Strain-level Analyses of Public Sequencing Data to Characterize Escherichia Coli Strain Sharing Between Children and Chickens in Mozambique

Escherichia coli causes diarrhea in children and can be transmitted from animals. Characterizing the scope of human-animal strain sharing is crucial for assessing potential health risks; however, conventional methods that assess single isolates are resource-intensive and lack sensitivity. Strain-level metagenomic analyses can reveal within-host strain diversity and between-host strain sharing. In this study, we aimed to determine whether E. coli strains we previously detected among chickens in Mozambique might pose meaningful risks to local children. To achieve this, we compared E. coli strains in chicken metagenomes to E. coli strains reported by others in children's stool in the same community during the same period (2014-2022) using the Strain Genome Explorer toolkit. At least one E. coli strain was shared between 37/23,937 (0.15%) chicken-human pairs. This approach represents a novel method for assessing the scope of bacterial strain sharing between human and animal populations within a community.