Characterization of Salmonella enterica serovar Enteritidis was refined by incorporating new data from isolates obtained from avian sources, from the spleens of naturally infected mice, and from the United Kingdom into an existing lipopolysaccharide (LPS) O-chain compositional database. From least to greatest, the probability of avian isolates producing high-molecular-mass LPS O chain ranked as follows: pooled kidney, liver, and spleen; intestine; cecum; ovary and oviduct; albumen; yolk; and whole egg. Mouse isolates were most like avian intestinal samples, whereas United Kingdom isolates were most like those from the avian reproductive tract and egg. Non-reproductive tract organ isolates had significant loss of O chain. Isogenic isolates that varied in ability to make biofilm and to be orally invasive produced different O-chain structures at 25°C but not at 37°C. Hens infected at a 91:9 biofilm-positive/-negative colony phenotype ratio yielded only the negative phenotype from eggs. These results indicate that the environment within the hen applies stringent selection pressure on subpopulations of S. enterica serovar Enteritidis at certain points in the infection pathway that ends in egg contamination. The avian cecum, rather than the intestines, is the early interface between the environment and the host that supports emergence of subpopulation diversity. These results suggest that diet and other factors that alter cecal physiology should be investigated as a means to reduce egg contamination.Salmonella enterica serovar Enteritidis is the leading cause of food-borne salmonellosis worldwide, in part because it is the only one of more than 2,000 serotypes that efficiently contaminates the hen egg and causes human illness (1, 48). S. enterica serovar Enteritidis resembles other pathogenic salmonellae with regard to known virulence mechanisms central to host cell invasion, survival, and growth in the host (7, 9-11, 15, 23, 36, 38, 46, 51, 52). It is important to determine differences between S. enterica serovar Enteritidis and other salmonellae because this information could help reduce egg contamination, specifically, compared to carcass contamination. The egg is produced, marketed, and used by the consumer differently from meat, which suggests that control strategies tailored to the egg industry are needed to realize reductions beyond those already achieved (5). Analysis of strain heterogeneity has established that egg-contaminating S. enterica serovar Enteritidis is predominantly clonal (25,28,31,32,35) but that it nonetheless generates substantial phenotypic variation that alters the incidence of egg contamination in infection models. Chemotyping of the lipopolysaccharide (LPS) O chain is a sensitive method of phenotypic analysis that combines stoichiometry with statistical analysis to produce clusters of data that correlate with LPS O-chain structure (41). Chemotyping has shown that S. enterica serovar Enteritidis efficiently produces high-molecular-mass (HMM) LPS O chain, whereas Salmonella enterica serovar ...