Journal of Clinical Microbiology最新文献

{"title":"Detection of ESBL-producing <i>Klebsiella oxytoca</i> complex with VITEK 2 system and screening cutoffs for implementing confirmatory tests.","authors":"Edgar I Campos-Madueno, Gisele Peirano, Claudia Aldeia, Maria V Elzi, Claudine Kocher, Laurent Poirel, Patrice Nordmann, Vincent Perreten, Johann D D Pitout, Andrea Endimiani","doi":"10.1128/jcm.00128-25","DOIUrl":"10.1128/jcm.00128-25","url":null,"abstract":"<p><p><i>Klebsiella oxytoca</i> complex (<i>Ko</i>C) are important nosocomial pathogens that can be reservoirs of transmissible extended-spectrum β-lactamase (ESBL) genes. Therefore, it is essential for clinical microbiology laboratories to distinguish between <i>Ko</i>C producing ESBLs (ESBL-<i>Ko</i>C) and those hyperproducing the natural OXY-type β-lactamases (hOXY-<i>Ko</i>C). We investigated the abilities of VITEK 2 with and without using the Advanced Expert System (AES) to detect ESBL producers among 44 well-characterized <i>Ko</i>C strains (including 11 ESBL-<i>Ko</i>C and 21 hOXY-<i>Ko</i>C). VITEK 2/AES showed 100% sensitivity (Se) and 64.7% specificity (Sp), whereas the VITEK 2 coupled by the Clinical Laboratory Standards Institute (CLSI) ESBL confirmatory tests (ESBL-CTs; i.e., disk-combination tests) showed 100% Se and 97.5% Sp to detect ESBL-<i>Ko</i>C. We also analyzed <i>Ko</i>C-specific screening cutoffs for ceftriaxone (CRO), cefpodoxime (CPD), ceftazidime (CAZ), cefotaxime (CTX), and aztreonam (ATM) to negate unnecessary ESBL-CTs. As a result, we propose the following screening cutoffs (minimum inhibitory concentration [MIC] and inhibition zone diameter): CRO, >4 µg/mL and ≤16 mm; CPD, >4 µg/mL and ≤10 mm; CAZ, >1 µg/mL and ≤22 mm (European Committee on Antimicrobial Susceptibility Testing [EUCAST] disk)/≤30 mm (CLSI disk); CTX, >4 µg/mL and ≤12 mm (EUCAST disk)/≤22 mm (CLSI disk); ATM, >1 µg/mL and ≤28 mm. Notably, all suggested cutoffs could assure 100% Se and high Sp/positive predictive values for our 44 <i>Ko</i>C strains. In conclusion, the AES performed poorly, while VITEK 2 with the CLSI ESBL-CTs yielded a reliable methodology to distinguish ESBL-<i>Ko</i>C from hOXY-<i>Ko</i>C. This study also proposed revised screening cutoffs for detecting ESBL-<i>Ko</i>C and reducing the unnecessary use of ESBL-CTs.IMPORTANCESpecies within the <i>Klebsiella oxytoca</i> complex (<i>Ko</i>C) are emerging clinical pathogens of increasing concern. These bacteria can acquire plasmid-mediated ESBL genes, seriously complicating antibiotic treatment and overall management of infected patients. Differentiating ESBL-producing from non-ESBL-producing <i>Ko</i>C isolates is therefore crucial. However, this task presents significant challenges for clinical laboratories. In this work, we showed that the automated VITEK 2 system equipped with its AES fails to differentiate the two groups of <i>Ko</i>C isolates. In contrast, VITEK 2 alone followed by the ESBL screen and phenotypic confirmatory tests provides accurate differentiation. Since this latter approach increases the diagnostic workload, we also proposed new screening cutoffs for key cephalosporins that may reduce the current high number of unnecessary confirmatory tests.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0012825"},"PeriodicalIF":6.1,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153293/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143993882","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":"<i>In vitro</i> activity of isavuconazole, ravuconazole, and comparison of the Sensititre YeastOne and CLSI broth microdilution methods against clinical isolates of <i>Trichosporon</i> species.","authors":"Shih-Hao Lo, Yi-Ting Tseng, Yee-Chun Chen, Mao-Wang Ho, Chen-Hsiang Lee, Po-Liang Lu, Shang-Yi Lin","doi":"10.1128/jcm.00319-25","DOIUrl":"10.1128/jcm.00319-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;This study aimed to evaluate the &lt;i&gt;in vitro&lt;/i&gt; activity of isavuconazole and ravuconazole against clinical &lt;i&gt;Trichosporon&lt;/i&gt; isolates. Additionally, we assessed the performance of the Sensititre YeastOne (SYO) assay compared to the reference Clinical and Laboratory Standards Institute (CLSI) broth microdilution (BMD) method for antifungal susceptibility testing. A total of 267 &lt;i&gt;Trichosporon&lt;/i&gt; clinical isolates were collected from multiple centers in Taiwan between 2008 and 2020. The MIC values for amphotericin B, fluconazole, itraconazole, posaconazole, and voriconazole obtained using the CLSI BMD were compared to those determined using SYO. Among the