The Department of Respiratory Medicine, the Second People's Hospital of Hefei and Hefei Second People's Hospital Affiliated to Bengbu Medical College, Hefei Hospital Affiliated to Anhui Medical University, Hefei, Anhui 230011, China.
Department of Microbiology, Immunology & Pathology, Des Moines University, Des Moines, IA, 50312, USA.
Curr Pharm Biotechnol. 2024;25(17):2266-2277. doi: 10.2174/0113892010246350231030042340.
BACKGROUND: Metagenomic next-generation sequencing (mNGS) demonstrates great promise as a diagnostic tool for determining the cause of pathogenic infections. The standard diagnostic procedures (SDP) include smears and cultures and are typically viewed as less sensitive and more time-consuming when compared to mNGS. There are concerns about the logistics and ease of transition from SDP to mNGS. mNGS lacks standardization of collection processes, databases, and sequencing. Additionally, there is the burden of training clinicians on interpreting mNGS results. OBJECTIVE: Until now, few studies have explored factors that could be used as early adoption candidates to ease the transition between SDP and mNGS. This study evaluated 123 patients who had received both SDP and mNGS and compared several variables across a diagnostic test evaluation. METHODS: The diagnostic test evaluation observed metrics such as sensitivity, specificity, positive and negative likelihood ratios (PLR, NLR), positive and negative predictive values (PPV, NPV), and accuracy. Factors included various sample sources such as bronchoalveolar lavage fluid (BALF), lung tissue, and cerebral spinal fluid (CSF). An additional factor observed was the patient's immune status. RESULTS: Pathogen detection was found to be significantly greater for mNGS for total patients, BALF sample source, CSF sample source, and non-immunocompromised patients (p<0.05). Pathogen detection was found to be insignificant for lung tissue sample sources and immunocompromised patients. Sensitivity, PLR, NLR, PPV, NPV, and accuracy appeared to be higher with mNGS for the total patients, BALF sample source, and non-immunocompromised patients when compared with SDP (p<0.05). CONCLUSION: With higher metrics in sensitivity, specificity, PLR, NLR, PPV, NPV, and accuracy for overall patients, mNGS may prove a better diagnostic tool than SDP. When addressing sample sources, mNGS for BALF-collected samples appeared to have higher scores than SDP for the same metrics. When patients were in a non-immunocompromised state, mNGS also demonstrated greater diagnostic benefits to BALF and overall patients compared to SDP. This study demonstrates that using BALF as a sample source and selecting non-immunocompromised patients may prove beneficial as early adoption factors for mNGS standard protocol. Such a study may pave the road for mNGS as a routine clinical method for determining the exact pathogenic etiology of lung infections.
背景：宏基因组下一代测序（mNGS）作为确定致病感染原因的诊断工具具有很大的潜力。标准诊断程序（SDP）包括涂片和培养，与 mNGS 相比，通常被认为灵敏度较低，耗时较长。人们对从 SDP 过渡到 mNGS 的后勤和便利性存在担忧。mNGS 在采集过程、数据库和测序方面缺乏标准化。此外，培训临床医生解读 mNGS 结果也是一项负担。
目的：到目前为止，很少有研究探讨可以作为早期采用的因素，以缓解 SDP 和 mNGS 之间的过渡。本研究评估了 123 名同时接受 SDP 和 mNGS 检测的患者，并在诊断测试评估中比较了几个变量。
方法：该诊断测试评估观察了灵敏度、特异性、阳性和阴性似然比（PLR、NLR）、阳性和阴性预测值（PPV、NPV）和准确性等指标。因素包括各种样本来源，如支气管肺泡灌洗液（BALF）、肺组织和脑脊液（CSF）。观察的另一个因素是患者的免疫状态。
结果：总患者、BALF 样本来源、CSF 样本来源和非免疫功能低下患者的 mNGS 病原体检测阳性率显著高于 SDP（p<0.05）。肺组织样本来源和免疫功能低下患者的病原体检测无显著性差异。与 SDP 相比，总患者、BALF 样本来源和非免疫功能低下患者的 mNGS 检测灵敏度、PLR、NLR、PPV、NPV 和准确性似乎更高（p<0.05）。
结论：对于所有患者，mNGS 在灵敏度、特异性、PLR、NLR、PPV、NPV 和准确性方面的指标更高，可能是一种优于 SDP 的诊断工具。在处理样本来源时，BALF 采集样本的 mNGS 似乎比 SDP 在相同指标上的得分更高。当患者处于非免疫功能低下状态时，mNGS 对 BALF 和总患者的诊断益处也大于 SDP。本研究表明，使用 BALF 作为样本来源并选择非免疫功能低下患者，可能有助于将 mNGS 标准方案作为早期采用的因素。这样的研究可能为 mNGS 作为确定肺部感染确切病因的常规临床方法铺平道路。
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