Farm-to-fork Changes in Poultry Microbiomes and Resistomes in Maputo City, Mozambique

Increasing demand for poultry has spurred poultry production in low- and middle-income countries like Mozambique. Poultry may be an important source of foodborne, antimicrobial resistant bacteria to consumers in settings with limited water, sanitation, and hygiene infrastructure. The ChEEP ChEEP (Chicken Exposures and Enteric Pathogens in Children Exposed through Environmental Pathways) study was conducted in Maputo City, Mozambique from 2019-2021 to quantify enteric pathogen exposures along the supply chain for commercial and local (i.e. scavenger) chicken breeds. Here, we performed metagenomic sequencing of total DNA from banked ChEEP ChEEP samples to characterize fecal and carcass microbiome and resistome diversity between chicken breeds and along the supply chain. Fecal samples (26) were collected from commercial and local chickens at production sites and markets, and carcass (49) and rinse bucket samples (26) from markets. We conducted taxonomic profiling and identified antimicrobial resistance genes (ARGs) from metagenomic sequence data, focusing especially on known human pathogens and high-risk ARGs. We estimated alpha diversity for each sample and compared by site and breed. We estimated Bray-Curtis dissimilarity between samples and examined clustering. We found that commercial and local chickens harbored distinct fecal pathogens and resistomes at production and market sites. Many bacterial pathogens and ARGs present in chicken fecal samples are also present on carcasses sold to consumers. Finally, commercial chicken carcasses contain high-risk ARGs that are not necessarily introduced from chicken feces. These results indicate markets are an important site of pathogen and ARG exposure.