Journal of Clinical Microbiology最新文献

{"title":"<i>Lactobacillus delbrueckii</i> subsp. <i>allosunkii</i> and <i>lactis</i> as emerging human uropathogens in elderly patients.","authors":"François Guérin, Mohamed Sassi, Francois Gravey, Asma Zouari, Benjamin Quenet, Maxime Lecourt, Pauline Ract, Charlotte Michaux, Michel Auzou, Christophe Isnard, Vincent Cattoir","doi":"10.1128/jcm.02072-24","DOIUrl":"10.1128/jcm.02072-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Lactobacillus delbrueckii&lt;/i&gt; has been considered a very rare cause of human urinary tract infections (UTIs). However, little is known about its clinical significance and antimicrobial susceptibility, and genomic data from clinical isolates are lacking. This study aimed at analyzing clinical, microbiological, and genomic data of &lt;i&gt;L. delbrueckii&lt;/i&gt; urinary isolates. All &lt;i&gt;L. delbrueckii&lt;/i&gt; isolates collected from patients hospitalized in a French university hospital from 2014 to 2016 were included. Clinical and biological data were gathered. Species identification was performed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, and MICs were determined using the broth microdilution method. Whole genome sequencing (WGS) was conducted (Illumina MiSeq 2 × 300 bp), and genomes were compared using three approaches (multilocus sequence typing [MLST], average nucleotide identity [ANI], and core genome single nucleotide polymorphism [SNP]). From 2014 to 2016, 48 isolates of &lt;i&gt;L. delbrueckii&lt;/i&gt; were recovered from the urine of 48 patients (mean age = 84 years; sex ratio M/F = 0.04). Nearly half (44%) of patients were diagnosed with a UTI, and all had significant cultures (≥10&lt;sup&gt;5&lt;/sup&gt; CFU/mL) with a positive direct examination in &gt;90% of cases. The majority of isolates were susceptible to most antibiotics (especially β-lactams), whereas they seemed intrinsically resistant to fosfomycin and metronidazole. Subspecies identification was consistent across the three approaches, showing that most &lt;i&gt;L. delbrueckii&lt;/i&gt; isolates belonged to subspecies &lt;i&gt;allosunkii&lt;/i&gt; (&lt;i&gt;n&lt;/i&gt; = 40; 83%), followed by subspecies &lt;i&gt;lactis&lt;/i&gt; (&lt;i&gt;n&lt;/i&gt; = 8; 17%). Two isolates were resistant to tetracycline (MIC &gt;16 mg/L) and both harbored the &lt;i&gt;tet&lt;/i&gt;(W) gene. This study demonstrates the uropathogenic role of &lt;i&gt;L. delbruekii&lt;/i&gt; subspecies &lt;i&gt;allosunkii&lt;/i&gt; and &lt;i&gt;lactis&lt;/i&gt;, particularly in elderly female patients.IMPORTANCEThis largest case series of urinary tract infections (UTIs) caused by &lt;i&gt;Lactobacillus delbrueckii&lt;/i&gt; clearly demonstrates the uropathogenic role of this species (especially the subspecies &lt;i&gt;allosunkii&lt;/i&gt;) in human UTIs, particularly in elderly female patients and those with underlying comorbidities. This study may change practice in two ways: (i) clinical laboratories, which typically consider lactobacilli from urine samples as contaminants, may need to reassess this practice; (ii) patient care can be improved by prescribing appropriate antibiotics for these underdiagnosed UTIs. &lt;i&gt;L. delbrueckii&lt;/i&gt; should be considered an actual pathogen when it is significantly found in the urine of predisposed patients with clinical and/or biological signs of infection. While matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry allows reliable identification of &lt;i&gt;L. delbrueckii&lt;/i&gt;, there is also a need for better discrimination between subspecies (especially &lt;i&gt;allosu","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"63 5","pages":"e0207224"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077209/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144026943","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":"Accuracy of real-time PCR assays for human papillomavirus using urine samples: a systematic review and meta-analysis.","authors":"Byeong-Min Park, Soohyun Kim, Jieun Choi, Yoonkyung Song, Seungman Park","doi":"10.1128/jcm.01352-24","DOIUrl":"10.1128/jcm.01352-24","url":null,"abstract":"<p><p>This study aims to assess the diagnostic accuracy of real-time PCR assays for detecting human papillomavirus (HPV) in urine samples through a systematic review