Data from: Ecological and genetic determinants of plasmid distribution in Escherichia coli

Bacterial plasmids are important carriers of virulence and antibiotic resistance genes. Nevertheless, we know little of the determinants of plasmid distribution in bacterial populations. Here we explored the factors affecting the diversity and distribution of the large plasmids of Escherichia coli in populations of cattle grazing on semi-natural grassland, a set of populations with low frequencies of antibiotic resistance genes. Critically, we also characterized the population genetic structure of bacterial hosts. This revealed structured E. coli populations with high diversity between sites and individuals but low diversity within cattle hosts. Plasmid profiles, however, varied considerably within the same E. coli genotype. Both ecological and genetic factors affected plasmid distribution: plasmid profiles were affected by site, E. coli diversity, E. coli genotype and the presence of other large plasmids. Notably 3/26 E. coli serotypes accounted for half the observed plasmid-free isolates indicating that within species variation can substantially affect carriage of the major conjugative plasmids. The observed population structure suggest that most of the opportunities for within species plasmid transfer occur between different individuals of the same genotype and support recent experimental work indicating that plasmid-host coevolution, and epistatic interactions on fitness costs are likely to be important in determining occupancy.