Journal of Clinical Microbiology最新文献

{"title":"Shedding of nontyphoidal <i>Salmonella</i> by asymptomatic convalescing children under 5 years as a risk factor for invasive disease in Mukuru informal settlement in Nairobi, Kenya.","authors":"Kelvin Kering, Kariuki Njaanake, Celestine Wairimu, Marianne Mureithi, Collins Kebenei, Georgina Odityo, Michael Mugo, Susan M Kavai, Cecilia Mbae, Kristin Weber, Michael Pietsch, Tanja Pilz, Oliver Drechsel, Andrea Thürmer, Torsten Semmler, Stephan Fuchs, Sandra Simon, Antje Flieger, Lothar H Wieler, Samuel Kariuki","doi":"10.1128/jcm.00750-24","DOIUrl":"10.1128/jcm.00750-24","url":null,"abstract":"<p><p>Nontyphoidal <i>Salmonella</i> (NTS) is a predominant cause of invasive disease in sub-Saharan Africa especially among children under 5 years. Asymptomatic fecal shedding of NTS is hypothesized to contribute to the human-to-human transmission of NTS especially in low-resource settings. However, the role of pathogen shedding in invasive disease is unknown. This study aimed to investigate the prevalence and duration of fecal shedding of NTS among children under 5 years convalescing from invasive NTS disease and among healthy individuals in the community. Children presenting with fever of ≥38°C with or without diarrhea were recruited at four health facilities in Nairobi, between June 2021 and August 2023. Blood and stool samples collected were subjected to culture for the isolation of NTS (<i>S</i>. Enteritidis and <i>S</i>. Typhimurium). Children with NTS culture-positive samples (index cases) were followed up post-acute disease where household contacts and controls provided stool samples for isolation of NTS. NTS prevalence among the 3,293 individuals recruited was 1.52%. Asymptomatic shedding post-treatment was observed in almost one-third (31%) of the 42 index cases followed up. Of the 13 with intestinal shedding, 7 were shedding NTS of the same sequence type (ST) as the one recovered during acute disease. The longest duration of intestinal shedding was 3 months post-treatment. Of the 241 healthy individuals recruited, 8 had asymptomatic shedding of NTS, and 2 of these were closely related to those recovered from index cases. These findings support the hypothesis of human-to-human transmission of NTS in sub-Saharan Africa highlighting the possible benefit of vaccine introduction.</p><p><strong>Importance: </strong>Asymptomatic fecal shedding of nontyphoidal <i>Salmonella</i> (NTS) is hypothesized to contribute to the human-to-human transmission of NTS especially in low-resource settings which could lead to invasive disease among high-risk populations, especially children. Our findings reiterate the hypothesis that human reservoirs could be important in the transmission of nontyphoidal <i>Salmonella</i> in sub-Saharan Africa. This underscores the importance of developing infection prevention measures which could include vaccine deployment and improving water, sanitation and hygiene infrastructure.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0075024"},"PeriodicalIF":5.3,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559038/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142501307","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":"GPT-4-based AI agents-the new expert system for detection of antimicrobial resistance mechanisms?","authors":"Christian G Giske, Michelle Bressan, Farah Fiechter, Vladimira Hinic, Stefano Mancini, Oliver Nolte, Adrian Egli","doi":"10.1128/jcm.00689-24","DOIUrl":"10.1128/jcm.00689-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The European Committee on Antimicrobial Susceptibility Testing (EUCAST) recommends two steps for detecting beta-lactamases in Gram-negative bacteria. Screening for potential extended-spectrum beta-lactamase (ESBL), plasmid-mediated AmpC beta-lactamase, or carbapenemase production is confirmed. We aimed to validate generative pre-trained transformer (GPT)-4 and GPT-agent for pre-classification of disk diffusion to indicate potential beta-lactamases. We assigned 225 Gram-negative isolates based on phenotypic resistances against beta-lactam antibiotics and additional tests to one or more resistance mechanisms as follows: \"none,\" \"ESBL,\" \"AmpC,\" or \"carbapenemase.