A one health genomic approach to exploring E. coli and AMR transmission within the Malawian national poultry supply chain, with consideration of host adaptability and antibiotic accessibility as drivers of transmission and prevalence.

Prevalence of antimicrobial resistance (AMR) in bacteria is global, with similar resistance patterns observed in bacteria from humans, animals, and the environment; and rates of drug resistant infections increasing.

Various types of E. coli can be transmitted between species, or their genes transferred between bacteria conferring AMR into new hosts when this happens.

Close interfaces between carriers of bacteria increases likelihood of transfer, however dissemination of E. coli and AMR throughout the livestock chain is not well understood, as there are multiple routes of transmission creating complexity in outlining the dynamics and determinants.

This study will examine transmission of E. coli and AMR in the Malawian national poultry supply chain across the human-animal-environment interfaces.

E. coli samples will be sequenced using nanopore sequencing to examine population structures and AMR genes; identifying potential E. coli types or genes that are transmitted through the supply chain, or between poultry, farmers and the local environment.

Machine learning techniques will be applied on the sequence dataset to investigate whether E. coli host adaptability features and AMR repertoires impact species transfer potential.

Additionally, farm accessibility to regional drug outlets will be mapped to ascertain if ease of antibiotic access is linked to AMR prevalence.