a prevalence of 14.3% for rhinovirus/enterovirus, followed by HPIV-3, adenovirus, and coronavirus. During the study period, 6% of patients received the standard of care extended respiratory panel order after a negative SARS-CoV-2/Flu/RSV result, duplicating SARS-CoV-2/Flu/RSV testing. Leveraging a flexible feature could have resulted in an estimated staff time reduction of 5,545 minutes for a second swab collection and running a second test, in addition to the cost of running two different panels during a single encounter. Local respiratory pathogen prevalence data can guide target selection in customized panels. The inclusion of high-prevalence targets can increase the likelihood of diagnosis from 12% to nearly 30%. Flexibility in customizing targeted pathogen panels could enhance diagnostic value while conserving institutional resources.IMPORTANCERapid and accurate identification of pathogens causing respiratory tract infections can aid in guiding treatment decisions, reducing healthcare costs, and supporting real-time surveillance of infectious diseases within a community. Limitations of clinical utility beyond SARS-CoV-2/Flu/RSV are primarily driven by cost and the lack of specific treatment options. There is a need to balance clinical gaps with testing cost and diagnostic stewardship. In this study, we evaluated the utility of flexible, customized respiratory viral panels and reportable targets within a broader set of available targets in an extended respiratory panel.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0031325"},"PeriodicalIF":6.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12239722/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144258128","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":"Performance of liquid Amies transport medium for the recovery of <i>Salmonella</i> and <i>Shigella</i> from stool compared to molecular testing.","authors":"Laura Collier, Morgan A Pence","doi":"10.1128/jcm.00453-25","DOIUrl":"10.1128/jcm.00453-25","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0045325"},"PeriodicalIF":6.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12239730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144215991","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}
Julie Rousselot, Laurence Millon, Emeline Scherer, Nathalie Bourgeois, Sebastien Imbert, Damien Dupont, Anne Debourgogne, Danièle Maubon, Anne Pauline Bellanger, Christopher R Thornton
{"title":"Detection of <i>Mucorales</i> antigen in bronchoalveolar lavage samples using a newly developed lateral-flow device.","authors":"Julie Rousselot, Laurence Millon, Emeline Scherer, Nathalie Bourgeois, Sebastien Imbert, Damien Dupont, Anne Debourgogne, Danièle Maubon, Anne Pauline Bellanger, Christopher R Thornton","doi":"10.1128/jcm.00226-25","DOIUrl":"10.1128/jcm.00226-25","url":null,"abstract":"<p><p>A murine IgG2b monoclonal antibody, named TG11, binding to an extracellular polysaccharide antigen secreted by all <i>Mucorales</i> fungi has been recently developed and integrated into a lateral-flow device (TG11-LFD). The aim of this study was to establish the clinical performance of TG11-LFD on bronchoalveolar lavage (BAL) fluids for the diagnosis of mucormycosis. Thirteen BAL samples from 13 patients with mucormycosis, all of which tested positive for <i>Mucorales</i> qPCR (<i>Mucor/Rhizopus</i> [<i>n</i> = 5], <i>Lichtheimia</i> [<i>n</i> = 2], <i>Rhizomucor</i> [<i>n</i> = 5], and <i>Cunninghamella</i> [<i>n</i> = 1]), were used to assess the TG11-LFD. We also selected 49 BAL samples from 25 patients with other invasive fungal infections (IFI) (aspergillosis, <i>Pneumocystis</i> infection, candidiasis, and possible IFI) and from 20 patients without IFI for use as negative controls. The intensities of the test and control lines were recorded using a Cube reader. The diagnostic performance was assessed by analyzing the receiver operating characteristics (ROC) curve with the Jamovi software package (version 2.6.13). The area under the curve of the ROC curve was 0.739. Using a threshold value positivity ≤531 artificial units, the TG11-LFD test has a sensitivity and specificity of 76.92% and 75.51%, respectively, a positive predictive value of 45.45%, and a negative predictive value of 92.5%. In this study, we evaluated the performance of TG11-LFD on clinical samples for the first time and demonstrated its significant potential for enhancing the rapid detection of mucormycosis. Combining antigen detection with qPCR, as successfully applied in the diagnosis