Resistomes from oxytetracycline-treated pigs are readily transferred to untreated pen mates

Pork is currently a major part of Danish food export and is also a key dietary source of protein across the world. Industrial pork production, however, comes with high antibiotic usage in many countries, including Denmark. This has created consumer demand for meat Raised Without Antibiotics (RWA). Previous work has demonstrated that levels of antibiotic resistance genes (ARGs) are indeed increased in antibiotically treated animals, but also suggest that these ARGs are transferred to untreated pen-mates. In a Danish commercial farm, we studied four groups of physically separated pigs: one group of only antibiotic treated pigs (n = 20), one group of only untreated pigs (n = 30 total, n = 15 analysed), and one group combining treated (n = 15) and untreated pigs (n = 15). These groups were followed for 16 weeks during which all pigs were profiled for both their faecal microbiome (through 16 S rRNA gene sequencing) and resistome (by use of a high-throughput qPCR platform targeting 82 ARGs and their variants). We found that the resistome of treated pigs was substantially enriched in resistance genes compared to untreated pigs but, importantly, observed that untreated pigs co-reared with treated pigs had levels of resistance genes approaching their treated pen mates, suggesting that the treated enterotype is readily transferred to the untreated animal. From this, we conclude that mixing of treated and untreated pigs causes spill-over of antibiotic resistant bacteria and/or resistance genes from treated pigs when these are co-reared. To optimize RWA production, treated and untreated pigs should be physically separated to limit the proliferation of ARGs.