and meta-analysis. A comprehensive search of PubMed, Embase, and Springer databases (2014-2024) was conducted. Studies comparing urine-based HPV tests with cervical samples as the reference standard were included. Diagnostic accuracy measures such as sensitivity, specificity, diagnostic odds ratio (DOR), likelihood ratios (LR+ and LR-), percent agreement, and Cohen's kappa were calculated. Heterogeneity was assessed using the Higgins' I² index, and subgroup analyses were performed based on HPV test type and urine volume. The study revealed that 15 studies met the inclusion criteria, with pooled sensitivity of urine-based HPV tests at 0.82 (95% CI, 0.78-0.86), specificity at 0.91 (95% CI, 0.87-0.94), positive LR at 9.5 (95% CI, 6.3-14.3), negative LR at 0.19 (95% CI, 0.16-0.24), DOR at 49 (95% CI, 32-75), and the area under the curve at 0.92 (95% CI, 0.90-0.94), with significant heterogeneity observed (I² >50%), particularly in sensitivity and specificity, and subgroup analysis indicating that urine volumes ≤20 mL demonstrated higher sensitivity compared to those >20 mL, despite this finding being based on a limited number of studies. Results suggest that urine-based HPV testing shows strong diagnostic accuracy and could be a viable alternative to cervical swabs, with potential benefits for increasing screening accessibility, especially in areas with limited healthcare resources, despite some variability and limitations in the data.IMPORTANCEThis study is significant as it thoroughly evaluates the diagnostic accuracy of real-time PCR assays for human papillomavirus (HPV) detection in urine samples through a rigorous systematic review and meta-analysis. By integrating data from multiple databases and comparing urine-based HPV tests with the established cervical sample reference standard, the study provides valuable insights into the effectiveness and reliability of non-invasive HPV screening methods. The findings demonstrate that urine-based tests exhibit high sensitivity and specificity, offering a promising alternative to traditional cervical swabs. This advancement has significant implications for increasing accessibility to HPV screening, particularly in under-resourced settings, thereby potentially enhancing cervical cancer prevention efforts on a broader scale. The study not only fills a critical gap in HPV screening methodologies but also supports the development of more inclusive and practical public health strategies for combating cervical cancer.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0135224"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077123/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752949","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":"Establishment of epidemiological cutoff values for <i>Fonsecaea pedrosoi</i>, the primary etiologic agent of chromoblastomycosis, and eight antifungal medications.","authors":"Dallas J Smith, Marcia S C Melhem, Jessy Dirven, Conceição Maria Pedrozo E Silva de Azevedo, Sirlei Garcia Marques, Bruna Jacomel Favoreto de Souza Lima, Vania Aparecida Vicente, Maria da Glória Teixeira Sousa, James Venturini, Nathan P Wiederhold, Amir Seyedmousavi, Philippe J Dufresne, Sybren de Hoog, Shawn R Lockhart, Ferry Hagen, Daniel Wagner de C L Santos","doi":"10.1128/jcm.01903-24","DOIUrl":"10.1128/jcm.01903-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Chromoblastomycosis, a fungal neglected tropical disease, is acquired through traumatic inoculation and is clinically characterized by a chronic granulomatous infection of the skin and subcutaneous tissue. &lt;i&gt;Fonsecaea pedrosoi&lt;/i&gt; is the most commonly reported etiologic agent globally. Itraconazole is considered first-line therapy, but successful treatment with terbinafine, voriconazole, and posaconazole has been reported. &lt;i&gt;F. pedrosoi&lt;/i&gt; minimum inhibitory concentration (MIC) data are limited, and epidemiological cutoffs (ECVs) are lacking; such data are important to help monitor antifungal resistance trends and guide initial antifungal selection. Thus, we performed antifungal susceptibility testing (AFST) on &lt;i&gt;F. pedrosoi&lt;/i&gt; isolates and determined the MIC distributions and ECVs. AFST on &lt;i&gt;Fonsecaea pedrosoi&lt;/i&gt; isolates was conducted at six laboratories from October 2023 to June 