Journal of Clinical Microbiology最新文献

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Host blood protein biomarkers to screen for tuberculosis disease: a systematic review and meta-analysis. 用于筛查结核病的宿主血液蛋白生物标志物:系统综述和荟萃分析。
IF 5.3 2区 医学
Journal of Clinical Microbiology Pub Date : 2024-11-13 Epub Date: 2024-10-24 DOI: 10.1128/jcm.00786-24
Mary Gaeddert, Kerstin Glaser, Bih H Chendi, Ayten Sultanli, Lisa Koeppel, Emily L MacLean, Tobias Broger, Claudia M Denkinger
{"title":"Host blood protein biomarkers to screen for tuberculosis disease: a systematic review and meta-analysis.","authors":"Mary Gaeddert, Kerstin Glaser, Bih H Chendi, Ayten Sultanli, Lisa Koeppel, Emily L MacLean, Tobias Broger, Claudia M Denkinger","doi":"10.1128/jcm.00786-24","DOIUrl":"10.1128/jcm.00786-24","url":null,"abstract":"<p><p>Non-sputum tests are needed to improve tuberculosis (TB) diagnosis and close the diagnostic gap. The World Health Organization's target product profile (TPP) for point-of-care (POC) screening tests requires a minimum sensitivity of 90% and a specificity of 70%. Our objective was to identify host blood protein biomarkers meeting TPP criteria. A systematic review was conducted and reported following PRISMA guidelines. Data extraction and quality assessment with Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) were completed for the included studies. Heterogeneity was assessed. For biomarkers reporting sensitivity and specificity in at least four studies, a random-effects meta-analysis was performed for biomarkers with similar cut-offs. We screened 4,651 citations and included 65 studies that enrolled 16,010 participants and evaluated 156 host proteins. Most (47/65) studies enrolled adult pulmonary TB (PTB), with 15 studies in adult extra-pulmonary TB and 5 in children. Small early-stage discovery studies with case-control design were common (24/65) and had a high risk of bias. For adult PTB, CRP, IP-10, NCAM-1, and SAA met TPP criteria in high-quality studies. There was a high degree of heterogeneity in biomarker cut-offs and study design. CRP at 10 mg/L cut-off was meta-analyzed from 10 studies; pooled sensitivity 86% [95% confidence interval (CI): 80-95] and pooled specificity 67% (95% CI: 54-79). In people living with HIV (six studies), CRP pooled sensitivity was 93% (95% CI: 90-95), and pooled specificity was 59% (95% CI: 40-78). We identified promising biomarkers that performed well in high-quality studies. Data overall are limited and highly heterogenous. Further standardized validation across subgroups in prospective studies is needed before translating into POC assays.</p><p><strong>Importance: </strong>To our knowledge, this is the first comprehensive systematic review of host blood protein biomarkers for tuberculosis (TB), and we identified promising biomarkers for a TB screening test.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0078624"},"PeriodicalIF":5.3,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559064/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142501305","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
Photo Quiz: Skin scraping of persistent lesion reveals the main course. 照片测验:刮除顽固病灶的皮肤可发现主要病变。
IF 6.1 2区 医学
Journal of Clinical Microbiology Pub Date : 2024-11-13 DOI: 10.1128/jcm.00220-24
Christopher Attaway, Jennifer Andrasko, Anisha Misra
{"title":"Photo Quiz: Skin scraping of persistent lesion reveals the main course.","authors":"Christopher Attaway, Jennifer Andrasko, Anisha Misra","doi":"10.1128/jcm.00220-24","DOIUrl":"10.1128/jcm.00220-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"62 11","pages":"e0022024"},"PeriodicalIF":6.1,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559008/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142621323","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
Evaluation of gradient strip diffusion for susceptibility testing of aztreonam-avibactam in metallo-β-lactamase-producing Enterobacterales. 评估梯度条带扩散法在产金-β-内酰胺酶肠杆菌中对阿曲南唑-阿维菌素的药敏试验。
IF 5.3 2区 医学
Journal of Clinical Microbiology Pub Date : 2024-11-13 Epub Date: 2024-09-30 DOI: 10.1128/jcm.00649-24
Jamie K Lemon, Cheryl Jankowsi-Romano, Scott Duong, Stefan Juretschko, Vincent A Streva
