Shared species, strains and resistome between humans and pigs: A metagenomic analysis

Pig farming is one of the most intensive human-animal interfaces, and farm workers carry gut microbiotas that differ from those of non-farmers. Whether this overlap reflects genuine strain transmission or shared environmental exposure is unclear. Using shotgun metagenomics, we profiled the gut microbiomes of pigs at three growth stages (suckling, weaning, fattening), their farmers, and non-farmer controls, at species and strain resolution, and characterized the resistome in parallel. Farmers shared more species with pigs than controls, with Prevotellaceae the most consistently enriched family. Strain-level analysis of 137 shared species showed that most (71%) maintain host-specific sub-species clades. Strain sharing ran an order of magnitude below species sharing and was confined to early growth stages; its direction could not be determined. Pigs and farmers shared a farm-associated resistome signature, including the beta-lactamase cfxA4 and the methyltransferases ermF and cfrE. ermF and tet(X) were carried together on the same clonal Tn4351-family transposon, present in 86% of farmers and 80% of pigs but only 19% of controls. We found no evidence for transmission of mobile genetic elements between pigs and farmers; the shared resistome is best explained by carriage within shared gut taxa. Species sharing, strain transmission, and resistance gene carriage thus reflect different scales of microbial exchange at the livestock-human interface. Our results argue against ongoing strain or mobile genetic element transmission from handled animals: the shared species and resistome are best explained by shared environmental exposure and by carriage of resistance genes within shared gut taxa.