2024. Species identification was previously confirmed by DNA sequence analysis. AFST was performed by CLSI M38 standard broth microdilution method for itraconazole, voriconazole, posaconazole, isavuconazole, ketoconazole, terbinafine, flucytosine, and amphotericin B. The ECVs were established using the iterative statistical method with ECOFFinder (version 2.1) following CLSI M57 guidelines. We analyzed MIC results from 148 &lt;i&gt;Fonsecaea pedrosoi&lt;/i&gt; isolates. The calculated ECVs were itraconazole, 0.5 µg/mL; voriconazole, 0.5 µg/mL; posaconazole, 0.5 µg/mL; isavuconazole, 1 µg/mL; ketoconazole, bimodal, no ECV determined; terbinafine, 0.25 µg/mL; flucytosine, rejected; and amphotericin, 8 µg/mL. These &lt;i&gt;Fonsecaea pedrosoi&lt;/i&gt; ECVs, obtained through a multicenter international effort, provide a baseline to better understand the &lt;i&gt;in vitro&lt;/i&gt; antifungal susceptibility profile of this species and monitor resistance. Clinicians and researchers can use these values to detect non-wild-type isolates with reduced susceptibility, reevaluate therapeutic options, and investigate potential clinical resistance if treatment failure occurs.IMPORTANCEChromoblastomycosis is a neglected tropical disease caused by an environmental, dematiaceous fungus. This fungal disease is acquired after a break in the skin that allows the fungus to enter, leading to a chronic infection in the skin and subcutaneous tissue. It is difficult to treat and often requires years of antifungal treatment. &lt;i&gt;Fonsecaea pedrosoi&lt;/i&gt; is the most reported causative agent globally. Limited antifungal susceptibility data exist for &lt;i&gt;F. pedrosoi&lt;/i&gt; making interpreting minimum inhibitory concentration (MIC) results difficult. We performed antifungal susceptibility testing on 148 &lt;i&gt;F&lt;/i&gt;. &lt;i&gt;pedrosoi&lt;/i&gt; isolates to establish MIC distributions and epidemiologic cutoff values (ECVs) for eight antifungals, including those commonly used to treat chromoblastomycosis. The calculated ECVs for the commonly used antifungals itraconazole and terbinafine were 0.5 and 0.25 µg/mL, respectively. ECVs can be helpful","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0190324"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077196/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143780150","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":"Rapid prediction of carbapenemases in <i>Pseudomonas aeruginosa</i> by imipenem/relebactam and MALDI-TOF MS.","authors":"Ana Candela, María Fernández-Billón, Pablo Aja-Macaya, Lucía González-Pinto, Pablo Arturo Fraile-Ribot, Esther Viedma, Isaac Alonso-García, Tania Blanco-Martín, Roberto Estévez-Alfaya, Ana Fernández-González, Alejandro Beceiro, Carla López-Causapé, Marina Oviaño, Germán Bou, Antonio Oliver, Jorge Arca-Suárez","doi":"10.1128/jcm.01105-24","DOIUrl":"10.1128/jcm.01105-24","url":null,"abstract":"<p><p><i>Pseudomonas aeruginosa</i> is a major nosocomial pathogen commonly involved in multidrug-resistant (MDR) infections that are very difficult to treat. Imipenem/relebactam is a new carbapenem/β-lactamase inhibitor combination with robust activity against <i>P. aeruginosa</i>. However, resistance is increasingly reported, and rapid detection is, therefore, crucial so that appropriate treatments can be prescribed. We have developed a rapid MALDI TOF-MS-based method that can accurately predict the presence of carbapenemases in <i>P. aeruginosa</i> using imipenem/relebactam. The method was developed using a retrospective and a prospective collection of 419 <i>P</i>. <i>aeruginosa</i> isolates (including recombinant isolates and WGS-characterized clinical strains) encompassing the most important β-lactam resistance mechanisms. The MALDI TOF-MS method is based on the detection of the hydrolysis of imipenem in the presence or absence of relebactam, measuring modifications in the mass spectra of imipenem after incubation with bacteria. The method was evaluated against a retrospective collection and then validated against 250 prospectively collected clinical isolates, showing a 98% (246/250) agreement between the phenotype and the MALDI-TOF MS hydrolysis result and a 100% accordance with the β-lactam resistance genotype. Some errors in detecting GES-producing isolates and in