Chlamydia pneumoniae infection is associated with atherosclerosis progression, destabilization of atherosclerotic lesions, and cardiovascular disease yet our understanding of how this organism may causally contribute to chronic diseases is not well understood. C. pneumoniae is an obligate intracellular prokaryotic bacterial pathogen that can modulate its interaction with host cells to produce either acute productive infection or chronic persistent infection. Isolates of C. pneumoniae exhibit a finite number of genomic polymorphisms suggesting that intra-strain heterogeneity reflect variants suited for growth or persistence in different in vivo environments or host cell types. We propose to compare respiratory and cardiac C. pneumoniae isolates, plaque, clone and analyze individual variants by polynucleotide polymorphism analysis to identify different genotypes that may be present within single strains or selected in different in vivo environments. We will then test these genotypes in models of in vitro infection to identify strains with propensities to cause chronic infection and atherosclerotic disease. Molecular genetic analysis of the growth of these genotypes using microarray gene expression profiling and quantitative real time polymerase chain reaction will identify subsets of genes that are predictive of acute and chronic diseases. These objectives will be accomplished according to two specific aims involving (1) plaquing, cloning and analyzing chlamydial variants obtained from respiratory and cardiovascular sites and, (2) molecular analysis of pathogen and host cell gene usage patterns during differing growth conditions. These investigations will provide useful information on the degree of genetic heterogeneity inherent in C. pneumoniae populations and how this heterogeneity may contribute to the pathogenesis of C. pneumoniae disease. Results also will have the practical application of providing information to obtain the identity of subsets of C. pneumoniae genes or their products that can be used to target the development of new diagnostic tools or intervention strategies to populations that are at risk of heart disease with a C. pneumoniae-mediated component and to the identification of chronic chlamydial infections in general.