{"title":"Evaluation of gradient strip diffusion for susceptibility testing of aztreonam-avibactam in metallo-β-lactamase-producing Enterobacterales.","authors":"Jamie K Lemon, Cheryl Jankowsi-Romano, Scott Duong, Stefan Juretschko, Vincent A Streva","doi":"10.1128/jcm.00649-24","DOIUrl":"10.1128/jcm.00649-24","url":null,"abstract":"<p><p>The emergence of metallo-β-lactamase (MBL)-producing Enterobacterales presents unique clinical treatment challenges. Recently developed β-lactam/ β-lactamase inhibitor combination agents, while effective against other carbapenemase-producing organisms, are notably ineffective against MBL producers. While MBLs do not hydrolyze monobactams (aztreonam), many MBL-producing organisms are resistant to aztreonam through alternate mechanisms, leaving cefiderocol as the sole monotherapy treatment option recommended for MBL producers. Recent guidelines for the treatment of MBL-harboring organisms have added combination therapy with aztreonam and ceftazidime-avibactam, using ceftazidime-avibactam as a source of the β-lactamase inhibitor avibactam. Current laboratory testing options for the combination of aztreonam-avibactam are limited to broth microdilution (BMD) and broth disk elution (BDE) methods, which are not practical in most clinical laboratories. In this study, we evaluated the performance of aztreonam/avibactam gradient strips on 103 MBL-producing Enterobacterales patient isolates as well as an additional 31 isolates from the CDC AR Bank. All MBL Enterobacterales patient isolates included in this study harbored a New Delhi metallo-β-lactamase (<i>bla</i><sub>NDM</sub>) gene. Essential agreement of gradient strip minimal inhibitory concentrations (MICs) for patient isolates compared to BMD was 93.2%. While there are no established breakpoints for aztreonam-avibactam, category agreement (CA) for patient isolates was 97.1% when using the CLSI aztreonam breakpoints. There were no major or very major errors observed. There were three minor errors. Precision for aztreonam-avibactam gradient strip diffusion was 100%. These data demonstrate that the use of gradient strip diffusion for aztreonam-avibactam MIC determination in MBL-producing Enterobacterales is a viable option for clinical laboratories.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0064924"},"PeriodicalIF":5.3,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559034/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142347641","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
Clinical performance evaluation of the BioFire Joint Infection Panel. BioFire 关节感染面板的临床性能评估。
IF 5.3 2区 医学
Journal of Clinical Microbiology Pub Date : 2024-11-13 Epub Date: 2024-10-09 DOI: 10.1128/jcm.01022-24
Rose A Lee
{"title":"Clinical performance evaluation of the BioFire Joint Infection Panel.","authors":"Rose A Lee","doi":"10.1128/jcm.01022-24","DOIUrl":"10.1128/jcm.01022-24","url":null,"abstract":"<p><p>The BioFire Joint Infection (JI) Panel offers a significant advancement in the rapid diagnosis of joint infections by facilitating the simultaneous detection of multiple bacterial and fungal pathogens, as well as resistance markers, directly from synovial fluid samples. An article published in the <i>Journal of Clinical Microbiology</i> by Moran et al. (J Clin Microbiol 62:e00182-24, 2024, https://doi.org/10.1128/jcm.00182-24) presents both prospective and retrospective analyses of the panel's real-world clinical application. The study highlights the panel's benefits, such as its rapid turnaround time and ability to identify challenging pathogens, while also discussing its limitations, particularly in detecting certain off-panel organisms.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0102224"},"PeriodicalIF":5.3,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559011/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390930","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
Oxford Nanopore's 2024 sequencing technology for Listeria monocytogenes outbreak detection and source attribution: progress and clone-specific challenges. 牛津纳米孔公司的 2024 测序技术用于李斯特菌疫情检测和来源归因:进展与特定克隆的挑战。
IF 5.3 2区 医学
Journal of Clinical Microbiology Pub Date : 2024-11-13 Epub Date: 2024-10-04 DOI: 10.1128/jcm.01083-24
Michael Biggel, Nicole Cernela, Jule Anna Horlbog, Roger Stephan
{"title":"Oxford Nanopore's 2024 sequencing technology for <i>Listeria monocytogenes</i> outbreak detection and source attribution: progress and clone-specific challenges.","authors":"Michael Biggel, Nicole Cernela, Jule Anna Horlbog, Roger Stephan","doi":"10.1128/jcm.01083-24","DOIUrl":"10.1128/jcm.01083-24","url":null,"abstract":"<p><p>Whole genome sequencing is an essential cornerstone of pathogen surveillance and outbreak detection. Established sequencing technologies are currently being challenged by Oxford Nanopore Technologies (ONT), which offers an accessible and cost-effective alternative enabling gap-free assemblies of chromosomes and plasmids. Limited accuracy has hindered its use for investigating pathogen transmission, but recent technology updates have brought significant improvements. To evaluate its readiness for outbreak detection, we selected 78 <i>Listeria