Optical methods for bacterial detection and characterization

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.

Tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversity

“…Further, flow cytometry can easily distinguish between live and dead cells if samples are stained with a live/dead stain at the time of collection ( Buysschaert et al, 2016 ; Duquenoy et al, 2020 ). The accuracy of spectrophotometry is also sometimes limited to a high detection limit and a small optical range which is further constrained by the background turbidity of the media ( McGoverin et al, 2021 ). Fibers with low solubility such as laminarin and xylan ( Guo et al, 2017 ) can alter the opacity of media and thus complicate the accurate detection of microbial growth ( Wang et al, 2010 ).…”

Spatio-temporal based deep learning for rapid detection and identification of bacterial colonies through lens-free microscopy time-lapses

“…fluorescence microscopy), have decisive advantages: non-invasive, rapid and non-destructive, they could potentially allow automated, reliable, low-cost and high-throughput diagnosis. These techniques are based on various optical properties such as scattering, absorption and emission, reflection or even phase contrast each of which allows for the study of numerous bacterial characteristics [ 17 , 18 ] ( S1 Table ). On the one hand, spectroscopic methods highlight bacterial biochemistry by collecting spectral data over a certain range through the use of absorption and emission (Fourier transform infrared spectroscopy) [ 19 ] or inelastic scattering (Raman microspectrocopy [ 20 , 21 ]).…”

Phase Contrast Image-Based Rapid Antimicrobial Susceptibility Testing of Bacteria in Liquid Culture Media

“…Phase contrast imaging converts phase differences to amplitude differences by interferometry [ 9 ], eliminating the need for sample labeling, reducing damage to the sample and offering the possibility of in situ imaging of biological cells and tissues in vivo [ 10 ]. A number of rapid AST methods based on optical imaging have emerged in recent years, and image-based methods not only allow for the minimum inhibitory concentration (MIC), but also for the morphology of bacteria [ 11 , 12 , 13 ]. The current image-based rapid AST methods are mainly divided into two categories: one is to use agarose to make solid media to immobilize bacteria [ 14 , 15 , 16 , 17 , 18 ] and then use a microscope to track their growth; however, this method is less adequate than liquid media in terms of both nutrition and antibiotic exchange.…”