A detection instrument determines whether a specimen container (e.g., blood culture bottle) is positive for presence of microbial agent growth therein. When the container is deemed positive it is made available (e.g, transferred or exposed to) to an automated instrument performing identification and/or characterization of the microbial agent. The identification and/or characterization instrument removes a portion of the sample from the specimen container and places it into a disposable separation and concentration device. The microbial agent is concentrated via optional selective lysis of non-microbial agent cellular material which may be present and centrifugation. A reading module reads the concentrated microbial agent using spectroscopic methods, e.g., measurements of intrinsic fluorescence. Such interrogation may occur while the microbial agent remains concentrated in the disposable device.