Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details.
Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details.
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DOI：
10.1186/s40168-017-0234-1
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发表时间：
2017-02-10
期刊：
影响因子：
15.5
通讯作者：
von Mering C
中科院分区：
文献类型：
--
作者：
Feigelman R;Kahlert CR;Baty F;Rassouli F;Kleiner RL;Kohler P;Brutsche MH;von Mering C
囊性纤维化（CF）是一种危及生命的遗传性疾病，其特征是由于气道内异常粘稠的粘液分泌物引起的慢性微生物肺部感染。CF的临床管理通常包括定期的尿道培养，以确定病原体并指导治疗。然而，基于培养的方法可能会错过非典型或生长缓慢的微生物。此外，由于有限的分类分辨率，分离的微生物通常不能在菌株水平上分类。在这里，我们表明，痰液DNA的非靶向宏基因组测序可以提供超出基于培养的诊断可能性的有价值的信息。我们对6名CF患者和11名对照样本（包括健康受试者和慢性阻塞性肺疾病患者）的痰液进行测序，而无需事先耗尽人类DNA或细胞大小选择，从而获得迄今为止CF呼吸道微生物的最无偏见和最全面的表征。我们详细描述了CF和健康肺微生物组，重建了几乎完整的病原体基因组，并证实CF肺始终表现出减少的微生物多样性。至关重要的是，当与现有的多位点序列分型数据库结合分析时，所获得的基因组序列能够详细鉴定确切的病原体菌株类型。我们还检测到了假定的致病岛和抗生素耐药性指标，与独立的临床试验一致。无偏见的痰液宏基因组学提供了肺部病原体微生物组的深入概况，这是对标准的基于培养的报告的补充，并且比标准的基于培养的报告更详细。此外，可以推断出优势病原体的功能和分类特征，包括抗生素耐药性，从而支持准确和非侵入性的临床诊断。本文的在线版本（doi：10.1186/s40168-017-0234-1）包含补充材料，可供授权用户使用。
Cystic fibrosis (CF) is a life-threatening genetic disorder, characterized by chronic microbial lung infections due to abnormally viscous mucus secretions within airways. The clinical management of CF typically involves regular respiratory-tract cultures in order to identify pathogens and to guide treatment. However, culture-based methods can miss atypical or slow-growing microbes. Furthermore, the isolated microbes are often not classified at the strain level due to limited taxonomic resolution. Here, we show that untargeted metagenomic sequencing of sputum DNA can provide valuable information beyond the possibilities of culture-based diagnosis. We sequenced the sputum of six CF patients and eleven control samples (including healthy subjects and chronic obstructive pulmonary disease patients) without prior depletion of human DNA or cell size selection, thus obtaining the most unbiased and comprehensive characterization of CF respiratory tract microbes to date. We present detailed descriptions of the CF and healthy lung microbiome, reconstruct near complete pathogen genomes, and confirm that the CF lungs consistently exhibit reduced microbial diversity. Crucially, the obtained genomic sequences enabled a detailed identification of the exact pathogen strain types, when analyzed in conjunction with existing multi-locus sequence typing databases. We also detected putative pathogenicity islands and indicators of antibiotic resistance, in good agreement with independent clinical tests. Unbiased sputum metagenomics provides an in-depth profile of the lung pathogen microbiome, which is complementary to and more detailed than standard culture-based reporting. Furthermore, functional and taxonomic features of the dominant pathogens, including antibiotics resistances, can be deduced—supporting accurate and non-invasive clinical diagnosis. The online version of this article (doi:10.1186/s40168-017-0234-1) contains supplementary material, which is available to authorized users.