monocytogenes</i> isolates from diverse lineages or known epidemiological clusters for sequencing with ONT's V14 Rapid Barcoding Kit and R10.4.1 flow cells. The most accurate of several tested workflows generated assemblies with a median of one error (SNP or indel) per assembly. For 66 isolates, the cgMLST profiles from ONT-only assemblies were identical to those generated from Illumina data. Eight assemblies were of lower quality, with more than 20 erroneous sites each, primarily caused by methylations at the GAAGAC motif (5'-GAAG<u>6mA</u>C-3'/5'-GT<u>4mC</u>TTC-3'). This led to inaccurate clustering, failing to group isolates from a persistence-associated clone that carried the responsible restriction-modification system. Out of 50 methylation motifs detected among the 78 isolates, only the GAAGAC motif was linked to substantially increased error rates. Our study shows that most <i>L. monocytogenes</i> genomes assembled from ONT-only data are suitable for high-resolution genotyping, but further improvements of chemistries or basecallers are required for reliable routine use in outbreak and food safety investigations.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0108324"},"PeriodicalIF":5.3,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559035/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371977","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
Persistent bloodstream infection in children: examining the role for repeat blood cultures. 儿童持续性血流感染:研究重复血液培养的作用。
IF 5.3 2区 医学
Journal of Clinical Microbiology Pub Date : 2024-11-13 Epub Date: 2024-10-04 DOI: 10.1128/jcm.00998-24
Christine M Puthawala, Richard S Feinn, José Rivera-Viñas, Hanna Lee, Thomas S Murray, David R Peaper
{"title":"Persistent bloodstream infection in children: examining the role for repeat blood cultures.","authors":"Christine M Puthawala, Richard S Feinn, José Rivera-Viñas, Hanna Lee, Thomas S Murray, David R Peaper","doi":"10.1128/jcm.00998-24","DOIUrl":"10.1128/jcm.00998-24","url":null,"abstract":"<p><p>Repeat blood cultures are common in children after an initial positive culture. However, in contrast to adults, there are little data to help guide clinicians when a repeat culture is necessary to assess for persistent bacteremia. This study identifies factors associated with persistent bloodstream infections (BSI) in children to inform diagnostic stewardship. This cross-sectional study of children less than 18 years with at least one positive blood culture over a 5-year period utilized a generalized linear equation model to predict patient and microbial factors associated with persistent BSI defined as a positive blood culture with the same organism >48 hours after the index culture. Four hundred and five patients had 502 positive blood cultures yielding 556 organisms. Sixty-seven (13.2%) cultures were persistently positive. Anaerobic organisms (0/37) and <i>Streptococcus</i> species (0/104) were never recovered from repeat cultures. <i>Staphylococcus aureus</i> (OR 9.45, CI 5.15-17.35) and yeast (OR 78.18, CI 9.45-646.6) were statistically associated with persistent BSI. Patients with prior positive cultures (OR 1.44, CI 1.12-1.84) or a central venous catheter (OR 2.20, 95% CI 1.04-3.92) were also at risk for persistence. Immune dysfunction and elevated inflammatory markers at the time of the index blood culture were not significantly associated with persistence. Yeast or <i>S. aureus</i> were associated with persistent BSI, while anaerobes and <i>Streptococcus</i> species were never persistent. Patient characteristics at the time of blood draw did not predict persistence other than having previous positive blood cultures or a central venous catheter. These data can inform when repeat blood cultures have clinical value and reduce the risk of unnecessary blood draws in children.</p><p><strong>Importance: </strong>We identify factors associated with bloodstream infection persistence in children. Our findings can help guide blood culture stewardship efforts in pediatric patients, especially in light of blood culture supply shortages.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0099824"},"PeriodicalIF":5.3,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559050/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371978","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
Candida guilliermondii fungemia: a 12-year retrospective review of antimicrobial susceptibility patterns at a reference laboratory and tertiary care center. Guilliermondii 念珠菌菌血症:参考实验室和三级医疗中心抗菌药敏感性模式的 12 年回顾性研究。
IF 5.3 2区 医学
Journal of Clinical Microbiology Pub Date : 2024-11-13 Epub Date: 2024-10-23 DOI: 10.1128/jcm.01057-24
