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Conventional procedures to detect microorganisms and toxins in food, water, and human specimens can take hours or days to perform and may provide inconclusive identification. The complex nature of many sample matrices as well as the presence of particulate matter in samples often severely reduces the sensitivity and specificity of conventional bacterial detection systems, especially those that rely on immunological reactions for capture or detection. Evanescent wave fiber-optic biosensors can identify such target analytes in minutes directly from complex matrix samples using robust antibody-based assays, significantly improving the detection sensitivity, selectivity, and speed. In addition, live microbial targets can be recovered from fiber-optic waveguides to determine microorganism viability, confirm identification, and preserve as evidence.