biostudies-literatureBruder EWeizmann Institute of ScienceAgence Nationale de la Recherche2587402https://www.ebi.ac.uk/biostudies/studies/S-EPMC12931692biostudies-literatureUnknown17(1)Patients with Crohn's disease exhibit abnormal intestinal colonization by <i>Proteobacteria</i>, particularly adherent-invasive <i>Escherichia coli</i> (AIEC). These bacteria predominate in the mucus, adhere to epithelial cells, colonize them, and survive inside macrophages. We recently demonstrated that the AIEC strain LF82 adapts to phagolysosomal stress through a two-step process: initial replication arrest generating stress-tolerant persisters, followed by the resumption of replication, leading to the formation of intracellular bacterial communities (IBCs) embedded in a biofilm-like matrix. Given the significant genomic diversity among strains with the AIEC phenotype, we performed a comparative genomic and functional analysis of 13 AIEC isolates from Crohn's disease patients in France Gut microbesPersistence mechanisms of Crohn's disease-associated adherent invasive &lt;i&gt;Escherichia coli&lt;/i&gt; within macrophages.PMC12931692WIS 714514-01ANR-10-LABX-54 MEMOLIFEEspeli OQuenech'Du NBuisson AChevarin CVazeille EGranotier MSingh PBarnich NBruder ENedjar HfalsePersistence mechanisms of Crohn's disease-associated adherent invasive &lt;i&gt;Escherichia coli&lt;/i&gt; within macrophages.Patients with Crohn's disease exhibit abnormal intestinal colonization by <i>Proteobacteria</i>, particularly adherent-invasive <i>Escherichia coli</i> (AIEC). These bacteria predominate in the mucus, adhere to epithelial cells, colonize them, and survive inside macrophages. We recently demonstrated that the AIEC strain LF82 adapts to phagolysosomal stress through a two-step process: initial replication arrest generating stress-tolerant persisters, followed by the resumption of replication, leading to the formation of intracellular bacterial communities (IBCs) embedded in a biofilm-like matrix. Given the significant genomic diversity among strains with the AIEC phenotype, we performed a comparative genomic and functional analysis of 13 AIEC isolates from Crohn's disease patients in France 2025-01-01T00:00:00Z2025 Dec2026-07-09T12:26:13.393Z2026-07-09T11:17:53.571ZS-EPMC129316924128756810.1080/19490976.2025.2587402