Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Front Cell Infect Microbiol. 2021 Oct 4;11:738074. doi: 10.3389/fcimb.2021.738074. eCollection 2021.
The usefulness of metagenomic next-generation sequencing (mNGS) in identifying pathogens is being investigated. We aimed to compare the power of microbial identification between mNGS and various methods in patients with acute respiratory failure.
We reviewed 130 patients with respiratory failure, and 184 specimens including blood, bronchoalveolar lavage fluid (BALF), sputum, pleural effusion, ascitic fluid, and urine were tested by mNGS and conventional methods (culture, PCR). We also enrolled 13 patients to evaluate the power of mNGS and pathogen targets NGS (ptNGS) in microbial identifications. Clinical features and microbes detected were analyzed.
mNGS outperformed the conventional method in the positive detection rate of (MTB) (OR, ∞; 95% CI, 1-∞; < 0.05), bacteria (OR, 3.7; 95% CI, 2.4-5.8; < 0.0001), fungi (OR, 4.37; 95% CI, 2.7-7.2; < 0.0001), mycoplasma (OR, 10.5; 95% CI, 31.8-115; = 0.005), and virus (OR, ∞; 95% CI, 180.7-∞; < 0.0001). We showed that 20 patients (28 samples) were detected with () by mNGS, but not by the conventional method, and most of those patients were immunocompromised. Read numbers of (), (), (), , (), and () in BALF were higher than those in other sample types, and the read number of () in blood was higher than that in BALF. We found that orotracheal intubation and type 2 diabetes mellitus (T2DM) were associated with a higher detection rate of bacteria and virus by mNGS, immunosuppression was associated with a higher detection rate of fungi and virus by mNGS, and inflammatory markers were associated with mNGS-positive detection rate of bacteria. In addition, we observed preliminary results of ptNGS.
mNGS outperformed the conventional method in the detection of MTB, bacteria, fungi, mycoplasma, and virus. Orotracheal intubation, T2DM, immunosuppression, and inflammatory markers were associated with a higher detection rate of bacteria, fungi, and virus by mNGS. In addition, ptNGS results were consistent with the detection of abundant bacteria, fungi, and mycoplasma in our specimens.
宏基因组下一代测序（mNGS）在鉴定病原体方面的有效性正在研究中。我们旨在比较 mNGS 与各种方法在急性呼吸衰竭患者中微生物鉴定的能力。
我们回顾性分析了 130 例呼吸衰竭患者，对 184 份标本（包括血液、支气管肺泡灌洗液（BALF）、痰液、胸腔积液、腹水和尿液）进行了 mNGS 和常规方法（培养、PCR）检测。我们还招募了 13 例患者，以评估 mNGS 和病原体靶向 NGS（ptNGS）在微生物鉴定中的能力。分析了临床特征和检测到的微生物。
mNGS 在 MTB（OR，∞；95%CI，1-∞；<0.05）、细菌（OR，3.7；95%CI，2.4-5.8；<0.0001）、真菌（OR，4.37；95%CI，2.7-7.2；<0.0001）、支原体（OR，10.5；95%CI，31.8-115；=0.005）和病毒（OR，∞；95%CI，180.7-∞；<0.0001）的阳性检测率方面优于常规方法。我们显示，20 例（28 个样本）患者通过 mNGS 检测到 ，但常规方法未检测到，且这些患者大多数存在免疫功能低下。BALF 中 、 、 、 、 、 （）的读长数高于其他样本类型，血液中 （）的读长数高于 BALF。我们发现，经口气管插管和 2 型糖尿病（T2DM）与 mNGS 检测到的细菌和病毒的阳性检出率较高相关，免疫抑制与 mNGS 检测到的真菌和病毒的阳性检出率较高相关，炎症标志物与 mNGS 检测到的细菌的阳性检出率相关。此外，我们观察到了 ptNGS 的初步结果。
mNGS 在检测 MTB、细菌、真菌、支原体和病毒方面优于常规方法。经口气管插管、T2DM、免疫抑制和炎症标志物与 mNGS 检测到的细菌、真菌和病毒的阳性检出率较高相关。此外，ptNGS 结果与我们标本中大量细菌、真菌和支原体的检测结果一致。
