Intracellular niche formation of Shigella

Supervisor Organisation PhD Awarding Entity: phd location
Institut Pasteur
Université de Paris Cité
Institut Pasteur, Paris, France

Research Focus

This project investigates how Shigella, the causative agent of human dysentery, invades enterocytes of the human colon. In particular, we will address how the pathogen uses a molecular weapon called the type 3 secretion system to subvert host pathways and compartments to model its intracellular niche. During these steps, in situ formed infection associated macropinosomes interact with the pathogen compartment that is called the bacterial containing vacuole. We will decipher this dynamic crosstalk using the advanced imaging approaches of the CLEXM consortium.

Cryo-SXT will provide information about the cellular context around the infection site, and the data will be correlated with cryo-ET data. It will bridge the information and resolution gap between cryo-fluorescence microscopy and cryo-ET, providing a detailed 3D view of the remodelling of cellular architecture upon infection. Nanoscale detail of the whole cellular context around the infectious event, combined with the high-resolution structural information from cryo-ET on the same sample/grid will be obtained. We will further implement analytical workflows to extract quantitative information on the compartments subverted by the pathogen during the invasion process.


This project uses cellular models to investigate the infection of enterocytes by Shigella. Fluorescence imaging provides information on the molecular factors involved in the host pathogen crosstalk. Both, confocal and super-resolution techniques are used. This will be correlated with electron microscopy in cryo conditions, large volume EM, as well as SXT.

Aim 1

We will use fluorescence biosensors to pinpoint the successive invasion steps of Shigella. Sensors will identify pathogen factors, as well as subverted host proteins and their modulation by the pathogen.

Aim 2

The fluorescence biosensors will be exploited within correlative workflows at large volumes (either by FIBSEM or SXT) and at high rsolution by cryo tomography.

Aim 3

Bioinformatics workflows will be used and developed to decipher the molecular crosstalk for the intracellular niche formation of Shigella

Pictures Attached

 Image description: A workflow for correlative light and electron microscopy to investigate the intracellular niches of Shigella. Samples are prepared for optical imaging on coverslips with an engraved coordinate system. Coordinates can be identified in the different imaging modalities, and are used to correlate the images from fluroecence and electron microscopy.


Role/Focus of PhD:

The PhD candidate will work on an interdisciplinary project that combines cutting-edge optical imaging with the ultrastructural approaches within the CLEXM consortium. Furthermore, the candidate will learn about the infection model. It is important that the candidate is self-motivated, able to manage interactions between different teams, and ready to learn advanced imaging techniques. Skills in infection biology, particularly on intracellular bacteria and some knowledge in imaging as well as biophysics will be beneficial.


Application Deadline: 18th August 2023 (Closed)