Abstract: A computer implemented method and system for improving drug treatment of patients in local communities by providing drug treatment protocols for particular disease states, such as Diagnosis Related Group (DRG) classifications. The protocol contains ranked recommendations for drug treatments of the disease state, and the computer system collects information about the risks and benefits of the drug treatments. The information collected about the treatments is used to modify the rankings of the drug treatments in the protocol. In one specific embodiment of the system, where the disease state has a microbial etiology and the treatments are antimicrobial drugs, the emergence of drug resistance is quickly detected by determining the percentage of microbial isolates that are found to be resistant to antimicrobial therapy in the community where the therapy is being provided (such as a community hospital or city-wide health care system).