Malus x robusta 5 (Mr5) is a wild apple accession highly resistant to fire blight caused by the bacterium Erwinia amylovora. Only few strains of E. amylovora are able to overcome the resistance, including the avrRpt2_EA deletion mutant ZYRKD3-1. The related wild type strain Ea1189, expressing the avrRpt2_EA is not able to break resistance of Mr5. The differential transcriptome comparison of Mr5 after inoculation with these two strains gives the opportunity to analyze the host-pathogen interaction of Erwinia amylovora and Mr5 in a system differing only in one single gene: the avrRpt2_EA effector gene.