Bacterial strain-sharing across human, animal, and the environment in Nairobi

To investigate strain-sharing patterns, we collected matched human stool, animal samples (poultry cloacal swabs and canine feces), and environmental samples (stored drinking water and household soil) from 50 households in Nairobi, Kenya. Using Pooling Isolated Colonies-seq (PIC-seq), we sequenced pools of up to five Escherichia coli colonies per sample to capture strain diversity, strain-sharing patterns, and the overlap of antibiotic resistance genes (ARGs) including their genomic context.