To model the drivers of AMR-transmission, we will undertake detailed, longitudinal microbiological surveillance of humans, animals and the environment to understand the dynamics of ESBL-E and ESBL-K and their ecological niche. We will characterise bacterial isolates, mobile genetic elements, genes and intrinsic mutations associated with AMR and DR-BSI samples through whole genome sequencing (WGS) in collaboration with the Wellcome Sanger Institute to reliably and reproducibly distinguish them.
Household sampling: We will collect geolocated samples from humans, animals and the environment from randomly selected households (hhs) in our study sites to determine community prevalence of ESBL-E and ESBL-K, and risk factors for acquisition.
A detailed description of all households is beyond the scope of this study. Instead,15% of hhs will be intensively characterised, sampling stool from all humans, all companion domestic animals, a sample of wild animals and from representative sources in of the broader environment, taking up to 50 samples on a 8-weekly basis for 6-months. The remainder will be sampled at a lower intensity, by taking up to 8 swabs/hh, 3 times in 6 months. These methods have been developed in collaboration with the Food, Water and Environment laboratories, Public Health England, Colindale.
We will also test environmental samples for antimicrobial and heavy metal residue in collaboration with the Centre for Ecology and Hydrology.