Etiology of Severe Pneumonia in Children in Alveolar Lavage Fluid Using a High-Throughput Gene Targeted Amplicon Sequencing Assay.
Etiology of Severe Pneumonia in Children in Alveolar Lavage Fluid Using a High-Throughput Gene Targeted Amplicon Sequencing Assay.
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DOI：
10.3389/fped.2021.659164
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发表时间：
2021
影响因子：
2.6
通讯作者：
Shen J
中科院分区：
文献类型：
--
作者：
Li F;Wang Y;Zhang Y;Shi P;Cao L;Su L;Zhu Q;Wang L;Lu R;Tan W;Shen J
目的：目的评价高通量基因靶向扩增子测序（TAS）技术检测重症社区获得性肺炎（SCAP）患儿肺泡灌洗液（ALF）中病原微生物的诊断价值。研究方法：对复旦大学附属儿童医院2019年1月1日至2019年3月31日收治的47例重症肺炎患者的48份冷冻ALF样本进行回顾性研究。通过多重PCR（Multi-PCR）检测和TAS检测对所有样本进行检测。将TAS样本组的结果与多重PCR和常规检测（CT）（包括培养、直接荧光抗体法（DFA）和单重聚合酶链反应（PCR））进行平行比较。结果：CT检出病原体39例，检出率为81.2%。结果显示，48份标本中，呼吸道合胞病毒（RSV）、腺病毒（ADV）、甲型流感病毒（FLUA）、B流感病毒（FLUB）、副流感病毒1-3型（PIV 1 -3）和人偏肺病毒（hMPV）8种常见呼吸道病毒检出率为31.2%（15/48）。以CT结果作为判定TAS结果的“金标准”，TAS检出病原体的比例为70.8%（34/48）。TAS和CT之间的病原体检出比例差异无统计学意义（p = 0.232）。TAS对CT诊断的敏感性和特异性为87.1%（95% CI，71.77-95.18%）和100.0%（95%CI，62.88 ~ 100%），阳性预测值（PPV）和阴性预测值（NPV）均为100.0%（95% CI，87.35-100%）和64.2%（95% CI，35.62-86.02%）。以Multi-PCR结果为“金标准”，TAS的总病原体检出率为83.3%（40/48），与Multi-PCR结果有显著性差异（p = 0.003）。TAS与Multi-PCR相比的敏感性和PPV分别为83.3%（95% CI，69.23-92.03%）和100.0%（95% CI，89.08-100%）。CT、多重PCR和TAS检测证实合并感染率较高。肺炎支原体（MP）和ADV是所有三种检测中最常检出的两种病原体。结论：与CT和Multi-PCR方法相比，TAS方法对ALF中细菌和病毒病原体的检测具有良好的性能。需要更多的研究来建立基于TAS读数或分析平台的解释标准。
Objective: To evaluate the diagnostic value of a high-throughput gene targeted amplicon sequencing (TAS) assay for detecting pathogenic microorganisms in alveolar lavage fluid (ALF) from children with severe community-acquired pneumonia (SCAP). Methods: A retrospective study was performed on 48 frozen ALF samples from 47 severe pneumonia cases admitted to Children's Hospital of Fudan University from January 1, 2019, to March 31, 2019. All samples were tested by a multiplex PCR (Multi-PCR) assay and a TAS assay. The results of the TAS panels were parallel compared with Multi-PCR and Conventional Tests (CT) including culture, direct fluorescent antibody method (DFA), and singleplex polymerase chain reaction (PCR). Results: The proportion of pathogens detection by CT was 81.2% (39/48). The 8 common respiratory viruses including respiratory syncytial virus (RSV), adenovirus (ADV), influenza A virus (FLUA), influenza B virus (FLUB), parainfluenza virus 1–3 (PIV1-3), and human Metapneumovirus (hMPV) were found in 31.2% (15/48) of the 48 samples by DFA. With the criteria of CT results used as “Golden Standard” for determing of TAS results, the proportion of pathogens detection by TAS was 70.8% (34/48). The difference of proportion of pathogens detection between TAS and CT was not statistically significant (p = 0.232). The sensitivity and specificity of TAS for pathogens detection based on CT were 87.1% (95% CI, 71.77–95.18%) and 100.0% (95% CI, 62.88–100%), the positive predictive value (PPV) and negative predictive value (NPV) were 100.0% (95% CI, 87.35–100%) and 64.2% (95% CI, 35.62–86.02%), respectively. While Multi-PCR results were used as “Golden Standard,” the total pathogens detection rate of TAS was 83.3% (40/48), which had a significant difference with that of Multi-PCR (p = 0.003). The sensitivity and PPV of TAS compared with Multi-PCR were 83.3% (95% CI, 69.23–92.03%) and 100.0% (95% CI, 89.08–100%), respectively. High rates of co-infection were proved by CT, Multi-PCR, and TAS. Mycoplasma pneumoniae (MP) and ADV were the two most frequently detected pathogens in all three assays. Conclusion: Compared with the CT and Multi-PCR methods, this TAS assay had a good performance in detecting bacteriological and viral pathogens from ALF. More research is needed to establish interpretation criteria based on TAS reads or analysis platforms.
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影响因子：
4.3
作者：
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DOI：
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发表时间：
2019-01-24
期刊：
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影响因子：
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