Transfer of IncB/O/K plasmid and bacteriophages from broiler chicken cecum to Salmonella Heidelberg

The chicken gastrointestinal tract harbors taxa of microorganisms that play roles in the health and disease status of the host. The cecum is the part of the GIT that carries the highest microbial densities, has the longest residence time of digesta and is a vital site for urea recycling and water regulation. The cecum provides a rich environment for bacteria to horizontally transfer genes between one another via mobile genetic elements (MGE) such as plasmids and bacteriophages. In this study, we used broiler chicken cecum as a model to investigate MGE that can be transferred from chicken cecal populations to Salmonella enterica serovar Heidelberg (S. Heidelberg). We performed whole genome sequencing on isolates recovered after 0.5, 6, 24 and 48 h of incubation in ceca under microaerophilic conditions. We provide insights on genetic changes associated with phage-mediated DNA exchange between strains of the same bacterial lineage and characterized lysogenized bacteriophages carrying putative “moron” or fitness factor genes in S. Heidelberg. Finally, we performed an in-depth characterization and comparative genomics of an IncB/O/K/Z-like (88 kb) AmpC plasmid encoding extended ß-lactamase producing gene (blaCMY-2) that conferred resistance to first, second and third generation cephalosporins acquired by one S. Heidelberg isolate.