Journal of Clinical Microbiology最新文献

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Evaluation of long-read 16S rRNA next-generation sequencing for identification of bacterial isolates in a clinical diagnostic laboratory. 长读16S rRNA新一代测序在临床诊断实验室中鉴定细菌分离物的评价。
IF 6.1 2区 医学
Journal of Clinical Microbiology Pub Date : 2025-05-14 Epub Date: 2025-04-22 DOI: 10.1128/jcm.01670-24
Victoria L Campodónico, Jean Ruelle, Anna Fitzgerald, Yehudit Bergman, Brenda Osborne, Dimitrios Bourdas, Jennifer Lu, Karen C Carroll, Patricia J Simner
{"title":"Evaluation of long-read 16S rRNA next-generation sequencing for identification of bacterial isolates in a clinical diagnostic laboratory.","authors":"Victoria L Campodónico, Jean Ruelle, Anna Fitzgerald, Yehudit Bergman, Brenda Osborne, Dimitrios Bourdas, Jennifer Lu, Karen C Carroll, Patricia J Simner","doi":"10.1128/jcm.01670-24","DOIUrl":"10.1128/jcm.01670-24","url":null,"abstract":"<p><p>Sanger sequencing of the first ~500 bp of the 16S rRNA gene is frequently used to identify bacterial pathogens that have ambiguous biochemical profiles or proteomic mass spectra. When diversity does not occur within that region, genus-level and/or species-level identification may not be possible, and a longer sequence or alternative target may be required to distinguish between genera/species. In this study, we evaluated a clinically relevant end-to-end solution for long-read (~1,500 nt) 16S rRNA next-generation sequencing by Oxford Nanopore Technologies (ONT) compared to a ~500 nt Sanger sequencing approach for the identification of 153 bacterial clinical isolates. Sequencing data were analyzed using the IDNS software from SmartGene and its proprietary 16S Centroid reference database (Centroid database) SmartGene software and the Centroid database. The agreement of the two platforms on species- and genus-level identification was determined, and discrepancies were resolved by whole-genome sequencing. ONT had a higher taxonomic resolution at the genus level (<i>P</i> < 0.01). When genus-level identification was achieved by both methods, concordance to the best matching genus was 100%. When species-level identification was achieved by both methods, concordance to the best matching species was 91%. The costs per test were ~$25.30 (when multiplexing 24 samples/run) and $74 for ONT and Sanger sequencing, respectively. The hands-on time spent performing sequencing was similar for both methods, but the turnaround time of ONT was significantly shorter than that of Sanger sequencing.IMPORTANCEThis study adds to existing literature by describing a validated end-to-end solution of 16S rRNA gene Oxford Nanopore sequencing for bacterial isolate identification, including sequencing run time evaluation, automated analysis (SmartGene 16S Identification App) and interpretation of results, that can be incorporated into clinical and public health laboratories with a simple and cost-effective workflow.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"63 5","pages":"e0167024"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077174/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144004035","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}
引用次数: 0
Ultrasensitive and highly specific detection of the Brucella genus and B. melitensis by CRISPR/Cas12b-multiple cross displacement amplification technique. 利用CRISPR/ cas12b -多重交叉位移扩增技术对布鲁氏菌属和梅利特芽孢杆菌进行超灵敏、高特异性的检测。
IF 6.1 2区 医学
Journal of Clinical Microbiology Pub Date : 2025-05-14 Epub Date: 2025-04-11 DOI: 10.1128/jcm.01532-24
Sha Mao, Xinggui Yang, Yue Wang, Fengming Chen, Hai Jiang, Yi Wang, Yingqian Kang, Shijun Li
