Controlling persistent infection and antimicrobial resistance in Shigella

Shigella is a major diarrhoeal pathogen, estimated to cause up to 165 million illnesses and 600,000 deaths yearly. There is no vaccine available that protects against shigellosis. Due to widespread antimicrobial resistance (AMR), Shigella is listed by the World Health Organisation as a priority pathogen.

Shigella generally induces an acute, self-limiting disease. However, surveillance data and my own work using the zebrafish model have recently demonstrated that Shigella can establish persistent infections. Persistent infections are not cleared completely by the host.

They represent a critical public health issue because they can become asymptomatic and are difficult to diagnose and eradicate. Persistently infected carriers also represent a reservoir that promotes further disease spreading.

The zebrafish model has helped to uncover important mechanisms underlying Shigella pathogenesis. Using this model, I demonstrated that Shigella can establish persistent infection in vivo. Significantly, Shigella establishing persistent infection also becomes antibiotic tolerant (infection is no longer eradicated by antibiotics), which facilitates the evolution of AMR.

My data also indicate an important role for macrophages in establishing persistent Shigella infection. Despite these novel insights, the mechanisms underlying persistent Shigella infection and its precise links to AMR are unknown.

Using a combination of models in vitro (THP1 macrophage-like cells and macrophages derived from human induced pluripotent stem cells (hiPSCs) or monocytes) and in vivo (zebrafish larvae), I will investigate persistent Shigella infection and how this facilitates AMR. My specific objectives are:

Objective 1. Characterise the niche of persistent Shigella infection. I will apply high-resolution microscopy and cell sorting to follow how persistent infection develops and study its intracellular localisation.

I will use sequencing technologies to profile the gene expression changes occurring in macrophages carrying persistent infection. I will also apply gene editing techniques to study further the role of the discovered host factors contributing to persistent infection. This objective will describe the persistent infection niche and identify the host factors underlying persistence.