\" Next, we customized a GPT-agent with EUCAST guidelines and breakpoint table (v13.1). We compared routine diagnostics (reference) to those of (i) EUCAST-GPT-expert, (ii) microbiologists, and (iii) non-customized GPT-4. We determined sensitivities and specificities to flag suspect resistances. Three microbiologists showed concordance in 814/862 (94.4%) phenotypic categories and were used in median eight words (interquartile range [IQR] 4-11) for reasoning. Median sensitivity/specificity for ESBL, AmpC, and carbapenemase were 98%/99.1%, 96.8%/97.1%, and 95.5%/98.5%, respectively. Three prompts of EUCAST-GPT-expert showed concordance in 706/862 (81.9%) categories but were used in median 158 words (IQR 140-174) for reasoning. Sensitivity/specificity for ESBL, AmpC, and carbapenemase prediction were 95.4%/69.23%, 96.9%/86.3%, and 100%/98.8%, respectively. Non-customized GPT-4 could interpret 169/862 (19.6%) categories, and 137/169 (81.1%) agreed with routine diagnostics. Non-customized GPT-4 was used in median 85 words (IQR 72-105) for reasoning. Microbiologists showed higher concordance and shorter argumentations compared to GPT-agents. Humans showed higher specificities compared to GPT-agents. GPT-agent's unspecific flagging of ESBL and AmpC potentially results in additional testing, diagnostic delays, and higher costs. GPT-4 is not approved by regulatory bodies, but validation of large language models is needed.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;The study titled \"GPT-4-based AI agents-the new expert system for detection of antimicrobial resistance mechanisms?\" is critically important as it explores the integration of advanced artificial intelligence (AI) technologies, like generative pre-trained transformer (GPT)-4, into the field of laboratory medicine, specifically in the diagnostics of antimicrobial resistance (AMR). With the growing challenge of AMR, there is a pressing need for innovative solutions that can enhance diagnostic accuracy and efficiency. This research assesses the capability of AI to support the existing two-step confirmatory process recommended by the European Committee on Antimicrobial Susceptibility Testing for detecting beta-lactamases in Gram-negative bacteria. By potentially speeding up and improving the precision of initial screenings, AI could reduce the time ","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0068924"},"PeriodicalIF":5.3,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559085/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142466616","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 LAMP-based assay for the identification of <i>Streptococcus pneumoniae</i> and <i>Streptococcus pseudopneumoniae</i> in clinical isolates.","authors":"Mariam Basheer, Katarina Sasic, Alice Carlsson, Nora Vestberg, Birgitta Henriques-Normark, Karin Blomqvist, Geneviève Garriss","doi":"10.1128/jcm.00912-24","DOIUrl":"https://doi.org/10.1128/jcm.00912-24","url":null,"abstract":"<p><p>The Gram-positive bacteria <i>Streptococcus pneumoniae</i> is part of the <i>Streptococcus mitis</i> group (SMG) and causes life-threatening infections, such as pneumonia, sepsis, and meningitis. The closely related <i>Streptococcus pseudopneumoniae</i> has recently been shown to cause respiratory tract infections, as well as invasive infections, especially in patients with comorbidities. Due to the genetic and phenotypic similarities of species belonging to the SMG, the identification of <i>S. pneumoniae</i> and <i>S. pseudopneumoniae</i> is difficult and unreliable using phenotypic tests, as well as matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and 16S rRNA sequencing. In this study, a loop-mediated isothermal amplification (LAMP)-based assay was developed using molecular markers specific for <i>S. pneumoniae</i> (SPN0001) and <i>S. pseudopneumoniae</i> (SPPN_RS10375). The LAMP assay was evaluated using a collection of SMG clinical isolates, concluding that the method provides a correct, reliable, and fast identification of both <i>S. pneumoniae</i> and <i>S. pseudopneumoniae</i> clinical isolates.