detecting different mutational resistance mechanisms associated with imipenem/relebactam resistance (MICs ranging from 4 to 8 mg/L) were observed. All results were obtained within 1 hour, positioning the MALDI-TOF-based test as a rapid and easy-to-perform method for detection of carbapenemases (except GES enzymes) in <i>P. aeruginosa</i>. Besides, implementation of the method in routine laboratory screening would facilitate the correct use of imipenem/relebactam to treat <i>P. aeruginosa</i> infections.IMPORTANCEWhile several rapid diagnostic methods have been developed for the detection of ESBLs and carbapenemases to improve treatment decision-making in Enterobacterales, there is a lack of approaches to rapidly identify resistance mechanisms and predict β-lactam susceptibility in <i>Pseudomonas aeruginosa</i>. Taking advantage of the mechanism of action and the high efficacy of the newly developed β-lactam/β-lactamase inhibitor combination imipenem/relebactam against <i>P. aeruginosa</i>, we developed a WGS-guided, MALDI-TOF-based algorithm that accurately predicts the presence of carbapenemase enzymes in this bacterium and aids in forecasting the imipenem/relebactam susceptibility profile. The implementation of this method in routine laboratory testing would provide significant support in the rapid decision-making for the use of imipenem/relebactam in severe <i>P. aeruginosa</i> infections.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0110524"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077086/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700645","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":"Identification and characteristics of mutations promoting occult HBV infection by ultrasensitive HBsAg assay.","authors":"Shi Song, Qian Su, Ying Yan, Huimin Ji, Huizhen Sun, Kaihao Feng, Abudulimutailipu Nuermaimaiti, Shana Halemubieke, Ling Mei, Xinru Liu, Zhuoqun Lu, Le Chang, Lunan Wang","doi":"10.1128/jcm.02071-24","DOIUrl":"10.1128/jcm.02071-24","url":null,"abstract":"<p><p>The significance of occult hepatitis B virus (HBV) infection (OBI) has been increasingly recognized while the underlying mechanisms remain incompletely understood. This study aimed to identify high-frequency OBI-related mutations in HBV surface antigen (HBsAg)-negative samples tested by the ultrasensitive Lumipulse G HBsAg-Quant assay. OBI samples were collected from 32 blood establishments across 14 provinces in China. Lumipulse G HBsAg-Quant assay was performed for the re-testing and reclassification of OBI. Mutations in genotypes B (GTB) and C (GTC) were analyzed to identify high-frequency single and combined mutations. Additionally, the efficacy of commercial reagents commonly employed in clinical diagnostics for detecting mutant HBsAg was evaluated. Western Blot was used for the confirmation of extracellular HBsAg as well as the detection of intracellular HBsAg. Hydrophilicity analysis and transmembrane distribution prediction of HBsAg were utilized for further validation. Single mutations at 17 sites and 9 combined mutations in GTB indicated a significantly elevated mutation frequency. In GTC, there were single mutations at 16 sites and 9 combined mutations. Several commercial reagents commonly demonstrated limited capacity toward mutant HBsAg with T123A/P, K141C, and P142R/I/K/L (GTB) and S114A/P (GTC). The findings indicated that mutations including T123A/C/K/S, S132G/Y, P142L/R/S/T, T143M, D144G, G145A, K160R+V168A, I4T+V168A, M103I+K122R, and M103I+Q181R (GTB), along with Q101H, M103I, R160K+C221Y (GTC), were associated with reduced levels of HBsAg both extracellularly and intracellularly. Additionally, K160R (GTB) and E2G (GTC) were associated with intracellular aggregation. This study elucidates the mutations associated with decreased extracellular HBsAg with ultrasensitive HBsAg assay, providing insight for further investigation into the mechanisms of OBI.</p><p><strong>Importance: </strong>The sensitivity of HBsAg detection reagents directly impacts the identification of occult hepatitis B virus (HBV) infection (OBI). This study aims to identify high-frequency OBI-related mutations in HBV surface antigen (HBsAg)-negative samples evaluated using a Fujirebio-Lumipulse ultrasensitive HBsAg assay and to investigate the implications of these mutations on the antigenicity of HBsAg, the detection capacities of various HBsAg assays, and the effects on intracellular and extracellular levels of HBsAg. Generally, our study offers a new perspective on OBI-related mutations by ultrasensitive HBsAg assay and lays the groundwork for further research on the OBI mechanism and the enhancement of HBsAg detection reagents.