seven antifungal agents tested using the CLSI BMD method, &lt;i&gt;T. asahii&lt;/i&gt; isolates (&lt;i&gt;n&lt;/i&gt; = 224) exhibited significantly higher MICs for fluconazole, voriconazole, isavuconazole, and ravuconazole compared to non-&lt;i&gt;T&lt;/i&gt;. &lt;i&gt;asahii&lt;/i&gt; isolates (&lt;i&gt;n&lt;/i&gt; = 43) (&lt;i&gt;p&lt;/i&gt; &lt; 0.05). Across all isolates, voriconazole demonstrated the lowest geometric mean (GM) MIC (0.06 mg/L). For &lt;i&gt;T. asahii&lt;/i&gt;, the MIC₅₀, MIC₉₀, and GM MICs for posaconazole, isavuconazole, and ravuconazole were within ±1 twofold dilution, while mode MICs showed slightly greater variation (MIC₅₀, MIC₉₀, mode, and GM MICs were 0.25, 0.5, 0.5, and 0.28 mg/L; 0.12, 0.5, 0.12, and 0.17 mg/L; and 0.25, 0.5, 0.25, and 0.21 mg/L, respectively). The consistency of the MIC measurements between the SYO and CLSI BMD methods was assessed for amphotericin B, fluconazole, itraconazole, posaconazole, and voriconazole. The highest agreement within ±1 twofold dilution for &lt;i&gt;T. asahii&lt;/i&gt; isolates was observed for posaconazole (94.2%). The essential agreement within ±2 twofold dilutions between both methods for all drugs was &gt;97%. In conclusion, isavuconazole and ravuconazole demonstrated favorable &lt;i&gt;in vitro&lt;/i&gt; activity against clinical &lt;i&gt;Trichosporon&lt;/i&gt; isolates, while the SYO assay showed good concordance with the CLSI BMD method.IMPORTANCEInvasive infections caused by &lt;i&gt;Trichosporon&lt;/i&gt; species pose significant therapeutic challenges, primarily due to their intrinsic resistance to echinocandins and the limited availability of effective treatment options. This study provides essential data on the &lt;i&gt;in vitro&lt;/i&gt; activity of newer azoles and comprehensively evaluates the performance and concordance of the Sensititre YeastOne (SYO) and CLSI broth microdilution (BMD) methods. The current study analyzed 267 &lt;i&gt;Trichosporon&lt;/i&gt; clinical isolates collected from multicenter settings in Taiwan. Our results demonstrate that both isavuconazole and ravuconazole exhibit favorable &lt;i&gt;in vitro&lt;/i&gt; activities against &lt;i&gt;Trichosporon&lt;/i&gt; species. For &lt;i&gt;T. asahii&lt;/i&gt;, the essential agreement between the SYO and CLSI BMD methods exceeded 97% for all tested antifungal agents, indicating that the SYO method exhibits good concordance for most &lt;i&gt;Trichosporon&lt;/i&gt; species. Further investigations are warranted to validate these findings and to asse","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0031925"},"PeriodicalIF":6.1,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153333/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143973528","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":"REL/DPA/AVI method: a novel approach for rapid detection of carbapenemase-producing Enterobacterales directly from positive blood cultures based on optical density.","authors":"Chuwen Zhao, Junqi Zhu, Yanping Xiao, Fuxing Li, Yunwei Zheng, Shumin Gu, Yaping Hang, Qiaoshi Zhong, Longhua Hu","doi":"10.1128/jcm.01960-24","DOIUrl":"10.1128/jcm.01960-24","url":null,"abstract":"<p><p>The high mortality rate associated with carbapenem-resistant Enterobacterales (CRE), particularly for bloodstream infections (BSI), underscores the urgent need for early identification and differentiation of its resistance mechanisms. In China, traditional phenotypic detection methods for carbapenemases, including the modified Carbapenem Inactivation Method (mCIM), EDTA Carbapenemase Inactivation Method (eCIM), and the carbapenemase inhibitor 3-aminophenylboronic acid (APB) and EDTA enhancement method (APB-EDTA method), are widely used; however, they are time consuming. The relebactam, dipicolinic acid, and avibactam sodium (REL/DPA/AVI) method is a novel phenotypic test for carbapenemase targeting to address these challenges. This method exploits the growth status differences of enzyme-producing bacteria under the combined action of imipenem and enzyme inhibitors (REL, DPA, and AVI) to identify Class A, B, and D carbapenemases at an early stage through optical density (OD) measurements. The REL/DPA/AVI method was optimized and evaluated using 213 contrived (seeded) blood cultures and compared to mCIM/eCIM and APB-EDTA methods. The REL/DPA/AVI method achieved results within 1.5 h (OD measurement) or 2 h (visual observation or OD measurement) from blood culture positivity. Sensitivities of detection of class A, B, D, and A + B carbapenemases at 1.5 h were 97.56% (40/41), 100% (82/82), 71.43% (5/7), and 100% (7/7), respectively. After 2 h, the sensitivity for detecting class D carbapenemases increased to 85.71% (6/7). Conversely, the sensitivities of mCIM/eCIM were 95.83% (46/48) and 97.56% (80/82) for serine β-lactamases and metallo-β-lactamases, respectively. However, the APB-EDTA method demonstrated a sensitivity of 95.1% (39/41), 87.8% (72/82), and 71.43% (5/7) for classes A, B, and A + B carbapenemases, respectively.