Journal of Clinical Microbiology最新文献

{"title":"The multiplexed single-tier InBios Lyme Detect Multiplex ELISA is more sensitive than standard two-tier tests in the early stages of Lyme disease.","authors":"Anna F Hickman, Allison F Weber, Elizabeth J Horn, Peter J Gwynne","doi":"10.1128/jcm.00629-25","DOIUrl":"https://doi.org/10.1128/jcm.00629-25","url":null,"abstract":"<p><p>There are nearly 500,000 cases of Lyme disease each year in the United States; 10%-20% of them result in the development of a debilitating chronic disease known as post-treatment Lyme disease. Existing standardized and modified two-tier tests (STT/MTT) suffer from poor detection rates in the first weeks of infection, where the antibody response, the basis of diagnosis, is developing but is not robust enough for detection. During this early window, false negative results are common, which leads to delayed treatment and increases the likelihood of developing severe symptoms. The InBios Lyme Detect Multiplex ELISA is a microarray-based assay designed to capture a set of commonly used diagnostic antibodies specific to <i>Borrelia burgdorferi</i> from human serum. The multiplex array captures common diagnostic antibodies, including those to C6, VlsE, and OspC, and has in-line controls. Diagnostic index scores are calculated from the relative abundance of controls and antibodies using a proprietary machine learning algorithm. The assay was evaluated here for reproducibility, accuracy, and performance. It was found to be reproducible using a group of 30 samples run in triplicate. The assay performed well in a blinded panel, correctly identifying all standard two-tier test-positive samples and controls while also detecting 21 of 79 samples that were clinically diagnosed but undetectable by standard Lyme serologic tests. There was one false positive from 66 look-alike disease samples and 146 healthy controls. The InBios assay has the potential to improve diagnostic sensitivity within the early weeks of infection while matching the specificity of current diagnostic tests.</p><p><strong>Importance: </strong>During initial Lyme disease infection, existing diagnostic tests have poor sensitivity, resulting in a high number of false-negative tests. This is due to the lag between infection and a robust immune response capable of being detected by such tests. With a multiplexed array of nine unique antibody targets specific for <i>Borrelia burgdorferi</i>, interpreted by a proprietary machine learning algorithm, the InBios Lyme Detect Multiplex ELISA has the potential to increase diagnostic sensitivity within the first few weeks of infection, reducing the number of false-negative tests. Improving diagnostic sensitivity during early infection would reduce the risk of developing severe symptoms, including post-treatment Lyme disease.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0062925"},"PeriodicalIF":5.4,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145251480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical and microbiologic features of <i>Achromobacter</i> species: a 10-year, multicenter experience.","authors":"David R Bayless, Mitchell G Dumais, Jack W McHugh, Nischal Ranganath, Madiha Fida, Supavit Chesdachai, Omar M Abu Saleh","doi":"10.1128/jcm.00724-25","DOIUrl":"10.1128/jcm.00724-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Achromobacter&lt;/i&gt; species are Gram-negative bacilli that predominantly affect individuals with cystic fibrosis or those with immunocompromising conditions. Clinical and microbiologic data on &lt;i&gt;Achromobacter&lt;/i&gt; species are limited due to the rarity of these organisms and challenges with species-level identification. We conducted a 10-year retrospective analysis (1 January 2013 to 14 March 2023) of all bloodstream and non-bloodstream &lt;i&gt;Achromobacter&lt;/i&gt; isolates identified at three tertiary-care Mayo Clinic locations (Minnesota, Arizona, and Florida). Additionally, we examined clinical characteristics of adult patients with &lt;i&gt;Achromobacter&lt;/i&gt; bloodstream isolates. A total of 1,598 &lt;i&gt;Achromobacter&lt;/i&gt; isolates, encompassing 1,545 non-bloodstream isolates and 53 bloodstream isolates, were identified. The most frequently identified species was &lt;i&gt;Achromobacter xylosoxidans&lt;/i&gt;, though species-level identification was not possible for many isolates. Among adult patients with &lt;i&gt;Achromobacter&lt;/i&gt; bloodstream infection, the mean age was 58.3 years (standard deviation ± 16.7), 73.1% had a central venous catheter, and 59.6% were immunocompromised. All-cause mortality was 10.2% at 30 days and 18.4% at 90 days. Bloodstream isolates exhibited greater than 90% susceptibility to meropenem, piperacillin-tazobactam, and trimethoprim-sulfamethoxazole. The respiratory tract was the most common source of non-bloodstream isolates (57.5%). Non-bloodstream isolates showed high susceptibility to imipenem (94.6%), piperacillin-tazobactam (92.8%), trimethoprim-sulfamethoxazole (92.1%), and meropenem (87.5%) while demonstrating significant resistance to fluoroquinolones and aminoglycosides. Our findings support the use of