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0091224"},"PeriodicalIF":6.1,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142621316","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":"Nomenclature for human and animal fungal pathogens and diseases: a proposal for standardized terminology.","authors":"Sybren de Hoog, Thomas J Walsh, Sarah A Ahmed, Ana Alastruey-Izquierdo, Maiken Cavling Arendrup, Andrew Borman, Sharon Chen, Anuradha Chowdhary, Robert C Colgrove, Oliver A Cornely, David W Denning, Philippe J Dufresne, Laura Filkins, Jean-Pierre Gangneux, Josepa Gené, Andreas H Groll, Jaques Guillot, Gerhard Haase, Catriona Halliday, David L Hawksworth, Roderick Hay, Martin Hoenigl, Vit Hubka, Tomasz Jagielski, Hazal Kandemir, Sarah E Kidd, Julianne V Kus, June Kwon-Chung, Shawn R Lockhart, Jacques F Meis, Leonel Mendoza, Wieland Meyer, M Hong Nguyen, Yinggai Song, Tania C Sorrell, J Benjamin Stielow, Rachel Vilela, Roxana G Vitale, Nancy L Wengenack, P Lewis White, Luis Ostrosky-Zeichner, Sean X Zhang","doi":"10.1128/jcm.00937-24","DOIUrl":"https://doi.org/10.1128/jcm.00937-24","url":null,"abstract":"<p><p>Medically important pathogenic fungi invade vertebrate tissue and are considered primary when part of their nature life cycle is associated with an animal host and are usually able to infect immunocompetent hosts. Opportunistic fungal pathogens complete their life cycle in environmental habitats or occur as commensals within or on the vertebrate body, but under certain conditions can thrive upon infecting humans. The extent of host damage in opportunistic infections largely depends on the portal and modality of entry as well as on the host's immune and metabolic status. Diseases caused by primary pathogens and common opportunists, causing the top approximately 80% of fungal diseases [D. W. Denning, Lancet Infect Dis, 24:e428-e438, 2024, https://doi.org/10.1016/S1473-3099(23)00692-8], tend to follow a predictive pattern, while those by occasional opportunists are more variable. For this reason, it is recommended that diseases caused by primary pathogens and the common opportunists are named after the etiologic agent, for example, histoplasmosis and aspergillosis, while this should not be done for occasional opportunists that should be named as [causative fungus] [clinical syndrome], for example, <i>Alternaria alternata</i> cutaneous infection. The addition of a descriptor that identifies the location or clinical type of infection is required, as the general name alone may cover widely different clinical syndromes, for example, \"rhinocerebral mucormycosis.\" A list of major recommended human and animal disease entities (nomenclature) is provided in alignment with their causative agents. Fungal disease names may encompass several genera of etiologic agents, consequently being less susceptible to taxonomic changes of the causative species, for example, mucormycosis covers numerous mucormycetous molds.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0093724"},"PeriodicalIF":6.1,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142621319","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":"Prospective evaluation of non-invasive saliva specimens for the diagnosis of syphilis and molecular surveillance of <i>Treponema pallidum</i>.","authors":"Kazuo Imai, Akihiro Sato, Masashi Tanaka, Yuki Ohama, Shu-Ichi Nakayama, Ryuha Omachi, Keita Takeuchi, Norihito Tarumoto, Mieko Tokano, Shigefumi Mesaki, Takuya Maeda, Yukihiro Akeda","doi":"10.1128/jcm.00809-24","DOIUrl":"10.1128/jcm.00809-24","url":null,"abstract":"<p><p>The promising diagnostic performance of molecular testing for syphilis using saliva and urine samples has been reported; however, further evaluation of its possible application for diagnosis and molecular surveillance is required. In addition, the development of a rapid and easy-to-perform molecular test for syphilis is important for its use in the clinical setting. We comprehensively evaluated the diagnostic and surveillance performance of two novel loop-mediated isothermal amplification (LAMP) assays using saliva and urine samples. Saliva, urine, and whole blood were collected from patients who underwent serological testing for syphilis at outpatient clinics. <i>Treponema pallidum</i> DNA in specimens was detected using quantitative PCR (qPCR), nested PCR, and novel LAMP assays. <i>T. pallidum</i> genotyping was conducted by multi-locus sequence typing (MLST). Of the 163 patients recruited, 98 were diagnosed with syphilis (primary: <i>n</i> = 35; secondary: <i>n</i> = 40; latent: <i>n</i> = 23). qPCR showed the highest sensitivity among the molecular tests performed with a sensitivity of 54.1% and 30.3% for all syphilis patients using saliva and urine samples, respectively. A novel method of LAMP combined with dry reagents and crude DNA extraction (Dry-LAMP) showed a probit detection limit of 37.4 copies/reaction within 45 min. The agreement rate between Dry-LAMP and qPCR for saliva was 95.7% (<i>κ</i> coefficient 0.90). The <i>T. pallidum</i> genotype was identified in 48 patients by MLST using saliva samples. Molecular analysis of saliva could be used as a supplementary diagnostic test for syphilis and molecular surveillance of the <i>T. pallidum</i> genotype. Dry-LAMP is expected to be helpful in the clinical diagnosis of syphilis.