Jack W McHugh, David R Bayless, Nischal Ranganath, Ryan W Stevens, Dalton R Kind, Nancy L Wengenack, Aditya S Shah
{"title":"<i>Candida guilliermondii</i> fungemia: a 12-year retrospective review of antimicrobial susceptibility patterns at a reference laboratory and tertiary care center.","authors":"Jack W McHugh, David R Bayless, Nischal Ranganath, Ryan W Stevens, Dalton R Kind, Nancy L Wengenack, Aditya S Shah","doi":"10.1128/jcm.01057-24","DOIUrl":"10.1128/jcm.01057-24","url":null,"abstract":"<p><p>The prevalence of invasive candidiasis caused by non-<i>albicans Candida</i> species is increasing. <i>Candida guilliermondii</i> is an infrequent cause of candidemia but has been associated with decreased susceptibility to triazoles. Clinical data related to the infection with <i>C. guilliermondii</i> are sparse. Our study evaluated the antifungal susceptibility testing (AST) for <i>C. guilliermondii</i> isolates submitted to a reference laboratory over a 12-year period (2012-2023). AST patterns were examined using Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) epidemiological cutoff values (ECVs) and breakpoints. Where isolates were identified from patients treated at our institution, retrospective chart review was performed to describe patient risk factors, treatment approaches, and outcomes associated with <i>C. guilliermondii</i> fungemia. One hundred twelve blood culture isolates of <i>C. guilliermondii</i> were identified, and clinical data were available for 21 fungemic patients. A significant number of isolates (9.8-20.5%) were observed to be non-wild type for various triazoles. All isolates were susceptible to micafungin. A majority (76.2%) of cases of <i>C. guilliermondii</i> fungemia treated at our tertiary care center were hospital-acquired, and two-thirds of patients were immunocompromised at the time of diagnosis. Ten of the 21 patients died within 60 days of fungemia, although mortality was directly or partially attributed to <i>C. guilliermondii</i> fungemia in only four cases (19.0%). Echinocandins may be used for empiric therapy for <i>C. guilliermondii</i> until the results of AST are available. Further research is required to determine appropriate clinical breakpoints for triazoles.</p><p><strong>Importance: </strong>Our study addresses a significant knowledge gap in the clinical management of this non-<i>Candida albicans</i> species. Our retrospective review includes comprehensive AST data for 112 <i>Candida guilliermondii</i> isolates, which is the largest number of isolates reported from the United States to date. Susceptibility data are supplemented by clinical outcomes, where isolates were identified for patients treated at Mayo Clinic. Key findings from our study include the observation that a notable proportion of <i>C. guilliermondii</i> isolates exhibit non-wild-type profiles for various triazoles. Importantly, all isolates remained susceptible to echinocandins, suggesting their efficacy as first-line therapy in the absence of timely susceptibility results. Furthermore, our study highlights the high mortality associated with <i>C. guilliermondii</i> fungemia in immunocompromised patients, emphasizing the urgent need for optimized treatment strategies.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0105724"},"PeriodicalIF":5.3,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559098/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142501302","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
An update on novel taxa and revised taxonomic status of bacteria isolated from aquatic host species described in 2022-2023. 关于 2022-2023 年描述的从水生宿主物种中分离的细菌的新分类群和修订分类地位的最新情况。
IF 5.3 2区 医学
Journal of Clinical Microbiology Pub Date : 2024-11-13 Epub Date: 2024-10-24 DOI: 10.1128/jcm.01043-24
Claire R Burbick, Sara D Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson
{"title":"An update on novel taxa and revised taxonomic status of bacteria isolated from aquatic host species described in 2022-2023.","authors":"Claire R Burbick, Sara D Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson","doi":"10.1128/jcm.01043-24","DOIUrl":"10.1128/jcm.01043-24","url":null,"abstract":"<p><p>The description of new taxa and nomenclature updates to currently known taxa from aquatic animal species continues. After a review of the literature from 2022 and 2023, multiple lists of bacteria, including members of Phylum <i>Planctomycetota</i>, were compiled. As with the previous review, most bacteria are oxidase-positive Gram-negative bacilli with familiar families including new taxa in <i>Aeromonadaceae</i>, <i>Flavobacteriaceae</i>, <i>and Vibrionaceae</i>. A number of Gram-positive bacilli are described including new taxa in the <i>Nocardioides</i>, <i>Paenibacillus</i>, and <i>Streptomyces</i> genera. Two anaerobic species are listed, and one new member of Family <i>Planctomycetaceae</i> is noted. Revised taxa are briefly mentioned. The majority of new and revised taxa are isolated from healthy aquatic animals, and therefore, the role of these new bacteria in health and disease is unknown. Bacteria with pathogenic association and potential production of bioactive substances are highlighted.