Identification of Pathogen Genomic Differences That Impact Human Immune Response and Disease during Cryptococcus neoformans Infection
Identification of Pathogen Genomic Differences That Impact Human Immune Response and Disease during Cryptococcus neoformans Infection
复制标题
DOI：
10.1128/mbio.01440-19
复制
发表时间：
2019-07-01
期刊：
影响因子：
6.4
通讯作者：
Nielsen, Kirsten
中科院分区：
文献类型：
--
作者：
Gerstein, Aleeza C.;Jackson, Katrina M.;Nielsen, Kirsten
患者在感染期间的预后是由于医疗质量、宿主免疫因素和感染病原体特征之间的复杂相互作用造成的。为了探索病原体基因型对人类生存、免疫反应和其他疾病参数的影响，我们检查了在乌干达进行的隐球菌最佳抗逆转录病毒治疗(COAT)试验期间收集的新生隐球菌分离株。我们测量了参与者的存活率、脑膜炎疾病参数、免疫学表型和病原体的体外生长特征。我们将这些临床数据与我们乌干达参与者群体中最常见的序列类型(ST)的38株新生葡萄球菌分离株的全基因组序列进行了比较，并与另外9种序列类型的另外18株菌株的序列进行了比较，这些序列类型代表了乌干达隐球菌临床分离株的已知遗传多样性。我们集中分析了ST93基因组中的652个多态，这些多态在着丝粒或极端端粒中不存在，并被预测具有适合性效应。Logistic回归和主成分分析确定了40个候选隐球菌基因和3个与人类生存、免疫反应或临床参数相关的假想RNA。我们用这些候选基因的17个可用的KN99α基因缺失菌株感染小鼠，发现35%(6/17)直接影响小鼠的存活。在影响小鼠存活的六个基因缺失中，有四个是新的。这种床边到工作台的翻译研究为未来研究人类隐球菌感染的毒力相关特征确定了重要的候选基因。重要的是，即使有最好的治疗，隐球菌性脑膜炎的死亡率也在20%到60%之间。疾病通常是由新生隐球菌真菌感染引起的，涉及人类宿主和真菌病原体之间的复杂相互作用。尽管以前的研究表明，影响人类疾病的病原体存在遗传差异，但事实证明，很难识别影响人类感染结局的特定新生葡萄球菌基因。在这里，我们利用感染了密切相关的新生葡萄球菌菌株的乌干达患者队列来检查病原体基因变异在几种人类疾病特征中的作用。使用病原体全基因组测序方法，我们发现40个新生链球菌基因与人类疾病有关。令人惊讶的是，这些基因中有许多是隐球菌特有的，具有未知的功能。我们还在感染的小鼠模型中显示了其中一些基因的缺失改变了疾病，证实了它们在疾病中的作用。这些发现特别重要，因为它们是第一次发现与人类隐球菌性脑膜炎相关的新生葡萄球菌基因，并为未来的研究奠定了基础，这些研究可能会导致旨在降低患者死亡率的新的治疗策略。
Patient outcomes during infection are due to a complex interplay between the quality of medical care, host immunity factors, and the infecting pathogen's characteristics. To probe the influence of pathogen genotype on human survival, immune response, and other parameters of disease, we examined Cryptococcus neoformans isolates collected during the Cryptococcal Optimal Antiretroviral Therapy (ART) Timing (COAT) Trial in Uganda. We measured human participant's survival, meningitis disease parameters, immunologic phenotypes, and pathogen in vitro growth characteristics. We compared those clinical data to whole-genome sequences from 38 C. neoformans isolates of the most frequently observed sequence type (ST), ST93, in our Ugandan participant population and to sequences from an additional 18 strains of 9 other sequence types representing the known genetic diversity within the Ugandan Cryptococcus clinical isolates. We focused our analyses on 652 polymorphisms that were variable among the ST93 genomes, were not in centromeres or extreme telomeres, and were predicted to have a fitness effect. Logistic regression and principal component analysis identified 40 candidate Cryptococcus genes and 3 hypothetical RNAs associated with human survival, immunologic response, or clinical parameters. We infected mice with 17 available KN99 alpha gene deletion strains for these candidate genes and found that 35% (6/17) directly influenced murine survival. Four of the six gene deletions that impacted murine survival were novel. Such bedside-to-bench translational research identifies important candidate genes for future studies on virulence-associated traits in human Cryptococcus infections.IMPORTANCE Even with the best available care, mortality rates in cryptococcal meningitis range from 20% to 60%. Disease is often due to infection by the fungus Cryptococcus neoformans and involves a complex interaction between the human host and the fungal pathogen. Although previous studies have suggested genetic differences in the pathogen impact human disease, it has proven quite difficult to identify the specific C. neoformans genes that impact the outcome of the human infection. Here, we take advantage of a Ugandan patient cohort infected with closely related C. neoformans strains to examine the role of pathogen genetic variants on several human disease characteristics. Using a pathogen whole-genome sequencing approach, we showed that 40 C. neoformans genes are associated with human disease. Surprisingly, many of these genes are specific to Cryptococcus and have unknown functions. We also show deletion of some of these genes alters disease in a mouse model of infection, confirming their role in disease. These findings are particularly important because they are the first to identify C. neoformans genes associated with human cryptococcal meningitis and lay the foundation for future studies that may lead to new treatment strategies aimed at reducing patient mortality.