</p><p><strong>Importance: </strong>The relebactam, dipicolinic acid, and avibactam sodium (REL/DPA/AVI) method has demonstrated significant success in identifying and differentiating carbapenemase-producing Enterobacterales (CPE) from positive blood cultures, exhibiting superior performance compared with existing technologies. Although numerous advanced technologies such as mNGS, Filmarray, Verigene, and NG-Test CARBA 5 DetecTool have been developed for carbapenemase typing of CPE in positive blood cultures, our method is distinguished by a significant economic advantage, with a cost of less than $1 USD per test. This substantial cost-effectiveness underscores the immense potential for widespread clinical applications.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0196024"},"PeriodicalIF":6.1,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153349/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143995049","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":"Alternative treponemal serology assays for diagnosis and confirmation of syphilis in a diagnostic laboratory: a retrospective evaluation of four agglutination assays and one ELISA.","authors":"Eloise Williams, Theo Karapanagiotidis, Suellen Nicholson, Helen Toma, Kim Lynn Vo, Celia Douros, Francesca Azzato, Peta Edler, Maryza Graham, Janet M Towns, Marcus Y Chen, Chuan K Lim, Deborah A Williamson","doi":"10.1128/jcm.01768-24","DOIUrl":"10.1128/jcm.01768-24","url":null,"abstract":"<p><p>The <i>Treponema pallidum</i> particle agglutination (TPPA) assay is no longer available in some settings. Here, we report the results of a clinical laboratory evaluation of alternative treponemal assays, including three <i>T. pallidum</i> hemagglutination assays (TPHAs), a <i>T. pallidum</i> IgG enzyme-linked immunosorbent assay (ELISA), and a detailed laboratory evaluation of the only TPHA with Australian regulatory approval. The clinical laboratory evaluation comprised 300 sera (120 TPPA reactive and 180 TPPA non-reactive) collected from individuals ≥18 years between 1 June 2021 and 1 June 2023. Median age was 33, 92% were from a sexually transmitted infection clinic, 71% were male, 15.3% were living with HIV and 5% were pregnant. Twenty-four percent had active untreated syphilis, 25% had prior treated syphilis, and 50.7% had no syphilis. Compared to TPPA, positive percent agreement (PPA) was 99.2% (95% confidence interval [CI], 95.4-99.9%), 100% (95% CI, 96.9-100%), 99.2% (95% CI, 95.4-99.9%), and 93.3% (95% CI, 87.4-96.6%), respectively, for the Arlington, Fortress, and Randox TPHAs, and Euroimmun IgG ELISA. Negative percent agreement (NPA) was 97.8% (95% CI, 94.4-99.1%) for each TPHA and 98.9% (95% CI, 96.0-99.8%) for the Euroimmun IgG ELISA. Clinical sensitivity of the Arlington and Fortress TPHAs for active untreated syphilis infection was equivalent to TPPA at 97.2% (95% CI, 90.4-99.5%) and clinical specificity of these assays was 99.3% (95% CI, 96.3-100%). In the evaluation of the NewBio TPHA, comprising 322 clinical serum and plasma samples and 22 quality assurance panel samples; overall PPA compared to TPPA was 100% (95% CI, 97.5-100%) and NPA 98.9% (95% CI, 94.1-98.9%). TPHAs are an acceptable alternative for confirmatory treponemal serology.IMPORTANCERates of syphilis, including congenital syphilis, are increasing globally, resulting in substantial morbidity and neonatal mortality. A key pillar of syphilis control is timely and accurate diagnosis. Serology is the primary diagnostic test for syphilis. Serological testing for syphilis has been impacted by a withdrawal of the <i>Treponema pallidum</i> particle agglutination (TPPA) assay from several geographical regions, including Australia and Europe. Here, we describe the clinical and laboratory performance of alternative treponemal serological assays, with a focus on alternative agglutination assays (<i>Treponema pallidum</i> hemagglutination assays, TPHAs) as these assays comprise alternative antigens to commercial treponemal immunoassays, require a small volume of sample input and do not require specific instrumentation. This study demonstrates that TPHAs have excellent clinical and analytical performance characteristics and provides confidence that these assays are an acceptable alternative in settings that no longer have access to the TPPA.