An automated instrument for identifying a microbial agent present in a specimen sample contained within a specimen container, comprising, in combination: a sample removal apparatus operative to automatically remove a test sample from the specimen container and add the test sample to a disposable separation device, the disposable separation device containing a density cushion with homogeneous density, and a robotic transfer mechanism coupled to the sample removal apparatus and preferably wherein the sample removal apparatus comprises a gripping structure coupled to the robotic transfer mechanism, the sample removal apparatus operative to grip said disposable sampling device and manipulate the disposable sampling device relative to the specimen container so as to vent the specimen container and withdraw the test sample into the sampling device; a separation and concentration station operative on the separation device after receiving the test sample so as to separate the microbial agent from other components that may be present in the test sample using the density cushion and concentrate the microbial agent within the separation device in the form of a pellet, wherein the separation and concentration station comprises a centrifuge, and wherein the centrifuge concentrates the microbial agent to form a pellet in the separation device; and an identification module to spectroscopically interrogate the pelleted microbial agent using intrinsic fluorescence while the pellet is contained within the separation device, said identification module further comprising a processing unit for executing instructions comparing measurements obtained from the sample with reference data from known microbial agents and identifying the microbial agent to the family, genus, species, and/or strain level. a sample removal apparatus operative to automatically remove a test sample from the specimen container and add the test sample to a disposable separation device, the disposable separation device containing a density cushion with homogeneous density, and a robotic transfer mechanism coupled to the sample removal apparatus and preferably wherein the sample removal apparatus comprises a gripping structure coupled to the robotic transfer mechanism, the sample removal apparatus operative to grip said disposable sampling device and manipulate the disposable sampling device relative to the specimen container so as to vent the specimen container and withdraw the test sample into the sampling device; a separation and concentration station operative on the separation device after receiving the test sample so as to separate the microbial agent from other components that may be present in the test sample using the density cushion and concentrate the microbial agent within the separation device in the form of a pellet, wherein the separation and concentration station comprises a centrifuge, and wherein the centrifuge concentrates the microbial agent to form a pellet in the separation device; and an identification module to spectroscopically interrogate the pelleted microbial agent using intrinsic fluorescence while the pellet is contained within the separation device, said identification module further comprising a processing unit for executing instructions comparing measurements obtained from the sample with reference data from known microbial agents and identifying the microbial agent to the family, genus, species, and/or strain level.