A robust, automated computational pipeline was used to design a system comprising a microarray for the identification of microorganisms and their antibiotic resistance profiles. This system and methods will facilitate the study of the epidemiology and microbial ecology of antibiotic resistance and be an invaluable tool to rapidly and simultaneously identify organisms and their antimicrobial resistance elements in environmental, food and clinical samples.
STATEMENT REGARDING GOVERNMENTAL SUPPORT
 This invention was made with Government support under Contract No. DE-AC03-05CH11231 awarded by the Department of Energy and under Grant No. U01 AI075410-01 awarded by the NIH/NIAID. The Government has certain rights in the invention.