Tracking disease progression in vivo is essential for the development of 
treatments against bacterial infection. Optical imaging has become a central 
tool for in vivo tracking of bacterial population development and therapeutic 
response. For a precise understanding of in vivo imaging results in terms of 
disease mechanisms derived from detailed postmortem observations, however, a 
link between the two is needed. Here, we develop a model that provides that link 
for the investigation of Citrobacter rodentium infection, a mouse model for 
enteropathogenic Escherichia coli (EPEC). We connect in vivo disease progression 
of C57BL/6 mice infected with bioluminescent bacteria, imaged using optical 
tomography and X-ray computed tomography, to postmortem measurements of colonic 
immune cell infiltration. We use the model to explore changes to both the host 
immune response and the bacteria and to evaluate the response to antibiotic 
treatment. The developed model serves as a novel tool for the identification and 
development of new therapeutic interventions.