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0176824"},"PeriodicalIF":6.1,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153291/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144002498","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":"Defining antimicrobial susceptibility testing methods and breakpoints among <i>Achromobacter</i> species.","authors":"Harley Harris, Haley Stambaugh, Emily Jacobs, Amira Bhalodi, Sukantha Chandrasekaran, Nicolynn C Cole, Jennifer Lu, Tsigereda Tekle, Romney Humphries, Patricia J Simner","doi":"10.1128/jcm.00264-25","DOIUrl":"10.1128/jcm.00264-25","url":null,"abstract":"<p><p><i>Achromobacter</i> species can cause opportunistic infections which are difficult to treat due to a variety of antimicrobial resistance (AMR) mechanisms. As such, antimicrobial susceptibility testing (AST) is a cornerstone to successful treatment for these organisms. Currently, there are no specific Clinical and Laboratory Standards Institute (CLSI) AST guidelines for <i>Achromobacter</i> species. The purpose of this study was to (i) establish tentative CLSI M45 MIC and disk diffusion (DD) breakpoints (BPs), (ii) evaluate the modified carbapenem inactivation method (mCIM), and (iii) understand the mechanisms mediating AMR among <i>Achromobacter</i> species. Contemporary MIC data from multiple sources were collated to define the tentative epidemiological cutoff values (tECVs), and the MIC distributions were used to inform the establishment of MIC BPs for various agents. A disk-to-MIC correlate study with 91 isolates from across the United States was completed by testing reference broth microdilution and DD from the same inoculum and applying the dBETS software to establish DD BPs. Lastly, the mCIM and whole-genome sequencing (WGS) were pursued. The tECVs for piperacillin-tazobactam, imipenem, and meropenem were 1, 2, and 0.5 µg/mL, respectively. Disk correlates met CLSI M23 acceptance criteria with a few exceptions related to a small number of isolates, resulting in high minor errors. WGS revealed that 82 (90.1%) isolates harbored a <i>bla</i>_OXA variant with <i>bla</i>_OXA-114 predominating (90.2%). Nineteen isolates harbored acquired beta-lactamase genes, including 16 <i>bla</i>_AXC, 2 <i>bla</i>_VIM-4, and 1 <i>bla</i>_AZM-1. The mCIM had a sensitivity of 100% and specificity of 87%. Upon review, the CLSI M45 committee set tentative MIC and DD BPs for piperacillin-tazobactam, imipenem, meropenem, and trimethoprim-sulfamethoxazole.IMPORTANCE<i>Achromobacter</i> species can cause opportunistic infections which may be difficult to treat due to a variety of antimicrobial resistance mechanisms. Antimicrobial susceptibility testing is a critical component of patient treatment for these infections. Currently, the Clinical and Laboratory Standards Institute M100 non-Enterobacterales susceptibility test interpretive criteria and methodology are utilized for <i>Achromobacter</i> by clinical laboratories and likely do not accurately predict susceptibility results for <i>Achromobacter</i> species. This study was designed to establish tentative MIC and disk diffusion breakpoints specific to <i>Achromobacter</i> species.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0026425"},"PeriodicalIF":6.1,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153331/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020876","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":"Development and validation of a blocking ELISA for measurement of rabies virus neutralizing antibody.","authors":"Yuewen Xiao, Meng Wu, Weidi Xu, Sheng Sun, Tingfang Liu, Yan Liu, Hongwei Li, Na Feng, Changchun Tu, Ye Feng","doi":"10.1128/jcm.02049-24","DOIUrl":"10.1128/jcm.02049-24","url":null,"abstract":"<p><p>Enzyme-linked immunosorbent assay (ELISA) is an effective approach for monitoring herd immunity of animals against rabies but not recommended to detect neutralizing antibody response of individual animals in the framework of international travel since its insufficient agreement with the globally recognized rabies virus (RABV) neutralizing tests. In this study, a blocking ELISA to specifically detect anti-RABV neutralizing antibody was developed using the purified RABV glycoprotein (G) expressed in HEK293T cells as coating antigen, and a labeled anti-G neutralizing monoclonal antibody as the blocking antibody. The overall agreement between the blocking ELISA and fluorescent antibody virus neutralization test