The invention provides multi-function instruments for automatically and simultaneously carrying out a variety of tests including identification of targets in specimens and antimicrobial susceptibility testing thereof. Application-specific cartridges are pre-loaded with all required reagents and allow for tests to be performed in a single testing device with no specimen preparation to, for example, rapidly detect infections, identify infectious pathogens, and analyze their susceptibility to various antimicrobial agents. Instruments include various stations for carrying out test steps that can be randomly accessed in any order dictated by the computer-controlled instrument. A carousel stores and incubates cartridges and, with a mechanical conveyor arm, transfers the cartridges between the required stations to carry out the tests. A plurality of different tests may be performed on a plurality of targets within an instrument, and the plurality of targets may be disposed in a single cartridge.