Disclosed herein are methods and systems for rapid detection of microorganisms such as Cronobacter spp. in a sample. A genetically modified bacteriophage is also disclosed which comprises an indicator gene in the late gene region. The specificity of the bacteriophage, such as Cronobacter-specific bacteriophage, allows detection of a specific microorganism, such as Cronobacter spp. and an indicator signal may be amplified to optimize assay sensitivity.