{"title":"Ultrasensitive and highly specific detection of the <i>Brucella</i> genus and <i>B</i>. <i>melitensis</i> by CRISPR/Cas12b-multiple cross displacement amplification technique.","authors":"Sha Mao, Xinggui Yang, Yue Wang, Fengming Chen, Hai Jiang, Yi Wang, Yingqian Kang, Shijun Li","doi":"10.1128/jcm.01532-24","DOIUrl":"10.1128/jcm.01532-24","url":null,"abstract":"<p><p>Brucellosis is caused by members of the <i>Brucella</i> spp. and remains one of the world's major zoonotic diseases. <i>Brucella melitensis</i> (<i>B. melitensis</i>) as the most contagious <i>Brucella</i> species cannot be ignored as an essential source of infection for brucellosis, especially in countries/regions dominated by animal husbandry. Thus, the identification of the <i>Brucella</i> genus and <i>B. melitensis</i> is crucial for rapid diagnosis of brucellosis to control disease transmission and clinical treatment. Here, we developed the CRISPR/Cas12b nuclease combined with a multiple cross displacement amplification (MCDA) assay (CRISPR-MCDA) for highly specific and sensitive detection of <i>Brucella</i> genus and <i>B. melitensis</i> in clinical applications. Two sets of specific primers were designed targeting the specific gene of <i>Brucella</i> genus (<i>Bcsp31</i>) and <i>B. melitensis</i> (<i>BMEII0466</i>), respectively. The CRISPR-MCDA assay showed high specificity and sensitivity in 28 non-<i>Brucella</i> isolates and 64 clinical samples. The detection limit of CRISPR-MCDA assay was 2 copies/μL in the plasmid dilution template, and the whole detection process took within 90 minutes with nanoparticle-based lateral flow biosensor (LFB) to validate experimental results. Taken together, the CRISPR-MCDA-LFB assay is a visual, sensitive, and highly specific detection technique that can be used as an attractive potential identification tool for <i>Brucella</i> genus and <i>B. melitensis</i>.IMPORTANCEThe prevention and control of Brucellosis urgently require rapid and accurate diagnostic methods. This work validates a new method for the simultaneous detection of <i>Brucella</i> genus and <i>B. melitensis</i>. The method can effectively reduce the chances of contamination and provides a more rapid, sensitive, and specific on-site detection of <i>Brucella</i>. It also offers a solution for the rapid screening of Brucellosis in resource-limited environments, which is crucial for effective disease prevention and control. This technology can also be widely applied to the rapid detection of other pathogens beyond <i>Brucella</i>.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"63 5","pages":"e0153224"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077202/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020009","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}
引用次数: 0
Impact of packed red blood cells versus fresh whole human blood on the growth of nutritionally variant streptococci and Streptococcus anginosus group during verification of the BACT/ALERT VIRTUO blood culture system. 在BACT/ALERT VIRTUO血液培养系统验证过程中,填充红细胞与新鲜全血对营养变异链球菌和血管链球菌群生长的影响
IF 6.1 2区 医学
Journal of Clinical Microbiology Pub Date : 2025-05-14 Epub Date: 2025-03-31 DOI: 10.1128/jcm.01987-24
Heather Glassman, Jasmine Ahmed-Bentley, Rebecca Buckman, Mark Carbungco, Colleen Fletcher, Kim Sy, Joyce Wong, Charlene Porter, Claudine Desruisseaux, Valery Lavergne, Suefay Liu, Anthony Lieu, Marthe K Charles
{"title":"Impact of packed red blood cells versus fresh whole human blood on the growth of nutritionally variant streptococci and <i>Streptococcus anginosus</i> group during verification of the BACT/ALERT VIRTUO blood culture system.","authors":"Heather Glassman, Jasmine Ahmed-Bentley, Rebecca Buckman, Mark Carbungco, Colleen Fletcher, Kim Sy, Joyce Wong, Charlene Porter, Claudine Desruisseaux, Valery Lavergne, Suefay Liu, Anthony Lieu, Marthe K Charles","doi":"10.1128/jcm.01987-24","DOIUrl":"10.1128/jcm.01987-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0198724"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077193/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752958","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}
引用次数: 0
Improvement of the diagnosis of intestinal protozoa using a multiplex qPCR strategy compared to classical microscopy: a prospective study on 3,500 stool samples over 3 years. 与传统显微镜相比,多重qPCR技术对肠道原生动物诊断的改善:一项对3500份粪便样本为期3年的前瞻性研究
IF 6.1 2区 医学