piperacillin-tazobactam, carbapenems, or trimethoprim-sulfamethoxazole as initial therapy for &lt;i&gt;Achromobacter&lt;/i&gt; infections. Further research is needed to better define the clinical and microbiologic characteristics of &lt;i&gt;Achromobacter&lt;/i&gt; infections.IMPORTANCE&lt;i&gt;Achromobacter&lt;/i&gt; is a rare but important genus of bacteria that tends to cause infection in those with cystic fibrosis, recurrent healthcare exposures, and/or an immunocompromising condition. There is limited data on the clinical profile of &lt;i&gt;Achromobacter&lt;/i&gt; infections as well as optimal antibiotic selection for affected patients. We conducted a retrospective study to improve understanding of the microbiologic and clinical characteristics of &lt;i&gt;Achromobacter&lt;/i&gt;. Our study consists of a 10-year survey of all &lt;i&gt;Achromobacter&lt;/i&gt; isolates processed by three Mayo Clinic tertiary-care centers in Minnesota, Florida, and Arizona from 2013 to 2023. We report multiple findings, including the clinical characteristics of patients with &lt;i&gt;Achromobacter&lt;/i&gt; bloodstream infection, the number of different &lt;i&gt;Achromobacter&lt;/i&gt; species identified, and the sources of isolates not obtained from blood cultures. We additionally present antimicrobial susceptibility results for &lt;i&gt;Achromobacter&lt;/","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0072425"},"PeriodicalIF":5.4,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505881/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086371","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":"An underestimated pathogen: <i>Corynebacterium</i> species.","authors":"Brooks I Mitchell, John E Markantonis","doi":"10.1128/jcm.01552-24","DOIUrl":"10.1128/jcm.01552-24","url":null,"abstract":"<p><p><i>Corynebacterium</i> species are a diverse group of organisms historically considered to be non-pathogenic, outside of the <i>C. diphtheriae</i> complex. Over the last few decades, this belief has been disproven with many notable non-diphtheriae <i>Corynebacterium</i> species being found to be pathogenic, often in certain clinical scenarios and/or anatomical sites. <i>C. striatum</i> and <i>C. jeikeium</i> are responsible for a large portion of bloodstream infections and orthopedic infections related to coryneform Gram-positive rods (GPRs). Eye and ear infections have commonly been attributed to <i>C. macginleyi</i> and <i>C. otitidis</i>, respectively. Pneumonia in critically ill and immunosuppressed individuals has been frequently reported by the <i>C. propinquum</i>/<i>pseudodiphtheriticum</i> group and occasionally in <i>C. striatum. C. urealyticum</i> is the primary pathogen associated with encrusted cystitis. Granulomatous lobular mastitis and breast abscesses have a strong association with <i>C. kroppenstedtii</i>. Erythrasma (<i>C. aurimucosum</i>/<i>minutissimum</i> group), trichobacteriosis (<i>C. flavescens</i>), and hidradenitis suppurativa are cutaneous disorders caused by or associated with <i>Corynebacterium</i> species. Biofilm formation by these bacteria leads to hardware/medical device-associated infections involving endovascular catheters, cerebrospinal fluid shunts, peritoneal dialysis catheters, and prosthetic joints. Clinical microbiology laboratories must be aware of this and optimize laboratory identification and reporting of these organisms when appropriate. Matrix-associated laser/adsorption ionization time-of-flight mass spectrometry, currently available in most large clinical microbiology laboratories, offers laboratories the ability to rapidly, accurately, and affordably accomplish this task.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0155224"},"PeriodicalIF":5.4,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506004/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144955957","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 laboratory billing process and its applications to molecular microbiology testing: guidance for laboratorians.","authors":"Meghan W Starolis, Hema Kapoor, Kristen L Jurcic Smith, Rachael M Liesman, Dawn R Zenefski","doi":"10.1128/jcm.00666-25","DOIUrl":"10.1128/jcm.00666-25","url":null,"abstract":"<p><p>The processes used by laboratories to seek reimbursement for services performed are complex and often unclear to laboratorians, a key group that has the clinical and technical knowledge to influence reimbursement. In this review, we provide a comprehensive overview of laboratory billing processes for insurance billing and hospital inpatient services, as well as the various procedure codes used in these processes. Understanding the health plan landscape is also of critical importance, as health plan policies and coverage decisions have downstream effects on accessibility of testing for patients. A detailed overview of health plans and how coverage determinations are made and communicated is discussed in this review. Lastly, we present actionable areas of opportunity in clinical microbiology where laboratorians, as well as test manufacturers, can focus on improving reimbursement (syndromic panels, antimicrobial resistance, and next-generation sequencing) to expand access to these evolving technologies and encourage adoption in clinical laboratories.