A broad-based remediation mechanism against MRFs and alternative fecal indicators such as multidrug resistant Pseudomonas aeruginosa, including nanotechnology formulations and methodologies that may be used to develop novel treatment strategies against certain drug resistant bacterial strains. The current invention relates to the treatment of drug resistant bacteria from nosocomial infections, for example in hospitals and in food animals. The invention uses hybrid nanomaterials comprising oligo-chitosan and zinc oxide formulated as nanoparticles and micelles. The inventors unexpectedly found unique properties of very small oligomers of chitosan that effectively treat multi-drug resistant bacteria without compromising the balance of the beneficial flora in the physiological and ecological microenvironments in a host. Also, the combination of chitosan with zinc oxide demonstrated synergistic and unexpected effects in remediation of important food-borne bacteria including the resistant types.