of aspergillosis, is likely to yield the most reliable diagnostic approach.IMPORTANCEMucormycosis is a severe emerging, invasive fungal disease caused by fungi in the order <i>Mucorales</i>. The mortality rate remains high at approximately 50%. Rapid diagnosis and prompt initiation of targeted treatment are associated with an improved prognosis. Gold standard diagnostic procedures have poor sensitivity and long turnaround times. <i>Mucorales</i> polymerase chain reaction in blood and respiratory samples has improved diagnosis, but this technique is not widely available due to high costs and the need for specialist equipment. A prototype lateral-flow device (TG11-LFD) incorporating a mouse monoclonal antibody, which binds to an extracellular polysaccharide antigen specific to <i>Mucorales</i> fungi, has been recently developed. In this study, we evaluated for the first time the performance of the TG11-LFD test on clinical bronchoalveolar lavage fluids for diagnosing mucormycosis. With 76.92% sensitivity and 75.51% specificity, this innovative, simple, and affordable approach shows great potential for improving the rapid diagnosis of mucormycosis.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0022625"},"PeriodicalIF":6.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12239717/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144325905","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}
Luani R Godoy, Mariam El-Zein, Elizaveta Padalko, Bo Verberckmoes, Bodine Van Eenooghe, Heleen Vermandere, Sónia Dias, Ana Gama, Bernardo Vega Crespo, Vivian Alejandra Neira, Eduardo L Franco, Adhemar Longatto-Filho
{"title":"Comparative performance of cobas 4800 HPV Test and Anyplex II HPV HR for high-risk human papillomavirus detection.","authors":"Luani R Godoy, Mariam El-Zein, Elizaveta Padalko, Bo Verberckmoes, Bodine Van Eenooghe, Heleen Vermandere, Sónia Dias, Ana Gama, Bernardo Vega Crespo, Vivian Alejandra Neira, Eduardo L Franco, Adhemar Longatto-Filho","doi":"10.1128/jcm.00200-25","DOIUrl":"https://doi.org/10.1128/jcm.00200-25","url":null,"abstract":"<p><p>Numerous molecular tests are available to detect human papillomavirus (HPV). We compared the analytical performance of cobas and Anyplex for detection of high-risk (HR) carcinogenic HPV genotypes, assessed the composition of HPV types (other than 16 and 18) that influenced cobas performance, and considered the impact of viral load on test performance. We used data from the Early Detection of Cervical Cancer in Hard-to-Reach Populations of Women Through Portable and Point-of-Care HPV Testing project, which involved collection (2019-2022) of cervicovaginal samples from 1,042 women aged 21-74 years in Belgium (<i>n</i> = 244), Portugal (<i>n</i> = 309), Brazil (<i>n</i> = 244), and Ecuador (<i>n</i> = 245). Samples were tested by cobas (provides individual results for HPV16 and HPV18 and a pooled result for 12 other HR-HPV types) and Anyplex (provides separate results for 14 HR-HPVs). We calculated HPV positivity by each test and compared performance between tests by calculating Cohen's kappa statistics. Based on 938 samples with complete data from both tests, positivity rates by cobas were 13.4%, 3.6%, 34.3%, and 45.3% for HPV16, HPV18, 12 pooled HR-HPVs, and any HR-HPV, respectively. Corresponding HPV positivity rates by Anyplex were 14.9%, 3.7%, 37.9%, and 50.0% for the same categories, respectively, with high concordance; kappa statistics were 0.90, 0.87, 0.82, and 0.85, respectively. Based on 355 samples that tested positive for at least 1 of the 12 pooled HR-HPVs, most types showed high agreement (80.9%-100.0%) between individual-Anyplex and pooled-cobas HPV results, except for HPV68 (61.3% agreement). Our findings suggest that the two commercial tests may have different performances, depending on the specific HPV types detected, emphasizing the need for continued research on conditions that may affect these tests, especially for less common or less studied HPV types.IMPORTANCEThis study compared two commercial tests-cobas and Anyplex-for detecting high-risk HPV types in women undergoing routine cervical cancer screening or referred for colposcopy. Both tests provide separate results for HPV16 and HPV18, but Anyplex also identifies the remaining 12 high-risk HPV types individually, while cobas groups them together. Overall, we found a high level of agreement between the two tests, supporting their use in clinical practice. However, differences in detecting certain HPV types, particularly those that are less common or less studied, emphasize the importance of choosing the right test. As more countries switch to HPV-based cervical cancer screening, using tests that provide detailed results could help improve risk assessment and optimize patient care.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0020025"},"PeriodicalIF":6.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144591365","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}
