Rapid identification and enumeration of bacteria are critical, given the surge of antibiotic-resistance, global exchange of food products, and the use of bacteria for bioremediation, pharmaceutical, and food production. In response, a wide range of methods are being developed that can be broadly classified as nucleic acid-based, structure-based, mass spectrometry-based, and optically based. Optical methods have generated interest given the potential for rapid, non-destructive, high-throughput, and amplification-free measurements that require minimal sample preparation. This Perspective reviews optical methods, which are applied to identification, enumeration, and greater understanding of bacteria routinely and more importantly at the cutting edge of research, with the aim of identifying gaps and opportunities for development. We have focused primarily on methods that directly measure bacteria and not their effect on the sample matrix or sensing, which requires a biorecognition element (i.e., label specific to some component of the bacterium). We identify gaps in the existing techniques and avenues for innovation. Finally, we suggest the parameters that should be considered and recorded when reporting the development of existing and new methods for bacterial characterization. This Perspective is intended for physicists interested in developing new optical methods for the study of bacteria and microbiologists in need of an optical technique for bacterial applications.

We present a novel microfluidic and optical system for the rapid detection and enumeration of bacteria cells. Our system uses a single microchannel with an integrated optical fibre to achieve large volume excitation and detection of bacteria cells in low concentration suspension.