Yersinia pestis, the causative agent of plague, is a high-priority pathogen that continues to cause outbreaks worldwide. The ability of Y. pestis to be transmitted via respiratory droplets and its history of weaponization has led to its classification as a Tier 1 Select Agent most likely to be used as a biological weapon. The most deadly form of disease caused by Y. pestis, pneumonic plague, results from the deposition of bacteria into the lungs and has mortality rates approaching 100% in the absence of treatment within 24 hours of the onset of symptoms. The Goldman lab has previously characterized pneumonic plague progression as biphasic, presenting with two distinct disease phases. Rapid bacterial growth during an initial pre-inflammatory phase transitions into the second pro-inflammatory phase where disease symptoms present and lead to death of the host. Using in vivo analyses and focusing on relevant cell types during pneumonic plague infection host pathways can be identified that may be manipulated to extend the 24 hour window for treatment of pneumonic plague. During pneumonic plague, the bacterium Yersinia pestis elicits the development of neutrophil-rich inflammatory lung lesions that continue to expand, eventually consolidating entire lobes of the lung during infection. This lesion development and persistence is poorly understood. In this dissertation I examine spatially distinct regions of lung lesions using laser capture microdissection and RNAseq to identify transcriptional differences between lesion microenvironments. I provide evidence that cellular pathways involved in leukocyte migration and apoptosis are down-regulated in the center of lung lesions compared to the periphery. Probing for the bacterial factor(s) important for the alteration in neutrophil survival, I provide evidence that Y. pestis increases neutrophil survival through a mechanism that is dependent on the type III secretion system effector YopM. Additionally, I investigate the roles of reactive oxygen and nitrogen species that are typically used as neutrophil defense mechanisms, and provide evidence that these molecules are important for controlling early establishment of Y. pestis in the lungs. This research explores the complexity of spatially distinct host-microbe interactions in vivo and emphasizes the importance of cell-relevant assays in understanding Y. pestis virulence.