Journal of Clinical Microbiology Pub Date : 2025-05-14 Epub Date: 2025-03-31 DOI: 10.1128/jcm.01610-24
Florence Robert-Gangneux, Xavier Duval, Clément Cazala, Sorya Belaz, Anne Dupuis, Hélène Guegan, Brice Autier, Jean-Pierre Gangneux
{"title":"Improvement of the diagnosis of intestinal protozoa using a multiplex qPCR strategy compared to classical microscopy: a prospective study on 3,500 stool samples over 3 years.","authors":"Florence Robert-Gangneux, Xavier Duval, Clément Cazala, Sorya Belaz, Anne Dupuis, Hélène Guegan, Brice Autier, Jean-Pierre Gangneux","doi":"10.1128/jcm.01610-24","DOIUrl":"10.1128/jcm.01610-24","url":null,"abstract":"<p><p>Commercial multiplex real-time PCR (qPCR assays) are now widely used for the diagnosis of intestinal protozoan infections, but few prospective studies evaluated their performances on large patient cohorts. We extracted data from our information system from 1 January 2021 to 15 March 2024 and included all stool samples analyzed in routine. Parasites were searched using a multiplex PCR (AllPlex Gastrointestinal Panel assay, Seegene) and microscopic examination with two concentration methods. Acid-fast staining was performed when <i>Cryptosporidium</i> detection was specifically requested. In total, 3,495 stools were analyzed from 2,127 patients. <i>Giardia intestinalis</i>, <i>Cryptosporidium</i> spp., <i>Entamoeba histolytica</i>, <i>Dientamoeba fragilis,</i> and <i>Blastocystis</i> spp. were found by multiplex qPCR in 45 (1.28%), 30 (0.85%), 9 (0.25%), 310 (8.86%), and 673 (19.25%) samples, respectively, alone or in combination (<i>n</i> = 909). In the vast majority of cases, PCR detected a protozoan on the first stool sample. Microscopy was positive for <i>G. intestinalis</i>, <i>Cryptosporidium</i> spp., <i>Entamoeba histolytica/dispar</i>, <i>D. fragilis,</i> and <i>Blastocystis</i> spp. in 25 (0.7%), 8 (0.23%), 24 (0.68%), 22 (0.63%), and 229 (6.55%), samples, respectively, alone or in combination (<i>n</i> = 286 samples). No samples were PCR-/Microscopy+ for <i>G</i>. <i>intestinalis</i>, <i>Cryptosporidium</i> spp., and <i>E. histolytica</i>, while <i>D. fragilis</i> and <i>Blastocystis</i> spp. were detected only with microscopy in 6 and 20 samples, respectively. Microscopy allowed the detection of parasites not targeted by the multiplex panel (5 <i>Cystoisospora belli,</i> 331 samples with non-pathogenic protozoa, and 68 samples with helminths). Overall, the multiplex PCR proved more efficient to detect protozoan parasites, but a microscopic technique should be performed when infection with <i>C. belli</i> (HIV-infected patients) or helminths is suspected (migrants and travelers).IMPORTANCEIn the era of increasing use of multiplex PCR panels for the diagnosis of intestinal protozoan infections, it is important to form an opinion on the positioning of those assays within a lab workflow. This study analyzes routine results obtained prospectively by microscopy and a commercial multiplex PCR over 3 years, and shows that the assay meets the expectations of a clinical laboratory for the detection of protozoan parasites of medical interest. It is recalled that <i>Cystoisospora belli</i> is not targeted by the multiplex assay, and that microscopy still remains necessary to detect helminths.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0161024"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077082/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752960","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}
引用次数: 0
A universal point-of-care immunochromatographic test for the serodiagnosis of hepatitis D. 用于D型肝炎血清诊断的通用点护理免疫层析试验。
IF 6.1 2区 医学
Journal of Clinical Microbiology Pub Date : 2025-05-14 Epub Date: 2025-04-11 DOI: 10.1128/jcm.01999-24
Thiciany Blener Lopes, Fabiana Fioravante Coelho, Tárcio Peixoto Roca, Jéssica Karoline Augusta Oliveira, Valérian Delagarde, Ségolène Brichler, Diana Paola Gómez Mendoza, Juan Miguel Villalobos Salcedo, Deusilene Souza Vieira, Frédéric Le Gal, Ricardo Tostes Gazzinelli, Ana Paula Fernandes