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0066625"},"PeriodicalIF":5.4,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505987/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144956136","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: How antibiotic pretreatment complicated the diagnosis of <i>Haemophilus influenzae</i> type a meningitis.","authors":"Kristen L Buehne, Lauren Lajos, Bert Lopansri, Abby Tate, Christian L Carlson, Diego Cerbian Chaustre, Sonia Mehra","doi":"10.1128/jcm.00540-25","DOIUrl":"10.1128/jcm.00540-25","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"63 10","pages":"e0054025"},"PeriodicalIF":5.4,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505880/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145251402","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>Corynebacterium striatum</i> infections in oncologic patients: clinical spectrum, resistance profiles, and evidence of nosocomial transmission.","authors":"Kenya Yukawa, Sohei Harada, Kohji Komori, Brian Hayama, Daisuke Ohkushi, Koichi Takeda, Taisuke Enokida, Akira Yarimizu, Kazumi Takehana, Kageto Yamada, Michihiko Goto, Kazuhiro Tateda","doi":"10.1128/jcm.00829-25","DOIUrl":"10.1128/jcm.00829-25","url":null,"abstract":"<p><p>Among <i>Corynebacterium</i> species, <i>Corynebacterium striatum</i> is relatively frequently involved in invasive human infections. In this study, we collected clinical information from patients diagnosed with <i>C. striatum</i> infection at a single cancer center and performed antimicrobial susceptibility testing and whole-genome sequencing of the causative strains. Of the 51 patients with <i>C. striatum</i> infections, 15 (29.4%) had postoperative intra-abdominal infections, eight (15.7%) had postoperative skin and soft tissue infections of the neck, and eight (15.7%) had osteoarticular infections. In 15 patients, <i>C. striatum</i> was detected concomitantly with other bacteria. The median duration of antimicrobial therapy was 25 days, with 43 patients (84.3%) showing clinical improvement by day 14. The crude mortality up to 90 days post-diagnosis was 15.7%. Vancomycin was the most commonly used definitive therapy, and 40 patients (78.4%) received multiple antimicrobial agents. Oral minocycline was often administered in patients requiring long-term treatment. Antimicrobial susceptibility testing of 53 strains, including two strains from follow-up cultures from the same patient, showed that most strains were susceptible to daptomycin and tetracyclines. However, non-susceptibility was noted in two strains (3.8%) for daptomycin and four strains (7.5%) for tetracyclines, each associated with <i>psgA2</i> mutation and <i>tet</i>(W) carriage. Core-genome single-nucleotide polymorphism analysis of the strains and epidemiological reviews of the source patients identified three suspected clusters of nosocomial transmission involving seven patients. This study demonstrated that <i>C. striatum</i> can cause a range of infections in patients with underlying diseases, such as malignancy, and that nosocomial spread of this pathogen may also occur.</p><p><strong>Importance: </strong>The use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, employed for bacterial species identification in this study, has enhanced the recognition of <i>Corynebacterium striatum</i> as an important human pathogen in clinical microbiology laboratories. Our study demonstrated that <i>C. striatum</i> is associated with various healthcare-associated infections, including those requiring prolonged antimicrobial therapy, and that nosocomial transmission of this pathogen can result in the development of infections. In addition, several agents other than vancomycin, such as teicoplanin, tetracyclines, and trimethoprim/sulfamethoxazole, have demonstrated favorable activities. The results of this study indicate the need for further research on the mechanisms and modes of nosocomial transmission of <i>C. striatum</i>, as well as the clinical efficacy of alternative agents to vancomycin, particularly those suitable for prolonged treatment, given the potential side effects associated with vancomycin use.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0082925"},"PeriodicalIF":5.4,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506117/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086311","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 diagnostic utility of Immunoglobulin G (IgG) avidity in distinguishing between past and acute infection of West Nile Virus (WNV).","authors":"Yaniv Lustig, Vicki Indenbaum, Ravit Koren, Shiri Katz-Likvornik, Osnat Halpern, Ella Mendelson","doi":"10.1128/jcm.00952-25","DOIUrl":"10.1128/jcm.00952-25","url":null,"abstract":"<p><p>Infection with West Nile Virus (WNV) can cause severe disease; however, due to immunoglobulin M (IgM) persistence and short viremia, confirmatory diagnosis of acute WNV infection often requires two consecutive samples and a laborious neutralization assay. Immunoglobulin G (IgG) avidity assay is being used to differentiate between