Data from: Metagenomic sequencing detects respiratory pathogens in hematopoietic cellular transplant patients

Rationale: Current microbiologic diagnostics often fail to identify the etiology of lower respiratory tract infections (LRTI) in hematopoietic cellular transplant recipients (HCT), which precludes the implementation of targeted therapies.
Objectives: To address the need for improved LRTI diagnostics, we evaluated the utility of metagenomic next generation sequencing (mNGS) of bronchoalveolar lavage (BAL) to detect microbial pathogens in HCT patients with acute respiratory illnesses.
Methods: We enrolled 22 post-HCT adults ages 19-69 years with acute respiratory illnesses who underwent BAL at the University of Michigan between January 2012 and May 2013. mNGS was performed on BAL fluid to detect microbes and simultaneously assess the host transcriptional response. Results were compared against conventional microbiologic assays.
Measurements and Main Results: Standard of care clinical diagnostics identified microbes in seven patients (32%), six of which were considered pathogens by treating physicians, and all of which were detected by mNGS. Previously unrecognized LRTI pathogens were also identified in six patients for whom standard testing was negative (human coronavirus 229E, human rhinovirus A, Corynebacterium propinquum and Streptococcus mitis); findings were confirmed by independent PCR and 16S rRNA sequencing. Relative to patients without infection, patients with infection had increased expression of immunity related genes (p=0.022) and significantly lower diversity of their respiratory microbiome (p=0.017).

研究背景：当前微生物诊断技术往往无法明确造血细胞移植受者（hematopoietic cellular transplant recipients, HCT）下呼吸道感染（lower respiratory tract infections, LRTI）的病原体病因，这一局限阻碍了靶向治疗的开展。
研究目的：为满足改进LRTI诊断方案的临床需求，本研究评估了支气管肺泡灌洗（bronchoalveolar lavage, BAL）液宏基因组下一代测序（metagenomic next generation sequencing, mNGS）用于检测急性呼吸道疾病HCT患者体内病原微生物的应用效能。
研究方法：本研究纳入2012年1月至2013年5月期间，于密歇根大学接受BAL检查的22例19~69岁HCT术后成人急性呼吸道疾病患者。对采集的BAL液开展mNGS检测，以同步识别微生物病原体并分析宿主转录应答特征，同时将mNGS结果与常规微生物学检测方法进行对比分析。
观测指标与主要结果：临床标准诊疗检测仅在7例患者（占比32%）中检出病原体，其中6例被经治医师判定为致病病原体，且上述所有病原体均被mNGS成功检出。另有6例常规检测结果为阴性的患者，经mNGS发现了此前未被识别的LRTI病原体，包括人冠状病毒229E、人鼻病毒A、近缘棒状杆菌和缓症链球菌，该检测结果经独立聚合酶链式反应（polymerase chain reaction, PCR）与16S rRNA测序验证。与未发生感染的患者相比，感染患者的免疫相关基因表达水平显著上调（p=0.022），且呼吸道微生物组多样性显著降低（p=0.017）。