State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
Department of Critical Care Medicine, The Fifth Medical Center of PLA General Hospital, Beijing, China.
J Transl Med. 2023 Oct 27;21(1):762. doi: 10.1186/s12967-023-04562-0.
Early availability of pathogen identification in urinary tract infections (UTIs) has critical importance in disease management. Metagenomic next-generation sequencing (mNGS) has the potential to transform how acute and serious infections are diagnosed by offering unbiased and culture-free pathogen detection. However, clinical experience with application of the mNGS test is relatively limited.
We therefore established a MinION-based mNGS pathogens diagnostic platform and evaluated its potential for clinical implementation in UTIs with clinical samples. 213 urine samples from patients with suspected UTIs were included and subjected to mNGS testing using the MinION platform. mNGS results were compared to the gold standard of clinical culture and composite standard of combining clinical testing, confirmatory qPCR testing, and clinical adjudication by doctors.
The mNGS exhibited a sensitivity of 81.4% and a specificity of 92.3%, along with a positive predictive value of 96.6%, a negative predictive value of 64.9%, and an overall accuracy of 84.4%, all of which were determined based on the gold standard of routine culture results. When assessed against the composite standard, the sensitivity and specificity both increased to 89.9% and 100%, respectively, while the accuracy rose to 92.4%. Notably, the positive predictive value and negative predictive value also saw improvements, reaching 100% and 76.8%, respectively. Moreover, this diagnostic platform successfully identified dsDNA viruses. Among the 65 culture-negative samples, the viral detection rate reached 33.8% (22/65) and was subsequently validated through qPCR. Furthermore, the automatic bioinformatics pipeline we developed enabled one-click analysis from data to results, leading to a significant reduction in diagnosis time.
These results demonstrate that the pathogen detection performance of mNGS is sufficient for diagnostic testing in clinical settings. As the method is generally unbiased, it can improve diagnostic testing of UTIs and other microbial infections.
尿路感染（UTI）病原体鉴定的早期获得对疾病管理具有至关重要的意义。宏基因组下一代测序（mNGS）有可能通过提供无偏倚和无需培养的病原体检测来改变急性和严重感染的诊断方式。然而，mNGS 测试的临床应用经验相对有限。
因此，我们建立了基于 MinION 的 mNGS 病原体诊断平台，并评估了其在 UTI 临床样本中的应用潜力。共纳入 213 例疑似 UTI 患者的尿液样本，使用 MinION 平台进行 mNGS 检测。将 mNGS 结果与临床培养的金标准和将临床检测、确认 qPCR 检测和医生临床判断相结合的综合标准进行比较。
mNGS 的敏感性为 81.4%，特异性为 92.3%，阳性预测值为 96.6%，阴性预测值为 64.9%，总准确率为 84.4%，均基于常规培养结果的金标准确定。当与综合标准进行评估时，敏感性和特异性均提高至 89.9%和 100%，准确性提高至 92.4%。值得注意的是，阳性预测值和阴性预测值也有所提高，分别达到 100%和 76.8%。此外，该诊断平台成功鉴定了双链 DNA 病毒。在 65 例培养阴性样本中，病毒检测率达到 33.8%（22/65），并通过 qPCR 进行了后续验证。此外，我们开发的自动生物信息学分析流程能够实现从数据到结果的一键分析，显著缩短了诊断时间。
这些结果表明，mNGS 的病原体检测性能足以满足临床诊断测试的要求。由于该方法通常无偏倚，因此可以提高 UTI 和其他微生物感染的诊断检测。
