Identification of Commensal <i>Escherichia coli</i> Genes Involved in Biofilm Resistance to Pathogen Colonization

<div><p>Protection provided by host bacterial microbiota against microbial pathogens is a well known but ill-understood property referred to as the barrier effect, or colonization resistance. Despite recent genome-wide analyses of host microbiota and increasing therapeutic interest, molecular analysis of colonization resistance is hampered by the complexity of direct <i>in vivo</i> experiments. Here we developed an <i>in vitro</i>-to-<i>in vivo</i> approach to identification of genes involved in resistance of commensal bacteria to exogenous pathogens. We analyzed genetic responses induced in commensal <i>Escherichia coli</i> upon entry of a diarrheagenic enteroaggregative <i>E. coli</i> or an unrelated <i>Klebsiella pneumoniae</i> pathogen into a biofilm community. We showed that pathogens trigger specific responses in commensal bacteria and we identified genes involved in limiting colonization of incoming pathogens within commensal biofilm. We tested the <i>in vivo</i> relevance of our findings by comparing the extent of intestinal colonization by enteroaggregative <i>E. coli</i> and <i>K. pneumoniae</i> pathogens in mice pre-colonized with <i>E. coli</i> wild type commensal strain, or mutants corresponding to identified colonization resistance genes. We demonstrated that the absence of <i>yiaF</i> and <i>bssS</i> (<i>yceP</i>) differentially alters pathogen colonization in the mouse gut. This study therefore identifies previously uncharacterized colonization resistance genes and provides new approaches to unravelling molecular aspects of commensal/pathogen competitive interactions.</p>