acute and past infection of several viral diseases but not of WNV. To test whether IgG avidity can be utilized for WNV diagnosis, serum samples from 103 past and 84 acute WNV-infected persons diagnosed in our laboratory according to WHO guidelines were subjected to IgG avidity. ROC curve analysis was applied to measure the diagnostic accuracy of WNV IgG avidity and establish the optimal cut-off. Mean avidity and geometric mean neutralization titers (GMTs) from acute and past infected cases were 26% (95% CI: 21-30) and 183 (95% CI: 144-235) and 63% (95% CI: 59-67) and 110 (95% CI: 82-147), respectively. Optimal avidity cut-off level to distinguish between acute and past infection was 35% with sensitivity, specificity, PPV, and NPV of 81% (95% CI: 72-88), 88% (95% CI: 81-93), 55% (95% CI: 42-67), and 96% (95% CI: 94-98), respectively. Our results suggest that IgG avidity can rule out acute WNV infections in patients with positive WNV IgM and IgG antibodies and replace the neutralization assay as a confirmatory assay in most cases. By using an avidity assay as part of the routine diagnostic protocol of WNV, the diagnosis of WNV will be simplified, rapid, and would substantially reduce the workload and diagnostic difficulty of this flaviviral infection.IMPORTANCEDiagnosing West Nile Virus (WNV) infection typically requires two serum samples collected weeks apart and a labor-intensive confirmatory test using live virus. Here, we evaluated immunoglobulin G (IgG) avidity assay, which measures the binding strength between WNV antigen and IgG antibodies, as a simpler diagnostic approach using only one sample. Our findings showed that IgG avidity reliably identifies past WNV infections but is less effective in confirming the acute phase. Crucially, this method can rule out acute infections and allow for a rapid and definitive diagnosis in most cases. IgG avidity assays offer a streamlined alternative, reducing the need for complex tests and prolonged timelines.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0095225"},"PeriodicalIF":5.4,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505976/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086316","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":"Comparison of core genome multi-locus sequencing typing pipelines for hospital outbreak detection of common bacterial pathogens.","authors":"Heather L Glasgow, Ying Zheng, Jessica N Brazelton, Li Tang, Randall T Hayden","doi":"10.1128/jcm.00646-25","DOIUrl":"10.1128/jcm.00646-25","url":null,"abstract":"<p><p>Microbial whole genome sequencing (WGS)-based methods have replaced conventional methods for genomic relatedness analysis in the investigation of or surveillance for infectious outbreaks. Analysis of WGS by core genome multi-locus sequence typing (cgMLST) has been proposed for standardized strain comparisons at high resolution and for longitudinal outbreak surveillance. We compared three commercial cgMLST software pipelines, Ridom SeqSphere+, 1928 Diagnostics' platform, and Ares Genetics ARESdb, for the identification of related (clustered) strains among 255 isolates of common bacterial pathogens, including <i>Acinetobacter baumannii, Escherichia coli, Enterococcus faecalis, Enterococcus faecium, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus,</i> and <i>Serratia marcescens</i>. Isolates were previously identified as clustered with at least one other isolate collected from the same patient or different patients. Concordance with SeqSphere+ for differentiating clustered from non-clustered isolate pairs using suggested thresholds was 100% for the 1928 platform and 99.5% for ARESdb overall and 91.8%, 96.1%, and 100% among same-patient clustered, different-patient clustered, and different-patient non-clustered isolate pairs, respectively, in ARESdb. ARESdb showed significantly greater allelic distances than SeqSphere+ and 1928 among same-patient clustered isolate pairs (mean [standard deviation, SD], 7.6 [7.17], 1.18 [1.56], and 1 [1.59]) and different-patient clustered isolate pairs (mean [SD], 8.34 [4.31], 3.61 [2.26], and 3.91 [2.67]) (<i>P</i> < 0.0001), but not among non-clustered isolate pairs. For all species analyzed with sufficient sample size, allelic distances of clustered isolate pairs were significantly higher in ARESdb. CgMLST analysis using commercial pipelines may result in different allelic distances but showed concordance using suggested clustering thresholds to determine relatedness among strains.IMPORTANCEMicrobial genetic relatedness analysis is commonly used to investigate suspected outbreaks among different patients with infections caused by the same species of pathogen and, increasingly, for outbreak surveillance to uncover unsuspected healthcare-associated transmission events among patients, enabling early intervention by infection prevention and control specialists to prevent further spread. Here, we compared three commercial software tools for bacterial relatedness analysis, which perform gene-by-gene comparisons to determine the degree of relatedness for several species of common pathogens. Such software tools potentially allow clinical laboratories to perform rapid and routine analysis for infection control purposes without the need for in-house bioinformatic expertize. This study evaluates the comparability of three of these software tools, while presenting a model for comparative analytic pipeline evaluation.