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0080924"},"PeriodicalIF":6.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142583235","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":"Evaluation of the QIAstat-Dx BCID GN and GPF kits for direct identification and antimicrobial resistance prediction from blood culture bottles.","authors":"Sally Ng, Chai Yuin Tan, Jing Yan Yah, Nur A'tikah Binte Osman, Ka Lip Chew","doi":"10.1128/jcm.01169-24","DOIUrl":"10.1128/jcm.01169-24","url":null,"abstract":"<p><p>Rapid multiplex PCR kits have been used for rapid identification of blood culture isolates and prediction of antimicrobial resistance. We performed an evaluation of the QIAstat-Dx BCID GN and GPF research use only (RUO) kits on positive blood culture bottles using routine laboratory testing as the reference standard. Positive blood culture bottles between November 2023 and January 2024 were tested with QIAstat-Dx BCID GN and GPF kits based on initial Gram stain results and compared against routine identification and phenotypic susceptibility testing. A total of 174 monomicrobial blood cultures were included in the final analysis. The 174 monomicrobial blood cultures composed of 129 BCID GN tests and 45 BCID GPF tests. The majority of on-target Gram-negative organisms in monomicrobial cultures were identified. One <i>Escherichia coli</i> isolate was not identified as such, although the pan-Enterobacterales target was positive. All on-target Gram-positive organisms in monomicrobial cultures were identified. Overall sensitivity and specificity of <i>tem/shv</i> for detection of aminopenicillin resistance in <i>E. coli</i> was 94.7% (18/19) and 95.8% (23/24). The presence/absence of <i>ctx-m</i> and <i>ampC</i> had 100% sensitivity and specificity for identification of third-generation cephalosporin resistance in <i>E. coli</i> and <i>Klebsiella pneumoniae</i>. The combination of <i>blaZ</i> and <i>mecA</i> gene detection was fully predictive of phenotypic susceptibility results to penicillin and cloxacillin for <i>Staphylococcus aureus</i>. Overall, the QIAstat-Dx BCID GN and GPF kits were able to identify on-target pathogens. Detected resistance mechanisms were highly predictive of β-lactam resistance. Prediction of resistance for non-β-lactam antimicrobial was more variable.</p><p><strong>Importance: </strong>This is one of the first evaluations of the QIAstat BCID kit and demonstrates high levels of correlation for both identification and antimicrobial resistance prediction.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0116924"},"PeriodicalIF":6.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142583229","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":"Evaluation of Fungitell (1,3)-β-D-glucan assay in tear samples for rapid diagnosis of fungal keratitis.","authors":"Yamini Tawde, Sourav Das, Shreya Singh, Soham Basak, Savitri Sharma, Amit Gupta, Shivaprakash M Rudramurthy, Geetika Yadav, Anup Ghosh","doi":"10.1128/jcm.01200-24","DOIUrl":"10.1128/jcm.01200-24","url":null,"abstract":"<p><p>Fungal keratitis (FK) is a serious suppurative and ulcerative corneal infection leading to blindness and vision loss. Rapid diagnosis of FK can contribute to prompt clinical management with early recovery. The study aimed to standardize the detection of (1,3)-β-D-glucan (BDG) and establish the diagnostic cut-off concentration in tears of suspected FK patients along with non-infected controls. This prospective multicentric study was conducted between the period of August 2022 and April 2024. Samples were collected from three tertiary eye-care facilities across India. All suspected FK patients were enrolled in the study. Prior to tear collection, the eye and eyelid were gently cleansed using sterile normal saline (NS) and lint-free tissue paper. Subsequently, 50 µL of sterile NS was instilled into the eye, followed by tear sample collection after 60 s using sterile fine microtips. Tear samples were collected from the contralateral eyes of the FK patients, and