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Infection outcome depends strongly on early events occurring immediately when bacteria start interacting with cells in the mucosal membrane. Hitherto reported transcription profiles on host-pathogen interactions are strongly biased towards<jats:italic>in vitro<\/jats:italic>studies. To detail the local<jats:italic>in vivo<\/jats:italic>genetic response to infection, we here profiled host gene expression in a recent experimental model that assures high spatial and temporal control of uropathogenic<jats:italic>Escherichia coli<\/jats:italic>(UPEC) infection within the kidney of a live rat.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Transcriptional profiling of tissue biopsies from UPEC-infected kidney tissue revealed 59 differentially expressed genes 8 h post-infection. Their relevance for the infection process was supported by a Gene Ontology (GO) analysis. Early differential expression at 3 h and 5 h post-infection was of low statistical significance, which correlated to the low degree of infection. Comparative transcriptomics analysis of the 8 h data set and online available studies of early local infection and inflammation defined a core of 80 genes constituting a \"General tissue response to early local bacterial infections\". Among these, 25% were annotated as interferon-\u03b3 (IFN-\u03b3) regulated. Subsequent experimental analyses confirmed a systemic increase of IFN-\u03b3 in rats with an ongoing local kidney infection, correlating to splenic, rather than renal<jats:italic>Ifng<\/jats:italic>induction and suggested this inter-organ communication to be mediated by interleukin (IL)-23. The use of comparative transcriptomics allowed expansion of the statistical data handling, whereby relevant data could also be extracted from the 5 h data set. Out of the 31 differentially expressed core genes, some represented specific 5 h responses, illustrating the value of comparative transcriptomics when studying the dynamic nature of gene regulation in response to infections.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Our hypothesis-free approach identified components of infection-associated multi-cellular tissue responses and demonstrated how a comparative analysis allows retrieval of relevant information from lower-quality data sets. The data further define marked representation of IFN-\u03b3 responsive genes and a prompt inter-organ communication as a hallmark of an early local tissue response to infection.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2164-12-123","type":"journal-article","created":{"date-parts":[[2011,2,22]],"date-time":"2011-02-22T07:19:10Z","timestamp":1298359150000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Comparative tissue transcriptomics reveal prompt inter-organ communication in response to local bacterial kidney infection"],"prefix":"10.1186","volume":"12","author":[{"given":"Jorrit","family":"Boekel","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"\u00d6rjan","family":"K\u00e4llskog","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Monica","family":"Ryd\u00e9n-Aulin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mikael","family":"Rhen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Agneta","family":"Richter-Dahlfors","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,2,21]]},"reference":[{"key":"9922_CR1","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1046\/j.1462-5822.2001.00101.x","volume":"3","author":"F B\u00e4ckhed","year":"2001","unstructured":"B\u00e4ckhed F, S\u00f6derh\u00e4ll M, Ekman P, Normark S, Richter-Dahlfors A: Induction of innate immune responses by Escherichia coli and purified lipopolysaccharide correlate with organ- and cell-specific expression of Toll-like receptors within the human urinary tract. 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