A Multi-Omics Approach to the Examination of Bacterial Co-pathogens

多种微生物感染与重要的人类疾病有关，包括慢性伤口感染， 肺部感染和菌血症，可能涉及不同种类的细菌，或细菌和病毒，或 细菌和真核生物。虽然在某些类型的疾病中存在共同病原体， 使用发病机制模型研究共同病原体相互作用的复杂性限制了我们对 不同病原体在这些疾病中的作用。拟议研究的科学前提是， 尽管多种微生物感染与传染病有关，但先前的实验研究集中在 单一病原体，通常不考虑宿主：病原体相互作用的存在下， 病原体或宿主微生物群的其他成员。因此，我们不仅要考虑联合国的影响， 病原体对肺部疾病和肺部感染，但也将扩大传统的实验室检测，以及 组织培养和小鼠模型，以更密切地概括宿主：病原体相互作用的复杂性。我们 将对气单胞菌属、E.大肠杆菌和/或志贺氏菌在大肠杆菌合并感染中的作用，以及流感的作用 病毒和肺炎链球菌对呼吸道合并感染。在目标1中，我们将使用比较基因组学 和宏基因组学，以提供洞察是否有基因/基因型，或微生物群落 与腹泻和/或这些肠道病原体的共病原体相互作用相关。在目标2中，我们将进一步 使用宿主和细菌的双重转录组学研究肠道共病原体的意义 双方研究共同病原体相互作用的影响，在人类肠道肠和小鼠模型与 简化的肠道微生物群。在目标3中，我们将通过描述 流感病毒对S.肺炎的呼吸道感染，通过执行双重转录 使用离体人肺上皮细胞模型和肺感染的体内小鼠模型进行分析。我们 中心假设是多种病原体的相互作用，细菌-细菌或细菌-病毒，可以导致 每种病原体的毒力模式发生改变，这反过来又会影响与宿主的相互作用， 并且在疾病的结果中起着重要作用。我们进一步假设，宿主的反应不同， 单一感染和合并感染。我们预计，在完成研究后，我们将确定： 病原体和宿主在共感染中的转录谱与单感染相比的差异， 感染，（ii）以前不知道参与这些重要疾病发病机制的基因， 病原体，和（iii）新的宿主途径驱动免疫和其他反应的共同感染。总体看 这项研究的发现将促进对细菌-细菌和细菌-病毒共病原体作用的认识 在肺部感染和肺部疾病，并将使未来的研究的作用，具体的真核细胞和 原核基因和途径在共同病原体和/或宿主：病原体相互作用参与这些疾病。 这些研究将确定未来研究的目标，作为新的治疗干预措施。

Polymicrobial infections have been linked to important human diseases including chronic wound infections, lung infections, and bacteremia, and can involve different species of bacteria, or bacteria and viruses, or bacteria and eukaryotes. Although the existence of co-pathogens in certain types of disease is established, the complexity of studying co-pathogen interactions using models of pathogenesis has limited our understanding of the role of the different pathogens in these diseases. The scientific premise of the proposed studies is that although polymicrobial infections are linked to infectious diseases, prior experimental studies have focused on single pathogens and have typically not considered the host:pathogen interactions in the presence of co- pathogens or with other members of the host's microbiota. Thus, we will consider not only the impact of co- pathogens on diarrheal illness and lung infections, but will also expand traditional laboratory assays, as well as tissue culture and mouse models to more closely recapitulate the complexity of host:pathogen interactions. We will investigate Aeromonas, E. coli, and/or Shigella in diarrheal co-infections, and the contributions of influenza virus and Streptococcus pneumoniae to respiratory co-infections. In Aim 1 we will use comparative genomics and metagenomics to provide insight into whether there are genes/genotypes, or microbial communities associated with diarrhea and/or co-pathogen interactions of these diarrheal pathogens. In Aim 2 we will further investigate the significance of diarrheal co-pathogens using dual transcriptomics on both the host and bacterial sides to study the impact of co-pathogen interactions in human intestinal enteroids and a mouse model with a simplified intestinal microbiota. In Aim 3, we will diversify our studies of co-infections by characterizing the impact of influenza virus on S. pneumoniae infection of the respiratory tract by performing dual transcriptional analyses with an ex vivo human lung epithelial cell model and an in vivo mouse model of lung infection. Our central hypothesis is that the interaction of multiple pathogens, bacterial-bacterial or bacterial-viral, can result in altered patterns of virulence of each of the pathogens, which will in turn influence interactions with the host, and have a significant role in the disease outcome. We further hypothesize that host responses differ between mono-infections and co-infections. We anticipate that upon completion of the studies we will have identified: (i) differences in the transcriptional profiles of the pathogens and the host in co-infection compared with mono- infection, (ii) genes that were not previously known to be involved in pathogenesis for these important pathogens, and (iii) novel host pathways driving immune and other responses to co-infections. Overall, the findings of this study will advance knowledge of the role of bacterial-bacterial and bacterial-viral co-pathogens in lung infections and diarrheal illness, and will enable future studies of the role of specific eukaryotic and prokaryotic genes and pathways in co-pathogen and/or host:pathogen interactions involved in these diseases. These studies will identify targets for future investigation as novel therapeutic interventions.