Abstract
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.
Highlights
Bacteria are ubiquitous in our everyday life, with applications in food production, as probiotics, and in the sustainable utilization of resources as well as their negative implications for food and water safety, food spoilage, and human, animal, and crop infections
Bacteria identified in this approach were E. coli K12, L. innocua, Sa. enterica serovar Typhimurium, and St. aureus,[226] and E. coli strains ATCC 25922, 35421, 11775, and 8739.65 A 93% correct classification rate based on support vector machines and ten-fold cross-validation was observed for differentiation of the four E. coli strains after just 6 h of colony growth.[65]
Optical coherence tomography of biofilms would benefit from the identification of molecular contrast agents that allow for greater differentiation of structures within biofilms, or seamless multiplexing with methods, such as fluorescence or Raman microscopy, to obtain molecular information
Summary
Bacteria are ubiquitous in our everyday life, with applications in food production, as probiotics, and in the sustainable utilization of resources as well as their negative implications for food and water safety, food spoilage, and human, animal, and crop infections. Perspective focuses on optical methods, which have been applied to identification, enumeration, and greater understanding of bacteria. These methods include monitoring of metabolic activity, antibiotic susceptibility testing (AST), and characterization of bacteria in matrices, such as biofilms. We suggest several 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
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