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（hematopoietic cellular transplant, HCT）受者下呼吸道感染（lower respiratory tract infection, LRTI）的病因，这使得针对性治疗方案难以实施。
研究目的：为满足优化LRTI诊断技术的需求，本研究评估了支气管肺泡灌洗（bronchoalveolar lavage, BAL）样本宏基因组下一代测序（metagenomic next-generation sequencing, mNGS）在罹患急性呼吸道疾病的HCT患者中检测病原微生物的应用价值。
研究方法：本研究纳入2012年1月至2013年5月于密歇根大学接受支气管肺泡灌洗的22名19~69岁HCT术后成人急性呼吸道疾病患者。对其BAL液开展mNGS检测，以识别微生物并同步分析宿主转录应答情况，并将检测结果与常规微生物学检测方法进行对比。
研究指标与主要结果：临床常规诊疗检测在7名患者（占比32%）中检出微生物，其中6名患者的检出物被主管医师认定为致病菌，且所有致病菌均被mNGS成功检出。在6份常规检测结果为阴性的样本中，mNGS还检出了此前未被识别的LRTI致病菌，包括人冠状病毒229E、人鼻病毒A、亲近棒杆菌（Corynebacterium propinquum）和轻型链球菌（Streptococcus mitis），上述发现均通过独立PCR及16S rRNA测序得到验证。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），且其呼吸道菌群多样性显著降低（p=0.017）。