DataSheet_1_Prospective Evaluation of a Rapid Clinical Metagenomics Test for Bacterial Pneumonia.docx

BackgroundThe diagnosis of bacterial pathogens in lower respiratory tract infections (LRI) using conventional culture methods remains challenging and time-consuming.ObjectivesTo evaluate the clinical performance of a rapid nanopore-sequencing based metagenomics test for diagnosis of bacterial pathogens in common LRIs through a large-scale prospective study.MethodsWe enrolled 292 hospitalized patients suspected to have LRIs between November 2018 and June 2019 in a single-center, prospective cohort study. Rapid clinical metagenomics test was performed on-site, and the results were compared with those of routine microbiology tests.Results171 bronchoalveolar lavage fluid (BAL) and 121 sputum samples were collected from patients with six kinds of LRIs. The turnaround time (from sample registration to result) for the rapid metagenomics test was 6.4 ± 1.4 hours, compared to 94.8 ± 34.9 hours for routine culture. Compared with culture and real-time PCR validation tests, rapid metagenomics achieved 96.6% sensitivity and 88.0% specificity and identified pathogens in 63 out of 161 (39.1%) culture-negative samples. Correlation between enriched anaerobes and lung abscess was observed by Gene Set Enrichment Analysis. Moreover, 38 anaerobic species failed in culture was identified by metagenomics sequencing. The hypothetical impact of metagenomics test proposed antibiotic de-escalation in 34 patients compared to 1 using routine culture.ConclusionsRapid clinical metagenomics test improved pathogen detection yield in the diagnosis of LRI. Empirical antimicrobial therapy could be de-escalated if rapid metagenomics test results were hypothetically applied to clinical management.

背景：采用传统培养方法对下呼吸道感染（LRI）中的细菌病原体进行诊断仍然具有挑战性和耗时性。目标：通过一项大规模的前瞻性研究评估基于快速纳米孔测序的宏基因组学检测在常见LRI中诊断细菌病原体的临床性能。方法：在2018年11月至2019年6月期间，我们在一项单一中心的、前瞻性队列研究中纳入了292名疑似患有LRI的住院患者。在现场进行快速临床宏基因组学检测，并将结果与常规微生物学检测结果进行比较。结果：从六种LRI患者中收集了171份支气管肺泡灌洗液（BAL）和121份痰液样本。快速宏基因组学检测的周转时间（从样本登记到结果）为6.4 ± 1.4小时，而常规培养的周转时间为94.8 ± 34.9小时。与培养和实时PCR验证测试相比，快速宏基因组学检测实现了96.6%的灵敏度和88.0%的特异性，并在161份培养阴性样本中的63份（39.1%）中鉴定出病原体。通过基因集富集分析观察到厌氧菌与肺脓肿之间的相关性。此外，通过宏基因组测序鉴定出38种在培养中失败的厌氧菌种。与常规培养相比，宏基因组测试提出的假设对34名患者进行了抗生素降级，而常规培养仅有1例。结论：快速临床宏基因组学检测提高了LRI诊断中的病原体检测产量。如果将快速宏基因组学检测结果假设应用于临床管理，则经验性抗菌治疗可以降低级别。