Proteins that were preferentially enriched by infection with WT Legionella compared to uninfected cells included those related to autophagy (ATG3, ATG16L and BECN1), endocytosis (RAB5C, RAB8A, HGS1 and TFRC), ER-to-Golgi trafficking (ERGIC1, SEC23A, COPG1 and COPG2) and the Golgi and trans-Golgi network (STT3A, STT3B, LMAN2, B4GALT1, RAB34, ARF3 and ARF4). Here, ATG16L1 is linked to infection.