c Yersinia enterocolitica is typically considered an extracellular pathogen; however, during the course of an infection, a significant number of bacteria are stably maintained within host cell vacuoles. Little is known about this population and the role it plays during an infection. To address this question and to elucidate the spatially and temporally dynamic gene expression patterns of Y. enterocolitica biovar 1B through the course of an in vitro infection, transcriptome sequencing and differential gene expression analysis of bacteria infecting murine macrophage cells were performed under four distinct conditions. Bacteria were first grown in a nutrient-rich medium at 26°C to establish a baseline of gene expression that is unrelated to infection. The transcriptomes of these bacteria were then compared to bacteria grown in a conditioned cell culture medium at 37°C to identify genes that were differentially expressed in response to the increased temperature and medium but not in response to host cells. Infections were then performed, and the transcriptomes of bacteria found on the extracellular surface and intracellular compartments were analyzed individually. The upregulated genes revealed potential roles for a variety of systems in promoting intracellular virulence, including the Ysa type III secretion system, the Yts2 type II secretion system, and the Tad pilus. It was further determined that mutants of each of these systems had decreased virulence while infecting macrophages. Overall, these results reveal the complete set of genes expressed by Y. enterocolitica in response to infection and provide the groundwork for future virulence studies.T he genus Yersinia includes three species that are pathogenic to humans: Y. pestis, the causative agent of the plague, as well as Y. enterocolitica and Y. pseudotuberculosis, both of which cause gastrointestinal diseases. Of the three organisms, Y. enterocolitica is the species most frequently isolated from humans (1). Y. enterocolitica infections are typically acquired through ingestion of the bacteria in contaminated food or water, especially raw or undercooked pork products (2). After ingestion, the bacteria travel through the gastrointestinal tract to the terminal ileum, where they are able to penetrate the M cells of the Peyer's patches and infect the mesenteric lymph nodes (1-3). This leads to a self-limiting gastroenteritis and mesenteric lymphadenitis in otherwise healthy patients (3). In immunocompromised patients or young children with developing immune systems, the bacteria can spread from the lymph nodes to systemic sites, leading to potentially fatal septicemia (1). Over half of all reported Y. enterocolitica infections occur in children under the age of five, the group that is most predisposed to developing the systemic form of the infection (4).Pathogenic Y. enterocolitica isolates can be divided into six distinct biovars based on several biochemical and physiological attributes (2, 5). Of the six biovars, the North American isolate, biovar 1B, is the most...