in detection of clinical serum samples (dogs = 658; cats = 508) was 97.43% (1,136/1,166), with a diagnostic specificity of 95.63% (219/229) and a diagnostic sensitivity of 97.87% (917/937). Further comparison with the commercial ELISA kits and inter-laboratory validation showed that the blocking ELISA had excellent specificity, sensitivity, and reproducibility. In conclusion, the developed method is a potential tool as an alternative to the virus neutralization test for the detection of canine and feline rabies neutralization antibodies following vaccination.IMPORTANCEThis study establishes a blocking enzyme-linked immunosorbent assay (ELISA) for detecting rabies neutralizing antibodies in dogs and cats, demonstrating high sensitivity, specificity, and no cross-reactivity. This method provides a reliable alternative to conventional neutralization assays, facilitating efficient large-scale rabies vaccination assessment, and thereby strengthening global rabies control efforts.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0204924"},"PeriodicalIF":6.1,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153311/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020879","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":"Assessing the sequencing success and analytical specificity of a targeted amplicon deep sequencing workflow for genotyping the foodborne parasite <i>Cyclospora</i>.","authors":"Anna C Peterson, David Jacobson, Travis Richins, Joel Barratt, Yvonne Qvarnstrom","doi":"10.1128/jcm.01811-24","DOIUrl":"10.1128/jcm.01811-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Epidemiological investigations of the foodborne parasitic illness cyclosporiasis can be aided by molecular techniques that enable the identification of genetically related clusters of &lt;i&gt;Cyclospora&lt;/i&gt; isolates. At the Centers for Disease Control and Prevention (CDC), routine &lt;i&gt;Cyclospora&lt;/i&gt; genotyping for the purpose of informing epidemiological outbreak investigations has occurred since 2018 using clinical stool specimens from case patients diagnosed with cyclosporiasis. This approach involves targeted amplicon deep sequencing of eight genotyping markers, followed by bioinformatic processing through a custom clustering algorithm. However, not all stool specimens submitted to the CDC for genotyping successfully amplify for at least five of the eight genotyping markers, the minimum required to be bioinformatically processed through the clustering algorithm. In this study, we utilized information from clinical stool specimens sent to the CDC from the years 2019 to 2023 to assess if the type of preservative, the age of the specimen, or the method used to diagnose the patient influenced the probability of successfully genotyping parasites from a fecal specimen. Additionally, we assessed the analytical specificity of the &lt;i&gt;Cyclospora&lt;/i&gt; genotyping workflow by analyzing samples positive for other intestinal parasites, including closely related non-human infecting &lt;i&gt;Cyclospora&lt;/i&gt; species and other coccidia. We found that stool specimens stored in preservatives had a greater likelihood of sequencing success over time relative to specimens without preservatives or those stored in non-nutritive transport media. Additionally, stool specimens from case patients diagnosed via microscopy-based methods were more likely to yield DNA of sufficient quality and quantity for genotyping compared to PCR or multiplex panels. Lastly, we determined that the genotyping workflow has an analytical specificity of 100%, as no non-human-infecting &lt;i&gt;Cyclospora&lt;/i&gt; or other parasites yielded sequence data at &gt;1 of the genotyping markers. This knowledge will help strengthen the quality of &lt;i&gt;Cyclospora&lt;/i&gt; genotyping data produced in the future, improving the utility of this data for supporting epidemiological investigations.IMPORTANCEDetermining the genetic relatedness among parasites causing foodborne illness, such as &lt;i&gt;Cyclospora&lt;/i&gt;, is a valuable tool to complement outbreak investigations. However, this molecular genotyping approach is limited by the quality and quantity of genetic data obtained from the samples being investigated. In this study, we demonstrate that the storage conditions of clinical stool specimens are correlated to the quality of sequence data produced for &lt;i&gt;Cyclospora&lt;/i&gt; genotyping. Our insights can be used to guide storage recommendations for stool specimens, which can improve the quality of foodborne illness outbreak investigations conducted in