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0207124"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077177/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752955","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":"Detection of human IgG antibodies against <i>Mycoplasma genitalium</i> using a recombinant MG075 antigen.","authors":"Anna Marie Overgaard Kildemoes, Olivia Sureya Seierø Rai, Elisabeth Probst Lyng Westermann, Henrik Frederik Bekkevold Johansen, Eva Bjørnelius, Carin Anagrius, Liang Ma, Ida Rosenkrands, Jørgen Skov Jensen","doi":"10.1128/jcm.01876-24","DOIUrl":"10.1128/jcm.01876-24","url":null,"abstract":"<p><p><i>Mycoplasma genitalium</i> is a sexually transmitted pathogen that can cause a range of reproductive tract diseases in both men and women. To disentangle the relationship between <i>M. genitalium</i> infection(s) and subsequent reproductive health complications at the population level, accurate serological tools are needed. The major challenge in developing specific <i>M. genitalium</i> serological tests is the extensive cross-reactivity with the closely related ubiquitous respiratory tract pathogen, <i>Mycoplasma pneumoniae</i>. In this report, we describe the development of an immunoblot assay based on a recombinant fragment of the <i>M. genitalium</i> MG075 protein present in lipid-associated membrane extracts. A sensitivity of 87.1% was achieved based on the testing antibody responses in sera from 101 adults with PCR-confirmed <i>M. genitalium</i> infection. A specificity of 95.2% was obtained through the evaluation of sera from 166 children under 15 years of age with and without <i>M. pneumoniae</i> infection, who were unlikely to have been exposed to sexually transmitted <i>M. genitalium</i>. The development of a serological assay capable of accurately distinguishing <i>M. genitalium</i> and <i>M. pneumoniae</i> will enable a better understanding of associations between <i>M. genitalium</i> and adverse reproductive sequelae.</p><p><strong>Importance: </strong><i>Mycoplasma genitalium</i> is the second most common sexually transmitted bacterial infection after chlamydia. The long-term consequences of the infection are still under investigation, but reliable tools for monitoring exposure by detection of antibodies have been lacking specificity due to the presence of cross-reacting antibodies to the closely related <i>Mycoplasma pneumoniae</i>. Here, we describe a novel diagnostic antigen with promising sensitivity (87%) and specificity (95%) based on testing of sera from patients with PCR-confirmed <i>M. genitalium</i> infection and children with and without <i>M. pneumoniae</i> infection, respectively. The MG075F1 antigen was expressed in <i>Escherichia coli</i>, and the recombinant antigen was used in a western line-blot. Due to the insolubility of the antigen, harsh denaturing conditions were needed, making an enzyme-linked immunosorbent assay (ELISA) format impossible. Future work should explore shorter fragments or protein engineering to allow for assay designs better suited for high-throughput screening.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"63 5","pages":"e0187624"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077152/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143968857","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: A renal abscess caused by ST35-KL108, a strain of multidrug-resistant hypervirulent <i>Klebsiella pneumoniae</i>.","authors":"Fang Qian, Dongyue Lyu, Jiazhen Guo, Ran Duan, Shuai Qin, Hanyu Sha, Huaiqi Jing, Xin Wang, Zhihai Chen","doi":"10.1128/jcm.02057-24","DOIUrl":"10.1128/jcm.02057-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"63 5","pages":"e0205724"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077192/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144039462","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":"Multi-center evaluation of the Selux next-generation