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

多菌感染与包括慢性伤口感染在内的重要人类疾病有关， 肺部感染和菌血症，可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共病原体的存在已被证实，但 使用致病模型研究共病原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 尽管多菌感染与传染病有关，但先前的实验研究主要集中在 单一病原体，通常没有考虑寄主：在存在共同病原体的情况下病原体相互作用 病原体或与宿主微生物区系的其他成员。因此，我们不仅会考虑联合- 对腹泻疾病和肺部感染的病原体，但也将扩大传统的实验室分析以及 组织培养和小鼠模型更接近地概括了宿主的复杂性：病原体的相互作用。我们 将调查腹泻合并感染中的气单胞菌、大肠杆菌和/或志贺氏菌，以及流感的影响 病毒和肺炎链球菌对呼吸道的联合感染。在目标1中，我们将使用比较基因组学 和元基因组学，以深入了解是否存在基因/基因类型或微生物群落 与腹泻和/或这些腹泻病原体的共病原体相互作用有关。在目标2中，我们将进一步 利用双重转录组技术研究腹泻共病原菌对宿主和细菌的意义 侧方研究共病原体相互作用对人类肠类和小鼠模型的影响 简化的肠道微生物区系。在目标3中，我们将通过描述联合感染的特征来多样化我们的联合感染研究 流感病毒双转录对肺炎链球菌呼吸道感染的影响 用体外人肺上皮细胞模型和体内小鼠肺部感染模型进行分析。我们的 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 在每种病原体的毒力模式改变中，这将反过来影响与宿主的相互作用， 并且在疾病的结局中起着重要作用。我们进一步假设宿主的反应不同于 单一感染和混合感染。我们预期在完成研究后，我们会确定：(I) 与单一感染相比，混合感染的病原体和宿主的转录图谱的差异 感染，(Ii)以前未知参与这些重要疾病的发病机制的基因 病原体，以及(Iii)驱动免疫和其他对联合感染的反应的新宿主途径。总体而言， 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了解 在肺部感染和腹泻疾病中的作用，并将使未来对特定的真核细胞和 共病原体和/或宿主中的原核生物基因和途径：参与这些疾病的病原体相互作用。 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.