those from healthy volunteers served as controls. The concentration of BDG in tears in varying dilutions was quantitatively measured using the Fungitell Assay Kit (Associates of Cape Cod, East Falmouth, Massachusetts). A total of 53 tear samples were analyzed at 1:10 and 1:20 dilutions. The receiver operating curve revealed an area under the curve (AUC) of 0.919 for the 1:10 dilution, with a cut-off value of 123 pg/mL, yielding a sensitivity of 100% and specificity of 84.85%. The corresponding Youden Index was 0.798. At the 1:20 dilution, the AUC was 0.898 with a cut-off of 84 pg/mL, achieving a sensitivity of 70% and specificity of 96.88% with a Youden Index of 0.670. Given the higher specificity at the 1:20 dilution, it was further validated in 145 tear samples. The validation cohort demonstrated a sensitivity of 95.56%, specificity of 83%, positive predictive value (PPV) of 71.67%, negative predictive value (NPV) of 97.65%, and diagnostic odds ratio of 112.4. Notably, a significantly higher BDG concentration (<i>P</i> < 0.0001) was observed in infected tear samples compared to controls (270.6 ± 128.5 vs 37.31 ± 31.32). Detection of BDG in tear samples is a new, non-invasive, and rapid technique showing excellent performance and can be effectively implemented for diagnosing FK in laboratories.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0120024"},"PeriodicalIF":6.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142583226","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":"Prospective, multi-site evaluation of the Cepheid Xpert Xpress CoV-2 <i>plus</i> test on nasal and nasopharyngeal swabs.","authors":"Alexander L Greninger, Allan Larcena, Amrish Patel, Brian Webster, Christina Ulen, Dallas F Green, Dana King, Deepesh Rubin Patel, Erin McElvania, Glenn Harnett, Imad Jandali, Jane Gibson, Jennifer Killion, Jibran Atwi, Kelly Bergmann, Lance Slade, Mary Allen Staat, Matthew Faron, Megan Washington, Rahul Patel, Rajasekaran Annamalai, Ronald Ackerman, William P Stewart, Yuliet Mora Amador, Deepa Rao, Xiaohong Liu, Aarthi Raman","doi":"10.1128/jcm.01219-24","DOIUrl":"10.1128/jcm.01219-24","url":null,"abstract":"<p><p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues its largely aseasonal spread with millions of cases per year. Highly sensitive, point-of-care testing is critical for rapid detection of coronavirus disease 2019 (COVID-19) cases and initiation of antiviral therapy to avert adverse health outcomes and reduce onward transmission of the virus. While hundreds of COVID-19 diagnostics received emergency use authorization from the FDA during the pandemic, significantly fewer have navigated the course to FDA clearance or approval. Here, we determined the clinical performance of the Cepheid Xpert Xpress CoV-2 <i>plus</i> for detection of SARS-CoV-2 in 3,750 anterior nasal swab (NS) specimens and nasopharyngeal swab (NPS) from 32 sites in comparison to the FDA-authorized BioFire Respiratory Panel 2.1. Three-quarters of specimens collected were tested on the Xpert Xpress CoV-2 <i>plus</i> in the point-of-care setting. Overall positive percent agreement (PPA) was 98.1% (95% CI: 96.7%-98.9%) and negative percent agreement (NPA) was 98.3% (97.7%-98.7%). Performance of the Xpert Xpress CoV-2 <i>plus</i> was slightly improved in NS compared to NPS specimens, with PPA of 99.3% versus 97.0% (Fisher's exact test, <i>P</i> = 0.06) and NPA of 98.3% versus 98.2% (<i>P</i> = 0.89), respectively. Assay PPA was similar between untrained and trained users (98.7% vs 97.3%, <i>P</i> = 0.75), while NPA was slightly improved for untrained users (99.0% vs 97.6%, <i>P</i> = 0.0003). This study showed that Cepheid Xpert Xpress COV-2 <i>plus</i> is highly sensitive and specific/has high PPA and NPA for detection of SARS-CoV-2 from both NS and NPS specimens.</p><p><strong>Importance: </strong>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to cause millions of infections and tens of thousands of deaths per year in the United States. While the FDA authorized hundreds of SARS-CoV-2 tests during the public health emergency, significantly fewer have made the transition to being cleared or approved. There continues to be a need for FDA-authorized point-of-care SARS-CoV-2 testing that can be performed by untrained users. We conducted a large prospective study of the Cepheid Xpert Xpress CoV-2 <i>plus</i> test for detection of SARS-CoV-2 in both nasal and nasopharyngeal swabs by trained and untrained users. The assay demonstrated excellent clinical performance characteristics and, as a result of this study, was cleared by the FDA.