The present invention provides compositions and methods for identifying molecules in samples that bind to molecules associated with pathogenic agents (e.g., infectious agents). In certain aspects, the invention may be used to identify individuals that have been exposed to one or more pathogenic agent or have generated antibodies in response to one or more pathogenic agent. In other aspects, the invention is directed to the identification of molecules of one or more pathogenic agent that may be used to generate immune responses in other individuals.