Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen, China.
Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands.
PLoS One. 2020 Jun 4;15(6):e0232610. doi: 10.1371/journal.pone.0232610. eCollection 2020.
Pneumonia is one of the most important causes of morbidity and mortality in children. Identification and characterization of pathogens that cause infections are crucial for accurate treatment and accelerated recovery. However, in most cases, the causative agent cannot be identified, which is partly due to the limited spectrum of pathogens covered by current diagnostics based on nucleic acid amplification. Therefore, in this study, we explored the application of metagenomic next-generation sequencing (mNGS) for the diagnosis of children with severe pneumonia. From April to July 2017, 32 hospitalized children with severe nonresponding pneumonia in Shenzhen Children's Hospital were included in this study. Blood tests were conducted immediately after hospitalization to assess cell counts and inflammatory markers, oropharyngeal swabs were collected to identify common pathogens by qPCR and culture. After bronchoscopy, bronchoalveolar lavage fluid (BALF) samples were collected for further pathogen identification using standardized diagnostic tests and mNGS. Blood tests were normal in 3 of the 32 children. In 9 oropharyngeal swabs, bacterial pathogens were detected, in 5 of these Mycoplasma pneumoniae was detected. Adenovirus was detected in 5 BALF samples, using the Direct Immunofluorescence Assay (DFA). In 15 cases, no common pathogens were found in BALF samples, using the current standard diagnostic tests, while in all 32 BALFs, pathogens were identified using mNGS, including adenovirus, Mycoplasma pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, cytomegalovirus and bocavirus. This study shows that, with mNGS, the sensitivity of detection of the causative pathogens in children with severe nonresponding pneumonia is significantly improved. In addition, mNGS gives more strain specific information, helps to identify new pathogens and could potentially help to trace and control outbreaks. In this study, we have shown that it is possible to have the results within 24 hours, making the application of mNGS feasible for clinical diagnostics.
肺炎是导致儿童发病和死亡的最重要原因之一。识别和鉴定导致感染的病原体对于准确治疗和加速康复至关重要。然而，在大多数情况下，无法确定病原体，这部分是由于目前基于核酸扩增的诊断方法所涵盖的病原体谱有限。因此，在本研究中，我们探索了宏基因组下一代测序（mNGS）在诊断儿童重症肺炎中的应用。2017 年 4 月至 7 月，我们纳入了深圳儿童医院 32 例住院的重症非反应性肺炎患儿。患儿入院后立即进行血液检查以评估细胞计数和炎症标志物，或采集咽拭子通过 qPCR 和培养来鉴定常见病原体。支气管镜检查后，收集支气管肺泡灌洗液（BALF）样本，通过标准化诊断测试和 mNGS 进一步鉴定病原体。32 例患儿中 3 例血液检查正常。9 例咽拭子中检测到细菌病原体，其中 5 例检测到肺炎支原体。5 例 BALF 样本中通过直接免疫荧光检测（DFA）检测到腺病毒。在 15 例病例中，使用当前标准诊断测试在 BALF 样本中未发现常见病原体，而在所有 32 例 BALF 样本中，均通过 mNGS 鉴定出病原体，包括腺病毒、肺炎支原体、肺炎链球菌、流感嗜血杆菌、卡他莫拉菌、巨细胞病毒和 bocavirus。本研究表明，使用 mNGS 可显著提高对重症非反应性肺炎患儿致病病原体的检测灵敏度。此外，mNGS 提供了更多的菌株特异性信息，有助于鉴定新的病原体，并有可能帮助追踪和控制疫情。在本研究中，我们表明可以在 24 小时内获得结果，这使得 mNGS 的应用在临床诊断上成为可能。
