Selection for antibiotic resistance in multistress environments

Synthetic microbial ecosystems Synthetic microbial ecosystems to study the selection for antibiotic resistance under changing hydration conditions. The burden of antibiotic resistance in the environment and its role in the development, transmission, and persistence is poorly understood. This is because the environment is the most dynamic and consequently the most confounding sector of the One Health triad. Especially soils harbour a huge diversity of bacteria, are highly heterogeneous in space and are subject to variable weather patterns. This leads to fluctuations in the environmental conditions experienced by bacteria. In addition, manure application itself induces manifold changes in the soil ecosystem. It introduces nutrients, several different antibiotics and bacterial species and other potential stressors (heavy metals, disinfectants).

As antibiotic resistance mechanisms are usually associated with fitness costs for bacteria, their frequency should decline in the absence of antibiotic selection. However, soil monitoring studies revealed that antibiotic resistance persists and both modelling and experiments showed that resistant individuals are (if at all) only slowly outcompeted by their non-resistant relatives.

To address the environmental fate of antibiotic resistance, it is crucial to understand how resistance is stabilized in bacterial populations and in particular under environmentally relevant conditions. Despite the different ecological and evolutionary mechanisms that facilitate the persistence of ABR, also the environmental conditions can act as a selective force. Different studies reported that sub-inhibitory concentrations (sub-MIC) of antibiotics select for antibiotic resistance. Such sub-MIC can result from the application and subsequent incorporation of manure into the soil. Some studies reported amounts of up to hundreds of mg/kg of Tetracyclines and Sulfonamides in pig and poultry slurry in Germany. Subsequent dilution in the soil matrix results in low-dose microhabitats in which sub-inhibitory effects occur together with other physical, chemical and biological stresses that impede bacterial fitness. In this project, we ask the question, to what extent antibiotic resistance is favoured in multistress environments. Specifically, we aim at testing the interacting effects of sub-MIC of antibiotics, resource availability and varying hydration conditions on the selection for antibiotic resistance. 

This project is carried out in collaboration with Prof. Dani Or and Dr. Robin Tecon at ETH Zurich.