phenotyping system for gram-negative direct-from-positive blood culture antimicrobial susceptibility testing.","authors":"Vincent Streva, Joseph Gajewski, Jacqueline Pento, Alamelu Chandrasekaran, Matt Green, Jill Lindley, Micahel Huband, Asmae El Ganbour, Kristen Roberts, Kelly Flentie, Jingzi Sherman, Eric Stern, Gregory J Berry","doi":"10.1128/jcm.01819-24","DOIUrl":"10.1128/jcm.01819-24","url":null,"abstract":"<p><p>Accurate and rapid antimicrobial susceptibility test (AST) results from positive blood cultures are crucial for patient care and combatting antimicrobial resistance. Although recent advancements in rapid direct-from-positive blood culture (PBC) identification platforms have enabled the provision of species-level identification and some resistance marker information within hours after blood culture positivity, AST results required for clinical decision-making often require 48 h after blood culture positivity. This study evaluated the Selux next-generation phenotyping system, including an automated PBC Separator and the Selux AST system in a multicenter clinical trial for their ability to perform AST directly from PBCs for gram-negative bacilli. The PBC separator produces McFarland equivalent inocula from positive blood cultures within 1 h, facilitating direct processing on the Selux AST system. The study evaluated 162 fresh clinical PBC samples, 307 seeded clinical samples, and 87 seeded challenge samples across 4 sites for each of the 17 antimicrobials included in the panel. The results demonstrate that the Selux system's clinical performance, reproducibility, and analytical performances are consistent when using positive blood cultures held for up to 16 h after positivity on the BACTEC and BacT/ALERT 3D and BacT/ALERT VIRTUO blood culture systems, including all major BACTEC and BacT/ALERT blood culture bottle types. These findings suggest that the PBC Separator with the Selux AST system is a valuable addition to the arsenal of tools available for rapid sepsis diagnosis and management.IMPORTANCETechnologies that consistently and substantially shorten the time between blood bottle positivity, organism identification, and complete AST results are crucial for ensuring that antimicrobial therapy can be tailored. The Selux PBC Separator and the Selux AST system perform rapid AST directly from positive blood culture bottles. This substantially shortens the gap between obtaining a positive blood bottle and organism identification and the availability of a fully actionable AST result.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0181924"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077214/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752964","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":"Automated whole genome sequencing platform for bacterial strain typing in clinical microbiology laboratories.","authors":"Rachel L Siddall, Jordan C Starkey, Robin Patel","doi":"10.1128/jcm.00178-25","DOIUrl":"10.1128/jcm.00178-25","url":null,"abstract":"<p><p>Nosocomial outbreaks impact patient safety and place an economic burden on healthcare facilities. Laboratory testing plays a crucial role in outbreak investigation and guides containment efforts. In recent years, whole genome sequencing (WGS) methods have replaced traditional typing methods due to higher resolution and simplified workflows. Though an improvement from previous methods, bacterial WGS is time-consuming with manual DNA extraction and library preparation and long sequencing times for paired-end sequence data. Here, a fully automated library preparation and sequencing solution, the Clear Dx^TM WGS platform (Clear Labs, San Carlos, CA), was compared to a more manual library preparation and sequencing approach using 226 isolates representing 18 bacterial species. Sequence data were analyzed using SeqSphere+ (Ridom, Münster, Germany), and the results of the two methods were compared. Of the 224 isolate sequences analyzed, 222 (99%) showed concordant isolate groupings, and, overall, the results of the two approaches were statistically similar by comparison of distance matrices. The automated workflow reduced turnaround time by 16-19 h and eliminated 3 h of manual labor while decreasing costs by an estimated 34%-57% depending on the number of isolates run. This study demonstrates the advantages of integrating automation into bacterial WGS workflows.IMPORTANCEAn automated platform for bacterial nucleic acid extraction and whole genome sequencing was compared to a manual method for bacterial strain typing. The two approaches yielded nearly equivalent results, with the automated approach providing improvement in turnaround time and cost, with less manual pipetting.