This disclosure concerns a pathogen inspection system that includes a handling system that presents single cells from a sample to at least one QCL laser source. The QCL laser source is configured to deliver light to a cell within the cells in order to induce vibrational bond absorption in one or more analytes within the cell. The system includes a detection facility that detects the mid-infrared wavelength light transmitted by the cell and identifies the cell as either a pathogen or not a pathogen.