Khouloud ARFAOUI's PhD thesis defence

Single-cell optical trapping for the typing of Escherichia coli using an optofluidic chip 

The rise of antimicrobial resistance has transformed the treatment of bacterial infections into a race against time, with projections suggesting it could become a leading cause of mortality worldwide by 2050. Addressing this challenge requires a deeper understanding of bacterial populations at the single-cell level, where phenotypic variability and early resistance-associated changes may emerge.

Conventional microbiological methods rely largely on population-averaged measurements and therefore overlook the heterogeneity present within bacterial populations. Rare or transient behaviours expressed by only a small fraction of cells may remain undetected despite their potential importance in adaptation and resistance. Detecting these signatures requires approaches capable of isolating and probing individual cells with high sensitivity.

Optical methods provide a promising framework for this purpose. Photonic structures enable strong confinement of light, enhancing sensitivity to subtle variations in cellular properties. Combined with microfluidics, they allow precise environmental control and continuous, non-invasive measurements at the single-cell level.

This work presents the development of optofluidic chips based on SOI photonic crystal optical resonators for the trapping and analysis of individual Escherichia coli cells. The devices integrate optical manipulation and sensitive detection within a microfluidic platform, enabling controlled investigations of cell-surface interactions and optical responses. The platform was applied to the characterization of 16 Escherichia coli strains at the single-cell level and to the evaluation of the discriminating capabilities of the optical approach. 

These developments contribute to the growing toolbox of optical methods for single-cell microbiology and open new perspectives for bacterial characterization.

Jury :

Taha BENYATTOU, directeur de recherche (INL CNRS) - rapporteur

Ahmad BSIESY, professeur des universités (Cime Nanotech) - examinateur

Sigolène LECUYER, chargée de recherche (ENS Lyon) - examinatrice

Isabelle LEDOUX-RAK, professeure des universités (ENS Cachan) - rapporteure

Pierre MARCOUX, ingénieur HDR (CEA Leti) - encadrant

Emmanuel PICARD, ingénieur (CEA IRIG) - encadrant

Valérie STAMBOULI-SENE, chargée de recherche (LMGP CNRS) - encadrante

Marc ZELSMANN, directeur de recherche (LTM CNRS) - directeur de thèse