Analytical and clinical validation of direct detection of antimicrobial resistance markers by plasma microbial cell-free DNA sequencing.

IF 6.1 2区 医学 Q1 MICROBIOLOGY
Journal of Clinical Microbiology Pub Date : 2024-10-16 Epub Date: 2024-08-28 DOI:10.1128/jcm.00425-24
Fred C Christians, Jamilla Akhund-Zade, Kristin Jarman, Shivkumar Venkatasubrahmanyam, Nicholas Noll, Timothy A Blauwkamp, Sivan Bercovici, Aga Zielinska, Amy L Carr, Arryn Craney, Matthew Pike, John Joseph Farrell, Sanjeet Dadwal, James B Wood, Efrat Matkovich, Staci McAdams, Frederick S Nolte
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引用次数: 0

Abstract

Sequencing of plasma microbial cell-free DNA (mcfDNA) has gained increased acceptance as a valuable adjunct to standard-of-care testing for diagnosis of infections throughout the body. Here, we report the analytical and clinical validation of a novel application of mcfDNA sequencing, the non-invasive detection of seven common antimicrobial resistance (AMR) genetic markers in 18 important pathogens. The AMR markers include SCCmec, mecA, mecC, vanA, vanB, blaCTX-M, and blaKPC. The AMR markers were computationally linked to the pathogens detected. Analytical validation showed high reproducibility (100%), inclusivity (54 to 100%), and exclusivity (100%). Clinical accuracy was assessed with 114 unique plasma samples from patients at seven study sites with concordant culture results for target bacteria from a variety of specimen types and correlated with available phenotypic antimicrobial susceptibility test results and genotypic results. The positive percent agreement (PPA), negative percent agreement (NPA), and diagnostic yield (DY) were estimated for each AMR marker. DY was defined as the percentage of tests that yielded an actionable result of either detected or not detected. The results for the combination of SCCmec and mecA for staphylococci were PPA 19/20 (95.0%), NPA 21/22 (95.4%), DY 42/60 (70.0%); vanA for enterococci were PPA 3/3 (100%), NPA 2/2 (100%), DY 5/6 (83.3%); blaCTX-M for gram-negative bacilli were PPA 5/6 (83.3%), NPA 29/29 (100%), DY 35/49 (71.4%); and blaKPC for gram-negative bacilli were PPA 0/2 (0%), NPA: 23/23 (100%), DY 25/44 (56.8%). The addition of AMR capability to plasma mcfDNA sequencing should provide clinicians with an effective new culture-independent tool for optimization of therapy.

Importance: This manuscript is ideally suited for the Innovative Diagnostic Methods sections as it reports the analytical and clinical validation of a novel application of plasma microbial cell-free DNA sequencing for direct detection of seven selected antimicrobial resistance markers in 18 target pathogens. Clearly, it has potential clinical utility in optimizing therapy and was incorporated into the Karius test workflow in September 2023. In addition, the workflow could readily be adapted to expand the number of target bacteria and antimicrobial resistance markers as needed.

通过血浆微生物无细胞 DNA 测序直接检测抗菌药耐药性标记物的分析和临床验证。
血浆微生物无细胞DNA(mcfDNA)测序作为诊断全身感染的标准检测方法的重要辅助手段,已被越来越多的人接受。在此,我们报告了 mcfDNA 测序新应用的分析和临床验证,即对 18 种重要病原体中 7 种常见抗菌药耐药性 (AMR) 遗传标记的无创检测。AMR 标记包括 SCCmec、mecA、mecC、vanA、vanB、blaCTX-M 和 blaKPC。AMR 标记通过计算与检测到的病原体建立了联系。分析验证结果表明,该方法具有很高的重现性(100%)、包容性(54% 至 100%)和排他性(100%)。对临床准确性的评估采用了 114 份独特的血浆样本,这些样本来自 7 个研究机构的患者,其目标细菌的培养结果与各种类型标本的培养结果一致,并与现有的表型抗菌药敏感性检测结果和基因型结果相关联。估算了每个 AMR 标记的阳性一致率 (PPA)、阴性一致率 (NPA) 和诊断率 (DY)。DY 的定义是得出检测到或未检测到的可操作结果的检测百分比。针对葡萄球菌的 SCCmec 和 mecA 组合检测结果为 PPA 19/20 (95.0%)、NPA 21/22 (95.4%)、DY 42/60 (70.0%);针对肠球菌的 vanA 检测结果为 PPA 3/3 (100%)、NPA 2/2 (100%)、DY 5/6 (83.3%)。3%);针对革兰氏阴性杆菌的 blaCTX-M 为 PPA 5/6 (83.3%)、NPA 29/29 (100%)、DY 35/49 (71.4%);针对革兰氏阴性杆菌的 blaKPC 为 PPA 0/2 (0%)、NPA: 23/23 (100%)、DY 25/44 (56.8%)。在血浆 mcfDNA 测序中加入 AMR 功能,将为临床医生优化治疗提供一种有效的、独立于培养的新工具:本稿件非常适合创新诊断方法栏目,因为它报告了血浆微生物无细胞 DNA 测序的新应用的分析和临床验证,该测序可直接检测 18 种目标病原体中的 7 种选定抗菌药耐药性标记物。显然,它在优化治疗方面具有潜在的临床实用性,并于 2023 年 9 月被纳入卡里乌斯检测工作流程。此外,该工作流程可根据需要随时调整,以扩大目标细菌和抗菌药耐药性标记物的数量。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Journal of Clinical Microbiology
Journal of Clinical Microbiology 医学-微生物学
CiteScore
17.10
自引率
4.30%
发文量
347
审稿时长
3 months
期刊介绍: The Journal of Clinical Microbiology® disseminates the latest research concerning the laboratory diagnosis of human and animal infections, along with the laboratory's role in epidemiology and the management of infectious diseases.
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