{"title":"A universal point-of-care immunochromatographic test for the serodiagnosis of hepatitis D.","authors":"Thiciany Blener Lopes, Fabiana Fioravante Coelho, Tárcio Peixoto Roca, Jéssica Karoline Augusta Oliveira, Valérian Delagarde, Ségolène Brichler, Diana Paola Gómez Mendoza, Juan Miguel Villalobos Salcedo, Deusilene Souza Vieira, Frédéric Le Gal, Ricardo Tostes Gazzinelli, Ana Paula Fernandes","doi":"10.1128/jcm.01999-24","DOIUrl":"10.1128/jcm.01999-24","url":null,"abstract":"<p><p>Hepatitis D is estimated to affect 12 million people worldwide and is caused by the hepatitis D virus (HDV), a defective virus that requires the presence of the hepatitis B virus (HBV) for infection. Here, we report a new recombinant antigen (DTH10.1) to detect anti-HDV IgG antibodies, designed to include a consensus sequence of the HDV antigen, based on bioinformatic analysis of the eight HDV genotypes. Using serum samples from patients living in the endemic area of the Brazilian Amazon basin, the enzyme-linked immunosorbent assay (ELISA) based on this protein displayed a sensitivity of 90.6% (95% CI: 84.2%-94.5%) and a specificity of 100% (95% CI: 94.2%-100.0%), while a rapid immunochromatographic test (ICT) showed a sensitivity of 91.3% (95% CI: 85.0%-95.1%) and specificity of 99.0% (95% CI: 94.5%-99.95%). Commercial monoclonal antibodies for HBV surface antigen (HBsAg) detection were then added to the test, resulting in a multiplex ICT with a sensitivity of 87.1% (95% CI: 81.3%-91.4%) for HBsAg and 95.2% (95% CI: 90.0%-97.8%) for anti-HDV IgG and specificity of 100% (95% CI: 91.0%-100.0%) and 98.0% (95% CI: 92.9%-99.6%), respectively. Finally, the three tests were evaluated against a panel of 79 patient samples infected, covering the eight HDV genotypes. The results indicated that all the DTH10.1-based tests were able to detect anti-IgG HDV antibodies with high sensitivity and specificity, regardless of the infecting HDV genotype. In conclusion, the prototypes developed for serodiagnosis of HDV using the DTH10.1 recombinant protein are promising tools for the universal diagnosis of HDV infection.IMPORTANCEThe manuscript outlines the complete strategy for developing tools for the diagnosis of hepatitis D, including an enzyme-linked immunosorbent assay (ELISA), an immunochromatographic test (ICT), and a multiplex ICT for the simultaneous detection of hepatitis B virus surface antigen and anti-hepatitis D virus (HDV) IgG antibodies. All the tests described are capable of detecting all eight HDV genotypes with high accuracy.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"63 5","pages":"e0199924"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143968852","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}
引用次数: 0
Pneumococcal genotype 23B1 as a driver of increased 23B serotype carriage, penicillin non-susceptibility, and invasive disease in Belgium: a retrospective analysis. 肺炎球菌基因型23B1是比利时23B血清型携带、青霉素非敏感性和侵袭性疾病增加的驱动因素:一项回顾性分析
IF 6.1 2区 医学
Journal of Clinical Microbiology Pub Date : 2025-04-09 Epub Date: 2025-03-12 DOI: 10.1128/jcm.01696-24
Lara Dierckx, Juan Pablo Rodriguez-Ruiz, Esra Ekinci, Liesbet van Heirstraeten, Laura Willen, Lize Cuypers, Philippe Beutels, Kirsten Maertens, Stefanie Desmet, Heidi Theeten, Surbhi Malhotra-Kumar
{"title":"Pneumococcal genotype 23B1 as a driver of increased 23B serotype carriage, penicillin non-susceptibility, and invasive disease in Belgium: a retrospective analysis.","authors":"Lara Dierckx, Juan Pablo Rodriguez-Ruiz, Esra Ekinci, Liesbet van Heirstraeten, Laura Willen, Lize Cuypers, Philippe Beutels, Kirsten Maertens, Stefanie Desmet, Heidi Theeten, Surbhi Malhotra-Kumar","doi":"10.1128/jcm.01696-24","DOIUrl":"10.1128/jcm.01696-24","url":null,"abstract":"<p><p><i>Streptococcus pneumoniae</i> serotype 23B, a non-vaccine serotype, has shown an increasing prevalence and penicillin non-susceptibility among carriage and invasive pneumococcal disease (IPD) isolates. Recently, a novel penicillin non-susceptible genotype has emerged, named 23B1. In the framework of the Belgian pneumococcal carriage study, we studied the prevalence of 23B<sub>0</sub>/23B1 among 586 23B strains (2016-2022) in 172 day care centers from 6- to 30-month-old children and among 130 pediatric 23B IPD isolates (2007-2021). Pneumococci were whole genome sequenced to determine the capsular polysaccharide genotype and sequence type (ST). Antimicrobial susceptibility testing determined penicillin and amoxicillin MICs, as well as resistance to co-trimoxazole and levofloxacin. 