Jun Ren, Jintao Xia, Mengyu Zhang, Chunhong Liu, Yuanyuan Xu, Jianing Wu, Yingzhu Li, Mingming Zhou, Shengjie Li, Wenjun Cao
{"title":"Automated identification of <i>Salmonella</i> serotype using MALDI-TOF mass spectrometry and machine learning techniques.","authors":"Jun Ren, Jintao Xia, Mengyu Zhang, Chunhong Liu, Yuanyuan Xu, Jianing Wu, Yingzhu Li, Mingming Zhou, Shengjie Li, Wenjun Cao","doi":"10.1128/jcm.00037-25","DOIUrl":"10.1128/jcm.00037-25","url":null,"abstract":"<p><p><i>Salmonella</i> serotyping is essential for epidemiological studies and clinical treatment guidance. However, traditional serological agglutination methods are time-consuming, technically complex, and difficult to adopt at scale. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a rapid and cost-effective microbial identification technique, but it cannot be used to differentiate <i>Salmonella</i> serotypes. This study aims to integrate MALDI-TOF MS with machine learning algorithms to develop and validate a model for <i>Salmonella</i> serotype identification, improving efficiency and simplifying workflows. A total of 692 <i>Salmonella</i> isolates from Children's Hospital, Zhejiang University School of Medicine (ZUCH) and Wanbei Coal-Electricity Group General Hospital (WCGH) were analyzed using MALDI-TOF MS, generating 2,048 spectra. The ZUCH data were randomly divided into training and internal validation sets. The WCGH data were used as an external validation set. Ten machine learning algorithms were evaluated for their ability to identify eight <i>Salmonella</i> serotypes (B, C1, C2/3, D, E, Not A-F, <i>Salmonella</i> Typhimurium, and <i>Salmonella</i> Enteritidis). From 192 initial features, 16 features were selected for the final model construction. XGBoost demonstrated the best discriminative ability (area under the receiver operating characteristic curve [AUC] = 0.9898, sensitivity = 0.88, and specificity = 0.98) for the training set. The streamlined XGBoost model achieved AUCs of 0.9662 and 0.9778 for the internal and external validation sets, respectively, accurately identifying <i>Salmonella</i> serotypes. To enhance usability, the model was deployed as a Streamlit-based application, facilitating interaction and broader application. MALDI-TOF MS combined with XGBoost provides a fast and accurate method for <i>Salmonella</i> serotype identification, offering an efficient solution for laboratory diagnostics and epidemiological studies.</p><p><strong>Importance: </strong><i>Salmonella</i> serotyping is vital for outbreak tracking and clinical guidance, but traditional methods are slow and laborious. This study combines matrix-assisted laser desorption ionization-time of flight mass spectrometry with machine learning (XGBoost) to enable rapid, accurate, and cost-effective serotyping. The streamlined model performed excellently in validation and was deployed as a user-friendly Streamlit app, enhancing usability. This innovation simplifies workflows, reduces diagnostic time, and supports scalable use in clinical and public health settings, improving outbreak response and epidemiological research.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0003725"},"PeriodicalIF":6.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12239726/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144266386","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}
Logan K Weyand, Brandi L Felts, E Frances Cassirer, Jonathan A Jenks, Daniel P Walsh, Thomas E Besser
{"title":"Correction for Weyand et al., \"Fatal interactions: pneumonia in bighorn lambs following experimental exposure to carriers of <i>Mycoplasma ovipneumoniae</i>\".","authors":"Logan K Weyand, Brandi L Felts, E Frances Cassirer, Jonathan A Jenks, Daniel P Walsh, Thomas E Besser","doi":"10.1128/jcm.00426-25","DOIUrl":"10.1128/jcm.00426-25","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0042625"},"PeriodicalIF":6.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12239714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144258125","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}