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0064625"},"PeriodicalIF":5.4,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506026/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144955976","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":"Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation of <i>Neisseria meningitidis</i> and <i>Salmonella enterica</i> when accounting for methylation-related errors.","authors":"Bert Bogaerts, Margo Maex, Florian Commans, Nathalie Goeders, An Van den Bossche, Sigrid C J De Keersmaecker, Nancy H C Roosens, Pieter-Jan Ceyssens, Wesley Mattheus, Kevin Vanneste","doi":"10.1128/jcm.00410-25","DOIUrl":"10.1128/jcm.00410-25","url":null,"abstract":"<p><p>Core-genome multi-locus sequence typing (cgMLST) is a well-established and standardized method for genomics-based cluster detection and phylogenomic analysis of bacteria. The reduced error rate of Oxford Nanopore Technologies (ONT) R10 sequencing has prompted many laboratories to explore incorporating this technology into their activities. However, conflicting reports exist on the performance of ONT R10 sequencing for cgMLST analysis. This study evaluates the suitability of ONT R10 data for cgMLST allele calling and cluster detection for bacterial outbreak investigation. ONT and Illumina sequencing data were generated for 24 <i>Neisseria meningitidis</i> and 24 <i>Salmonella enterica</i> isolates. For ONT, both the rapid barcoding kit (RBK) and the rapid PCR barcoding kit (RPB) were used. The percentage of loci called in the ONT-only assemblies was very high for both species. However, the proportion of mismatched alleles to the hybrid assemblies was substantially higher for the <i>Neisseria</i> ONT-only assemblies with the RBK kit, resulting in incorrect cluster assignments. The large majority of these mismatched alleles were due to incorrect base calls at methylated positions, which did not affect the ONT data generated using the RPB kit or any of the <i>Salmonella</i> ONT-only assemblies. In conclusion, ONT R10 sequencing shows great potential as a viable method for cgMLST analysis, but methylation-related errors can affect performance for certain species and strains. When properly corrected for, ONT R10 had the same performance for cgMLST analysis as Illumina, and both could be used interchangeably. These results support the integration of ONT R10 sequencing into routine public health and clinical workflows.</p><p><strong>Importance: </strong>This study evaluates the suitability of Oxford Nanopore Technologies R10 sequencing for core-genome multi-locus sequence typing (cgMLST), a widely used method in (clinical) outbreak investigation and bacterial strain tracking. We have sequenced 24 <i>Neisseria meningitidis</i> and 24 <i>Salmonella enterica</i> strains, including confirmed outbreak cases, using Illumina and ONT R10 sequencing to evaluate the performance for cgMLST analysis. We used a PCR-based and native barcoding protocol for the ONT sequencing, which enabled us to demonstrate a substantial species-dependent impact of methylation-related errors on the performance. However, we demonstrate that when these errors are properly addressed, ONT R10 can be used for accurate cgMLST-based clustering, including integration with strains sequenced using Illumina. Our findings support the use of ONT R10 as an alternative to Illumina sequencing for cgMLST analysis in routine public health practice.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0041025"},"PeriodicalIF":5.4,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144956171","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":"Standardized surveillance of blood culture contamination rates: moving toward a universal standard.","authors":"Fizza Manzoor, Sarah E Turbett","doi":"10.1128/jcm.00981-25","DOIUrl":"10.1128/jcm.00981-25","url":null,"abstract":"<p><p>Blood culture contamination (BCC) is a major healthcare challenge with no standardized process to monitor and report rates by individual healthcare facilities in the United States. A new study by V. Fabre, Y.- J. Hsu, K. C. Caroll, A. M. Milstone, et al. (J Clin Microbiol 63:e0053025, 2025, https://doi.org/10.1128/jcm.00530-25) characterizes blood culture contamination rates, surveillance methods, reporting practices, and preventative strategies across 52 centers in the United States. The study highlights a need for standardized surveillance metrics and target thresholds within and across hospitals to help facilitate accurate benchmarking, provide feedback on existing processes, support antimicrobial and diagnostic stewardship efforts, and allocate resources to reduce BCC events.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0098125"},"PeriodicalIF":5.4,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506060/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145000631","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}