Whole exome sequencing of germline DNA was performed and subsequent polymorphisms in genes known and putatively involved in the innate immune response to fungi were identified

Disease can be conceptualized as the result of interactions between infecting microbe and holobiont, the combination of a host and its microbial communities. It is likely that genomic variation in the host, infecting microbe, and commensal microbiota are key determinants of infectious disease clinical outcomes. However, until recently, simultaneous, multiomic investigation of infecting microbe and holobiont components has rarely been explored. Herein, we characterized the infecting microbe, host, micro- and mycobiomes leading up to infection onset in a leukemia patient that developed invasive mucormycosis. We discovered that the patient was infected with a strain of the recently described Mucor velutinosus species which we determined was hypervirulent in a Drosophila challenge model and has a predisposition for skin dissemination. After completing the infecting M. velutinosus genome and genomes from four other Mucor species, comparative pathogenomics was performed and assisted in identifying 66 M. velutinosus-specific putatively secreted proteins, including multiple novel secreted aspartyl proteinases which may contribute to the unique clinical presentation of skin dissemination. Whole exome sequencing of the patient revealed multiple non-synonymous polymorphisms in genes critical to control of fungal proliferation, such as TLR6 and PTX3. Moreover, the patient had a non-synonymous polymorphism in the NOD2 gene and a missense mutation in FUT2, which have been linked to microbial dysbiosis and microbiome diversity maintenance during physiologic stress, respectively. In concert with host genetic polymorphism data, the micro- and mycobiome analyses revealed that the infection developed amid a dysbiotic microbiome with low α-diversity, dominated by staphylococci. Additionally, longitudinal mycobiome data showed that M. velutinosus DNA was detectable in oral samples preceding disease onset. Our genome-level study of the host-infecting microbe-commensal triad extends the concept of personalized genomic medicine to the holobiont-infecting microbe interface thereby offering novel opportunities for using synergistic genetic methods to increase understanding of infectious diseases pathogenesis and clinical outcomes.EGA study EGAS00001001542

疾病可被理解为侵染微生物与全功能生物群（holobiont）——即宿主与其微生物群落的组合——之间相互作用的结果。宿主、侵染微生物以及共生微生物群的基因组变异，大概率是决定传染病临床结局的关键因素。然而直至近期，针对侵染微生物与全功能生物群组分的同步多组学研究仍鲜有开展。本研究对一名罹患侵袭性毛霉病的白血病患者感染发作前的侵染微生物、宿主、细菌微生物组与真菌微生物组（mycobiome）进行了表征分析。本研究发现该患者感染了近期被描述的绒状毛霉（Mucor velutinosus）菌株，经果蝇攻毒模型验证该菌株为强毒株，且具有皮肤播散的倾向。在完成侵染性绒状毛霉基因组以及另外4种毛霉属物种的基因组组装后，本研究开展了比较病原基因组学分析，成功鉴定出66种绒状毛霉特异性的推定分泌蛋白，其中包含多种新型分泌天冬氨酸蛋白酶，这类蛋白酶或与该菌株皮肤播散的独特临床表型相关。对该患者的全外显子组测序结果显示，其体内多个调控真菌增殖的关键基因存在非同义多态性，例如TLR6与PTX3基因。此外，该患者的NOD2基因存在非同义多态性，FUT2基因存在错义突变；既往研究表明，这两类变异分别与微生物群失调以及生理应激状态下微生物组多样性维持相关。结合宿主遗传多态性数据，细菌与真菌微生物组分析结果显示，该患者的感染发生于以葡萄球菌属为主、α多样性较低的失调微生物群环境中。此外，纵向真菌微生物组测序数据显示，在疾病发作前的口腔样本中即可检测到绒状毛霉的DNA。本研究针对宿主-侵染微生物-共生微生物三者开展的基因组层面研究，将个性化基因组医学的概念拓展至全功能生物群-侵染微生物互作界面，为利用协同遗传方法加深对传染病发病机制与临床结局的理解提供了全新思路。EGA研究编号：EGAS00001001542