23B carriage was stable during 2016 ̶ 2022 except in the 2020-2021 winter season when it increased. The proportion of genotype 23B1 compared to 23B<sub>0</sub> decreased from 2016 ̶ to 2022 but remained consistently higher than 23B<sub>0</sub>. In 2020-2021, an increase in the proportion of 23B1 was reflected in an overall increase in 23B carriage. All increases in 23B IPD cases were almost entirely driven by 23B1. The median penicillin MICs were significantly different for 23B<sub>0</sub> (0.03 mg/L) and 23B1 (0.25 mg/L). In 2021, increased intermediate levofloxacin susceptibility was noted in 23B. 23B1-associated ST2372 was the most prevalent ST in carriage and IPD during 2013-2022. We show that an increase in 23B carriage among children was paralleled in pediatric IPD in Belgium, reiterating the utility of pneumococcal surveillance in the day care population. Serotype 23B is reported worldwide as an important pediatric non-PCV13 serotype with reduced penicillin susceptibility, with 23B1 as the presumed driver for the increased prevalence.IMPORTANCEDuring the COVID-19 pandemic, the 23B serotype of <i>Streptococcus pneumoniae</i> has increased in prevalence in healthy carriage isolates from Belgian day care centers and pediatric (younger than 18 years of age) invasive pneumococcal disease (IPD) isolates. Additionally, an increase in penicillin non-susceptibility was also observed within this serotype. Recently, a genetic variant of 23B, named 23B1, was discovered, which is known to be related to decreased penicillin susceptibility. We showed that increases in 23B prevalence in healthy carriage and IPD cases always coincided with 23B1 expansions, leading to higher penicillin non-susceptibility rates. Increases in 23B in the day care population paralleled pediatric 23B IPD increases, indicating the vital role of day care monitoring of pneumococcal carriage. Countries should stay vigilant for prevalence increases in <i>S. pneumoniae</i> serotype 23B, given the decreased susceptibility to penicillin and co-trimoxazole of the 23B1 variant.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0169624"},"PeriodicalIF":6.1,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11980397/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
External quality assessment of molecular detection and variant typing of SARS-CoV-2 in European expert laboratories in 2023. 2023年欧洲专家实验室SARS-CoV-2分子检测和变异分型外部质量评价
IF 6.1 2区 医学
Journal of Clinical Microbiology Pub Date : 2025-04-09 Epub Date: 2025-03-14 DOI: 10.1128/jcm.01538-24
Kim C Heimsch, Kamelia R Stanoeva, Ramona Mögling, Annette Kraus, Eeva K Broberg, Jan Felix Drexler, Chantal B E M Reusken, Adam Meijer, Christian Drosten, Victor M Corman
{"title":"External quality assessment of molecular detection and variant typing of SARS-CoV-2 in European expert laboratories in 2023.","authors":"Kim C Heimsch, Kamelia R Stanoeva, Ramona Mögling, Annette Kraus, Eeva K Broberg, Jan Felix Drexler, Chantal B E M Reusken, Adam Meijer, Christian Drosten, Victor M Corman","doi":"10.1128/jcm.01538-24","DOIUrl":"10.1128/jcm.01538-24","url":null,"abstract":"<p><p>The COVID-19 pandemic highlighted the importance of laboratory preparedness. Regular monitoring of diagnostic tools via external quality assessments (EQAs) is key to maintaining robust public health response service. We hereby conducted a third SARS-CoV-2 EQA assessing the diagnostic capabilities of European expert public health laboratories. A 10 samples panel containing Alpha (used in previous