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Elastic light scattering for fast identification of pathogens

Abstract : The current health situation across the world is of great concern. There is an urgent need for novel and innovative diagnostic methods that would speed up accurate treatments decisions and be of significant utility for public health in the fight against antibiotic resistance.This Ph. D. work aims to better understand the Elastic Light Scattering (ELS) method for microbial identification. This phenotypic technique is based on the elastic scattering of a coherent light beam by a microorganism colony growing on its culture plate. The resulting scattering pattern can be considered as the phenotypic signature of the microorganism. Then this image is translated using mathematical descriptors so that it can be compared to a database previously obtained using learning algorithms.Part of this work was dedicated to the improvement of the optical design so that the instrument can handle opaque culture media widely used in clinical diagnosis. Then two approaches were proposed to model the interaction between light and bacterial colonies. A first geometrical approach could help us, using ray tracing algorithms, to estimate the numerical aperture needed for the acquisition depending on the colonies morphologies. The second approach, based on scalar diffraction theory, highlighted the importance of the biomass distribution inside the colonies. Macro-structures resulting from cells arrangement play a great role in the scattering patterns formation indeed. In addition, the features extraction step from images using a Bessel-Fourier basis significantly improved the description accuracy. A systematic approach comprising the optimization of the learning algorithm and a dimensionality reduction technique was proposed. Great improvements of classification rates were achieved. Among them: a Gram+/Gram-/Yeasts discrimination at 98.1% was obtained over 15 species. Finally the use of coherent lighting for the reading of antibiotics susceptibility test by means of dynamic speckle analysis was introduced and showed promising results.
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https://tel.archives-ouvertes.fr/tel-01782956
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Submitted on : Wednesday, May 2, 2018 - 11:19:11 AM
Last modification on : Thursday, June 11, 2020 - 5:04:06 PM

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  • HAL Id : tel-01782956, version 1

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Valentin Genuer. Elastic light scattering for fast identification of pathogens. Optics / Photonic. Université Grenoble Alpes, 2017. English. ⟨NNT : 2017GREAT096⟩. ⟨tel-01782956⟩

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