the future. Additionally, we showed that the current &lt;i&gt;Cyclospora&lt;/i&gt; genotyping tool used b","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0181124"},"PeriodicalIF":6.1,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144021016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Brief Case: hidden intruders-serendipitous discovery of an infection after appendicitis surgery.","authors":"Nada Ben Halima, Brice Autier, Federica Attaianese, Maya Husain, Florence Robert-Gangneux, Estelle Sabourin, Nadia Guennouni, Eric Dannaoui, Marie-Elisabeth Bougnoux","doi":"10.1128/jcm.00193-25","DOIUrl":"10.1128/jcm.00193-25","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"63 6","pages":"e0019325"},"PeriodicalIF":6.1,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153299/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144266389","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":"Determination of the performance of a novel diagnostic test for <i>Clostridioides difficile</i> toxins A and B using latent class analysis.","authors":"Jeremy Li, Nandini Dendukuri, Yves Longtin, Alice Banz, Charles Frenette, Philippe Gervais, Mark A Miller, Anne-Marie Bourgault, Noah L Dawang, Vivian G Loo","doi":"10.1128/jcm.01807-24","DOIUrl":"10.1128/jcm.01807-24","url":null,"abstract":"<p><p>The diagnosis of <i>Clostridioides difficile</i> infection (CDI) remains challenging. Nucleic acid amplification tests (NAAT) targeting the <i>C. difficile</i> (CD) toxin B gene suffer from suboptimal specificity for CDI due to CD asymptomatic colonization. Enzyme immunoassays (EIAs) that detect the presence of CD toxins are more specific for CDI but suffer from low sensitivity. To address this challenge, assays detecting CD toxins were developed using single-molecule array (SIMOA) technology, which have much lower limits of toxin detection than conventional EIAs. In this study, stool specimens from 708 symptomatic patients were aliquoted for testing by cell cytotoxicity neutralization assay (CCNA), toxigenic culture, NAAT, conventional CD toxin EIA, and SIMOA CD toxin EIAs. Using latent class analysis, we calculated the sensitivity and specificity of each of these diagnostic tests for detecting, separately, the presence of CD bacterium, CD toxin gene, and CD toxin. We estimated that the prevalence of CDI in our cohort was 14% (95% credible interval [CI]: 0.11-0.17). While the specificity of NAAT for detecting the presence of CD toxin was 95% (95% CI: 0.94-0.97), its positive predictive value was poor due to the low prevalence of CDI. The specificity of the conventional CD toxin EIA for CDI was excellent, but the sensitivity was only 48% (95% CI: 0.41-0.55). In comparison, the sensitivities of the SIMOA toxins A and B EIAs were 76% (95% CI: 0.67-0.84) and 77% (95% CI: 0.67-0.84), respectively, while maintaining excellent specificity. We conclude that SIMOA CD toxin EIAs are significantly more sensitive than conventional CD toxin EIAs.</p><p><strong>Importance: </strong><i>Clostridioides difficile</i> infection (CDI) is the most important infectious cause of hospital-associated diarrhea worldwide, but its diagnosis remains challenging. Nucleic acid amplification tests (NAATs) targeting the <i>C. difficile</i> (CD) toxin B gene have suboptimal specificity due to the presence of CD asymptomatic colonization, while enzyme immunoassays (EIAs) that detect the toxin itself are much more specific but are limited by low sensitivity. New assays for detecting CD toxins were developed using single-molecule array (SIMOA) technology, which have much lower limits of toxin detection than conventional EIAs, potentially improving the sensitivity of these conventional EIAs while remaining highly specific. In this study, we use latent class analysis to evaluate the sensitivity and specificity of different diagnostic tests for CD, including the novel SIMOA toxin assays, in detecting the different CD targets: the presence of CD bacterium, the presence of CD toxin gene, and the presence of CD toxin.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0180724"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752951","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":"Reaffirming DEI as a central value of JCM.","authors":"Romney M Humphries, Alexander J McAdam","doi":"10.1128/jcm.00372-25","DOIUrl":"10.1128/jcm.00372-25","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0037225"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077182/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752966","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}