Trap and track: designing self-reporting porous Si photonic crystals for rapid bacteria detection

Abstract

The task of rapid detection and identification of bacteria remains a major challenge in both medicine and industry. This work introduces a new concept for the design of self-reporting optical structures that can detect and quantify bacteria in real-time. The sensor is based on a two-dimensional periodic structure of porous Si photonic crystals in which the pore size is adjusted to fit the target bacteria cells (Escherichia coli). Spontaneous bacteria capture within the pores induces measurable changes in the zero-order reflectivity spectrum collected from the periodic structure. Confocal laser microscopy and electron microscopy confirm that the Escherichia coli cells are individually imprisoned within the porous array. A simple model is suggested to correlate the optical readout and the bacteria concentration and its predictions are found to be in good agreement with experimental results. In addition, we demonstrate that sensing scheme can be easily modified to potentially allow monitoring of concentration, growth and physiological state of bacteria cells. This generic platform can be tailored to target different microorganisms by tuning the array periodicity and its surface chemistry for rapid and label-free detection outside the laboratory environment.

Demonstration ofde novochemotaxis inE. coliusing a real-time, quantitative, and digital-like approach

“…Where ψ is the phase delay between the source beam and the reflected one, λ is wavelength, L is the depth of the Si pores, and n 0 is the refractive index of the medium filling the pores. Through frequency analysis using application of a fast Fourier transform (11), the value of 2n 0 L can be calculated. Thus 2n 0 L refers the optical path difference, commonly termed effective optical thickness (EOT) and provides a measure for monitoring changes in refractive index that correspond to bacterial colonization within the silicon pores.…”

“…To do this, we implemented a two-pronged approach: first, we computationally designed novel chemoreceptors using the “Rosetta” bioinformatics software suite, and second, we developed a novel chemotaxis detection tool, which facilitates rapid, quantitative, and “digital-like” detection of attractants and repellants by monitoring the light reflective interference from nanostructured PSi-based optical transducer. (11) We demonstrate the feasibility of our approach, by using Rosetta to produce several candidate Tar-LBD mutants that had a high probability of binding histamine. We then show using “digital chemotaxis” and more traditional chemotaxis assays that one of the variants that received a high score by Rosetta was indeed able to respond to histamine in a specific manner.…”

Antifungal susceptibility testing ofAspergillus nigeron silicon microwells by intensity-based reflectometric interference spectroscopy

“…1D-i and 1D-ii). Whereas in previous works [28][29][30][31][32][33] the values of 2nL were monitored over time, in this assay, the intensity of the reflected light is tracked, as A. niger tends to grow on top of the silicon microwells resulting in a decrease in peak intensity. The percent change in peak intensity of the fast Fourier spectrum, ΔI, of the reflected light over time is calculated as:…”

“…This platform is based on the optical sensing of reflected light from a micropatterned diffraction grating. 28 Previously, phase-shift reflectometric interference spectroscopic measurements (PRISM) was demonstrated to monitor antibiotic susceptibility and the behavior of bacteria within microstructured arrays. [29][30][31][32][33] Reflectance spectra of the arrays were collected over time in order to infer values of 2nL, in which n represents refractive index of the medium within the arrays and L represents the height of the microstructures.…”

Sticky Situations: Bacterial Attachment Deciphered by Interferometry of Silicon Microstructures

“…[36,37] In this method, bacterial cells colonize on diffractive, patterned Si microstructures, while zero-order reflectance spectra are continuously collected during illumination with a broadband white light source. [36][37][38][39][40] The resulting reflectance spectra exhibit optical interference fringes as the incident light is separated such that part of the beam is reflected by the top of the Si microstructures and the rest is reflected by the bottom of the Si microstructures. As bacteria occupy the empty spaces within the microstructures, the refractive index of the filling medium increases, resulting in increased values of optical path difference corresponding to 2nL, in which n represents the refractive index of the filling medium and L refers to the height of the grating.…”