Enterobacter sakazakii is an opportunistic pathogen and an occasional contaminant in powdered infant formula. Interaction between specific probiotics and E. sakazakii may reduce the risk of infection. The aim of this study was to characterize in vitro the ability of probiotics (alone and in combinations) to inhibit, compete with and displace the adhesion of E. sakazakii to immobilized human mucus and to assess their capacity to aggregate with pathogen. Specific probiotic strains have proved to aggregate E. sakazakii cells and, through competitive exclusion, inhibition and displacement of the adhered pathogen, were able to inhibit E. sakazakii action on intestinal mucus. The ability to inhibit and to displace adhered pathogen depended on both the probiotic and the pathogen, suggesting that several complementary mechanisms are involved in the processes. We suggest that the selection of specific probiotic strains and their combinations may be a useful means of counteracting E. sakazakii contamination in infant formula and thus to reduce the risk of emerging infection. This approach may also allow the development of new probiotic combinations to counteract the risks associated with other pathogens by improving the intestinal barrier against pathogens.