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0121924"},"PeriodicalIF":6.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142583239","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":"Serum antigen tests for the diagnosis of invasive aspergillosis: a retrospective comparison of five <i>Aspergillus</i> antigen assays and one beta-D-glucan assay.","authors":"Thilo Schub, Isabel Klugherz, Johannes Wagener, Juergen Prattes, Martin Hoenigl, Sebastian Suerbaum, Jürgen Held, Karl Dichtl","doi":"10.1128/jcm.00950-24","DOIUrl":"https://doi.org/10.1128/jcm.00950-24","url":null,"abstract":"<p><p>Invasive aspergillosis (IA) is a life-threatening infection. Early and specific diagnosis is pivotal to ensure adequate therapy. Antigen testing from blood is a widespread and convenient diagnostic approach. Various tests for the detection of <i>Aspergillus</i> antigen as well as for the panfungal antigen β-1,3-D-glucan (BDG) are available, for which comprehensive comparisons are still lacking. Blood samples of 82 proven/probable (11/71) IA patients and 52 controls were tested using two enzyme-linked immunosorbent assays (ELISAs) (Bio-Rad and Euroimmun), one chemiluminescent immunoassay (CLIA) (Vircell), one BDG assay (Fujifilm Wako), and two point of care (PoC) assays (Immy sōna and OLM). PoC assays were evaluated visually and used automated read out systems. Of the 82 IA patients, 37 had received solid organ transplantation (SOT) and 25 hematopoietic stem cell transplant (HSCT). Sensitivities and specificities for the eight test systems ranged from 27% to 71% and from 64% to 100%. Estimating a 10% prevalence of IA, test performance would have resulted in positive and negative predictive values of 14%-100% and 91%-95%. Areas under the curve (AUCs) for all tests except GM were below 0.7. When the cut-off values for quantitative tests were normalized to a specificity close to 95%, sensitivities ranged from 14% to 40%. The use of automated read out systems for the PoC assays had a significant impact. Combining different tests did not result in better test strategies. Sensitivity of <i>Aspergillus</i> antigen testing from single serum samples is low. Due to specificity issues, the majority of tests is not suited for screening purposes. The different assays can meet different needs in different diagnostic settings.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0095024"},"PeriodicalIF":6.1,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567528","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":"Update on novel validly published and included bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2023.","authors":"Arianna Carella, Karen C Carroll, Erik Munson","doi":"10.1128/jcm.01004-24","DOIUrl":"https://doi.org/10.1128/jcm.01004-24","url":null,"abstract":"<p><p>Taxonomy is a systematic practice in which microorganisms are granted names to facilitate and standardize multi-disciplinary communication. We summarize novel bacterial taxa derived from human clinical material that were published in peer-reviewed literature and/or included by the <i>International Journal of Systematic and Evolutionary Microbiology</i> during calendar year 2023, as well as taxonomic revisions that have been published/included by the same entity. While the majority of newly discovered facultative and anaerobic organisms were derived from microbiome surveillance, noteworthy novel taxa in the realm of pathogenicity potential include those related to <i>Aerococcus</i> spp., several <i>Corynebacterium</i> spp., <i>Exercitatus varius</i> gen. nov., sp. nov., and <i>Mycoplasma phocimorsus</i> sp. nov. With respect to nomenclature revision, the <i>Bacillus</i> and <i>Clostridium</i> genera continue to be visited annually. Creation of novel anaerobic Gram-negative bacillus genera <i>Hallella</i>, <i>Hoylesella</i>, <i>Leyella</i>, <i>Segatella</i>, and <i>Xylanibacter</i> impacted several <i>Bacteroides</i> spp. and <i>Prevotella</i> spp. Additional studies are necessary to ascertain the clinical significance of several of these microbes.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0100424"},"PeriodicalIF":6.1,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567717","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}