Clinical Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo, China.
Infection Technology Platform, Dian Diagnostics Group Co., Ltd., Hangzhou, China.
Front Cell Infect Microbiol. 2024 Aug 27;14:1451440. doi: 10.3389/fcimb.2024.1451440. eCollection 2024.
Although the emerging NGS-based assays, metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS), have been extensively utilized for the identification of pathogens in pulmonary infections, there have been limited studies systematically evaluating differences in the efficacy of mNGS and multiplex PCR-based tNGS in bronchoalveolar lavage fluid (BALF) specimens.
In this study, 85 suspected infectious BALF specimens were collected. Parallel mNGS and tNGS workflows to each sample were performed; then, we comparatively compared their consistency in detecting pathogens. The differential results for clinically key pathogens were confirmed using PCR.
The microbial detection rates of BALF specimens by the mNGS and tNGS workflows were 95.18% (79/83) and 92.77% (77/83), respectively, with no significant difference. mNGS identified 55 different microorganisms, whereas tNGS detected 49 pathogens. The comparative analysis of mNGS and tNGS revealed that 86.75% (72/83) of the specimens were complete or partial concordance. Particularly, mNGS and tNGS differed significantly in detection rates for some of the human herpesviruses only, including (P<0.001), (P<0.001), (P<0.05) and (P<0.01), in which tNGS always had higher detection rates. Orthogonal testing of clinically critical pathogens showed a total coincidence rate of 50% for mNGS and PCR, as well as for tNGS and PCR.
Overall, the performance of mNGS and multiplex PCR-based tNGS assays was similar for bacteria and fungi, and tNGS may be superior to mNGS for the detection of DNA viruses. No significant differences were seen between the two NGS assays compared to PCR.
尽管新兴的基于 NGS 的检测方法，宏基因组下一代测序（mNGS）和靶向下一代测序（tNGS），已被广泛用于鉴定肺部感染中的病原体，但对于 mNGS 和基于多重 PCR 的 tNGS 在支气管肺泡灌洗液（BALF）标本中检测病原体的效果差异，仅有有限的研究进行了系统评估。
本研究共收集了 85 例疑似感染性 BALF 标本。对每个样本平行进行 mNGS 和 tNGS 工作流程，然后比较它们在检测病原体方面的一致性。使用 PCR 对临床上关键病原体的差异结果进行了确认。
mNGS 和 tNGS 工作流程对 BALF 标本的微生物检测率分别为 95.18%（79/83）和 92.77%（77/83），无显著差异。mNGS 鉴定出 55 种不同的微生物，而 tNGS 检测出 49 种病原体。mNGS 和 tNGS 的比较分析显示，86.75%（72/83）的标本完全或部分一致。特别是，mNGS 和 tNGS 在某些人类疱疹病毒的检测率上存在显著差异，包括 （P<0.001）、 （P<0.001）、 （P<0.05）和 （P<0.01），其中 tNGS 的检测率总是更高。对临床上关键病原体的正交检测显示，mNGS 和 PCR 的总符合率为 50%，tNGS 和 PCR 的总符合率也为 50%。
总体而言，mNGS 和基于多重 PCR 的 tNGS 检测方法对细菌和真菌的性能相似，而 tNGS 可能优于 mNGS 检测 DNA 病毒。与 PCR 相比，两种 NGS 检测方法之间没有观察到显著差异。