EQA), BA.4, BA.5, and BQ.1.18 variants along with human seasonal coronaviruses and negative controls was produced and validated. Participants were invited by the European Centre for Disease Prevention and Control (ECDC) and asked to submit results and assay details via electronic forms. Thirty-eight laboratories from 31 European countries participated. Most (<i>n</i> = 32, 84%) identified all panel samples correctly and used in-house (11, 29%), commercial assays (22, 58%), or both (5, 13%). Compared to previous EQAs, correct detection of the SARS-CoV-2 samples in the panels increased: 8 (12%) in 2020, 45 (75%) in 2021, and 34 (90%) laboratories in 2023, respectively. The number of participants decreased to an average of one laboratory per country (range 1-3) compared to two (1-7) laboratories in both previous EQAs. The usage of commercial assays gradually increased in contrast to the usage of in-house or both approaches. The capacity for SARS-CoV-2 molecular diagnostics has markedly improved in Europe as evidenced by three consecutive EQAs carried out by expert public health laboratories. Routine monitoring of diagnostic and surveillance assays via EQAs remains key to maintaining rapid public health laboratory response systems.IMPORTANCEExternal quality assessments (EQAs) are crucial to ensure the reliability and consistency of diagnostic laboratories. They provide an objective framework for evaluating the performance of testing systems, enabling laboratories to identify weaknesses and implement improvements promptly. In the context of SARS-CoV-2, EQAs have become even more critical due to the high demand for accurate molecular diagnostics and the emergence of new variants. Accurate detection and typing of variants are especially essential for monitoring viral evolution. EQAs help standardize methodologies, ensuring that results across laboratories remain comparable and trustworthy. Moreover, they play a pivotal role in minimizing errors such as false positives or negatives. In this rapidly evolving landscape, regular EQAs are indispensable for maintaining high-quality standards in molecular diagnostics and variant surveillance. We demonstrate here that regular EQAs improve the molecular detection of SARS-CoV-2 in European laboratories.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0153824"},"PeriodicalIF":6.1,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11980390/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Nanopore sequencing for precise detection of Mycobacterium tuberculosis and drug resistance: a retrospective multicenter study in China. 纳米孔测序精确检测结核分枝杆菌和耐药性:一项中国多中心回顾性研究。
IF 6.1 2区 医学
Journal of Clinical Microbiology Pub Date : 2025-04-09 Epub Date: 2025-03-19 DOI: 10.1128/jcm.01813-24
Shanshan Yu, Ning Liu, Zhouhua Xie, Yi Zeng, Hua Wang, Qian Wang, Peibo Li, Haoran Li, Jinhao Sun, Qingdong Zhu, Weiwei Gao, Hongcang Gu, Fuyou Liu, Peisong Xu, Yunfei Wang, Liang Li, Yu Pang
{"title":"Nanopore sequencing for precise detection of <i>Mycobacterium tuberculosis</i> and drug resistance: a retrospective multicenter study in China.","authors":"Shanshan Yu, Ning Liu, Zhouhua Xie, Yi Zeng, Hua Wang, Qian Wang, Peibo Li, Haoran Li, Jinhao Sun, Qingdong Zhu, Weiwei Gao, Hongcang Gu, Fuyou Liu, Peisong Xu, Yunfei Wang, Liang Li, Yu Pang","doi":"10.1128/jcm.01813-24","DOIUrl":"10.1128/jcm.01813-24","url":null,"abstract":"<p><p>Tuberculosis (TB) management in endemic regions often grapples with resource constraints, including the scarcity of <i>Mycobacterium tuberculosis</i> (<i>M.tb</i>) culture laboratories. The emergence of <i>M.tb</i> strains with complex drug resistance profiles necessitates rapid and comprehensive drug susceptibility testing (DST) to guide patient treatment. However, traditional phenotypic DST (pDST) for <i>M.tb</i> is costly and time-consuming. In this study, we retrospectively enrolled 829 participants from six specialized TB treatment hospitals in China from September 2022 to July 2023. The diagnostic performance of TBseq test, a