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0104324"},"PeriodicalIF":5.3,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11558999/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142501304","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 novel machine-learning aided platform for rapid detection of urine ESBLs and carbapenemases: URECA-LAMP. 用于快速检测尿液中 ESBLs 和碳青霉烯酶的新型机器学习辅助平台:URECA-LAMP。
IF 5.3 2区 医学
Journal of Clinical Microbiology Pub Date : 2024-11-13 Epub Date: 2024-10-24 DOI: 10.1128/jcm.00869-24
L Ricardo Castellanos, Ryan Chaffee, Hitendra Kumar, Biniyam Kahsay Mezgebo, Pawulos Kassau, Gisele Peirano, Johann D D Pitout, Keekyoung Kim, Dylan R Pillai
{"title":"A novel machine-learning aided platform for rapid detection of urine ESBLs and carbapenemases: URECA-LAMP.","authors":"L Ricardo Castellanos, Ryan Chaffee, Hitendra Kumar, Biniyam Kahsay Mezgebo, Pawulos Kassau, Gisele Peirano, Johann D D Pitout, Keekyoung Kim, Dylan R Pillai","doi":"10.1128/jcm.00869-24","DOIUrl":"10.1128/jcm.00869-24","url":null,"abstract":"<p><p>Pathogenic gram-negative bacteria frequently carry genes encoding extended-spectrum beta-lactamases (ESBL) and/or carbapenemases. Of great concern are carbapenem resistant <i>Escherichia coli</i>, <i>Klebsiella pneumoniae</i>, <i>Pseudomonas aeruginosa,</i> and <i>Acinetobacter baumannii</i>. Despite the need for rapid AMR diagnostics globally, current molecular detection methods often require expensive equipment and trained personnel. Here, we present a novel machine-learning-aided platform for the rapid detection of ESBLs and carbapenemases using Loop-mediated isothermal Amplification (LAMP). The platform consists of (i) an affordable device for sample lysis, LAMP amplification, and visual fluorometric detection; (ii) a LAMP screening panel to detect the most common ESBL and carbapenemase genes; and (iii) a smartphone application for automated interpretation of results. Validation studies on clinical isolates and urine samples demonstrated percent positive and negative agreements above 95% for all targets. Accuracy, precision, and recall values of the machine learning model deployed in the smartphone application were all above 92%. Providing a simplified workflow, minimal operation training, and results in less than an hour, this study demonstrated the platform's feasibility for near-patient testing in resource-limited settings.IMPORTANCEExtended-spectrum beta-lactamases (ESBL) and carbapenemases confer resistance to third-generation cephalosporins and carbapenems in pathogenic Gram-negative bacteria such as <i>Escherichia coli</i>, <i>Klebsiella pneumoniae</i>, <i>Pseudomonas aeruginosa,</i> and <i>Acinetobacter baumannii</i>. Conventional antimicrobial susceptibility testing is based on phenotypic methods, and results can take several days to be obtained. Current genotypic detection methods can be rapid but require expensive equipment and trained personnel. In this study, we present a novel machine learning-aided platform for the rapid detection of ESBLs and carbapenemases using Loop-mediated isothermal Amplification (LAMP). The validation of the platform demonstrated percent positive and negative agreements above 95% for all targets. The newly developed platform provided a simplified workflow, minimal technical training, and results in less than an hour. This study demonstrated the platform's feasibility for rapid testing of ESBL and carbapenemases in bacteria and urine specimens.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0086924"},"PeriodicalIF":5.3,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559160/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142501303","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
Approaches to developing and implementing a molecular diagnostics stewardship program for infectious diseases: an ASM Laboratory Practices Subcommittee report. 制定和实施传染病分子诊断监管计划的方法:ASM 实验室规范小组委员会报告。
IF 5.3 2区 医学
Journal of Clinical Microbiology Pub Date : 2024-11-13 Epub Date: 2024-10-21 DOI: 10.1128/jcm.00941-24
Frances Valencia-Shelton, Neil Anderson, Elizabeth L Palavecino, Maria E Navas, Paige M K Larkin, Rosemary She, Laura M Filkins
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