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"63 5","pages":"e0017825"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077132/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144021061","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":"Diagnostic accuracy of the Daye diagnostic tampon compared to clinician-collected and self-collected vaginal swabs for detecting HPV: a comparative study.","authors":"Valentina Milanova, Michelle Gomes, Kalina Mihaylova, John Luke Twelves, Jan Multmeier, Hana McMahon, Hannah McCulloch, Kate Cuschieri","doi":"10.1128/jcm.01852-24","DOIUrl":"10.1128/jcm.01852-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Cervical cancer screening is vital for achieving global elimination of this preventable disease. Vaginal self-sampling (VSS) for human papillomavirus (HPV) has the potential to increase screening uptake, particularly among individuals who may be underserved by clinician collection. Expanding self-sampling options with accurate, acceptable collection devices is essential. The Daye diagnostic tampon (DDT) offers an innovative approach, utilizing a tampon for HPV-based detection. This study assessed the diagnostic accuracy of DDT in detecting high-risk HPV infections, using vaginal clinician-collected swabs (CCS) as the reference standard. In this UK-based study, 260 participants provided CCS and VSS (with Copan FLOQSwabs) and DDT samples for HPV testing. Samples were analyzed using the Aptima HPV assay, which detects 14 high-risk HPV types. The sensitivity, specificity, positive predictive value, and negative predictive value of the DDT were evaluated against the CCS. Invalidity rates-HPV-negative results with negative internal controls-were compared across sampling methods. The DDT showed a sensitivity of 82.9% [95% confidence interval (CI): 72.4%-89.9%], specificity of 91.6% (CI: 86.4%-94.9%), and overall accuracy of 89.0% (CI: 84.4%-92.4%) relative to CCS. McNemar's test showed no significant difference between CCS and DDT results (&lt;i&gt;P&lt;/i&gt; = 0.845). Valid result rates were highest for DDT (99.2%), followed by VSS (95.4%) and CCS (90.8%). The DDT demonstrates comparable accuracy to CCS for detecting high-risk HPV. This novel device shows promise as a self-sampling method. Furthermore, complementary research should focus on assessing DDT's clinical performance in detecting HPV associated with cervical disease endpoints.IMPORTANCECervical cancer remains a leading preventable cause of cancer death globally, with persistent disparities in screening access. Self-sampling for HPV has emerged as a critical tool to improve screening uptake, particularly among underserved populations, yet device acceptability and diagnostic reliability remain barriers to equitable implementation. This study demonstrates that the Daye diagnostic tampon (DDT), a novel, tampon-based self-sampling method, achieves diagnostic accuracy comparable to clinician-collected swabs (sensitivity 82.9% and specificity 91.6%) while yielding fewer invalid results (0.8%) than conventional swabs. By aligning with a familiar menstrual product, the DDT addresses usability concerns that hinder confidence in existing self-sampling devices, as evidenced by 70.5% participant preference in focus groups. These findings advance progress toward World Health Organisation (WHO) cervical cancer elimination targets by validating a culturally resonant, high-performance alternative to clinic-based sampling. The DDT's potential to expand screening access, especially in low-resource settings or among individuals avoiding pelvic exams, could transform preventive care landscapes, reducing disparities in","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"63 5","pages":"e0185224"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077143/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144023657","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}