targeted-nanopore sequencing assay, was compared head-to-head with <i>M.tb</i> culture, acid-fast bacillus smear, quantitative polymerase chain reaction, and Xpert MTB/RIF Ultra by using clinical diagnosis as the reference standard. Subsequently, pDST for seven anti-TB drugs (rifampicin, isoniazid, ethambutol, streptomycin, levofloxacin, amikacin, and capreomycin) was performed. The resistance predictions provided by the TBseq test were compared with pDST results, which were used as a reference standard. The performance estimates of TBseq test were quantified through sensitivity, specificity, positive predictive value, negative predictive value, and the area under the receiver operating characteristic curve (AUC), providing a comprehensive assessment of its diagnostic accuracy. We found that TBseq test demonstrated significantly superior diagnostic performance for TB compared to other methods, achieving a sensitivity of 90.9% (95% CI: 88.9%-93.0%), specificity of 93.0% (95% CI: 97.2%-99.5%), and an AUC of 0.92 (95% CI: 0.876-0.963). TBseq test also exhibited robust predictive capabilities for drug resistance to the seven anti-TB drugs, with sensitivity and specificity consistently above 90% for all drugs. The AUC values ranged from 0.919 to 0.998, indicative of high diagnostic accuracy in forecasting drug resistance.IMPORTANCEOur results show that TBseq test offers excellent identification performance for tuberculosis (TB), significantly outperforming <i>Mycobacterium tuberculosis</i> (<i>M.tb)</i> culture, acid-fast bacillus (AFB) smear, qPCR, and Xpert MTB/RIF. Its diagnostic accuracy for anti-TB drug resistance is also superior, with sensitivity and specificity above 90% for all drugs tested. This method can be integrated into routine clinical diagnostic workflows, enabling early diagnosis and reporting of drug resistance simultaneously.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0181324"},"PeriodicalIF":6.1,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11980377/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Biographical Feature: Ruth Ella Moore, Ph.D. 传记特征:露丝·艾拉·摩尔,博士。
IF 6.1 2区 医学
Journal of Clinical Microbiology Pub Date : 2025-04-09 Epub Date: 2025-02-27 DOI: 10.1128/jcm.01863-24
Marian C Johnson-Thompson
{"title":"Biographical Feature: Ruth Ella Moore, Ph.D.","authors":"Marian C Johnson-Thompson","doi":"10.1128/jcm.01863-24","DOIUrl":"10.1128/jcm.01863-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0186324"},"PeriodicalIF":6.1,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11980371/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143515817","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}
引用次数: 0
A call for the United States to continue investing in science. 呼吁美国继续对科学进行投资。
IF 6.1 2区 医学
Journal of Clinical Microbiology Pub Date : 2025-04-09 Epub Date: 2025-02-27 DOI: 10.1128/jcm.00348-25
Ira Blader, Felicia Goodrum, Michael J Imperiale, Arturo Casadevall, Cesar A Arias, Andreas Baumler, Carey-Ann D Burnham, Christina A Cuomo, Corrella S Detweiler, Graeme N Forrest, Jack A Gilbert, Susan Lovett, Stanley Maloy, Alexander McAdam, Irene Newton, Gemma Reguera, George A O'Toole, Patrick D Schloss, Ashley Shade, Marvin Whiteley
{"title":"A call for the United States to continue investing in science.","authors":"Ira Blader, Felicia Goodrum, Michael J Imperiale, Arturo Casadevall, Cesar A Arias, Andreas Baumler, Carey-Ann D Burnham, Christina A Cuomo, Corrella S Detweiler, Graeme N Forrest, Jack A Gilbert, Susan Lovett, Stanley Maloy, Alexander McAdam, Irene Newton, Gemma Reguera, George A O'Toole, Patrick D Schloss, Ashley Shade, Marvin Whiteley","doi":"10.1128/jcm.00348-25","DOIUrl":"10.1128/jcm.00348-25","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0034825"},"PeriodicalIF":6.1,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11980381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143515776","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}
引用次数: 0
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