PRJNA557844
16S rRNA gene metabarcoding of faecal samples from a production cycle on a commercial pig unit
There is considerable concern regarding the increasing threat to human health from drug resistant bacterial infections. The major driver for the development of these drug resistant infections is the use of antibiotics in humans and animals. Each time an antibiotic is used, a wide variety of bacteria including pathogenic ('bad'), commensal ('good') and environmental bacteria will be killed by the drug, however some of these bacteria will survive because they will have become resistant to the antibiotic used. Bacteria can become resistant either through a random change in their genes (mutation) or by acquiring a new gene(s) from another bacteria (horizontal gene transfer). The ability of bacteria to share antibiotic resistance genes is of considerable concern as it is possible that commensal and environmental bacteria could act as a reservoir of resistance genes that could be acquired by pathogenic bacteria. The more antibiotics that are used, the more likely it is that these resistance genes will become established within a broad range of bacteria and environments.Approximately 590 tonnes of antibiotics are used in humans and 420 tonnes in animals in the UK each year. Accurate data regarding use in animals is not available, however poultry and pig farming represent a significant proportion of this use. Whilst the use of antibiotics as growth promoters is banned in the EU, they are still used for group level treatments of farm animals. Our understanding as to how antibiotic use in farm animals relates to the levels of antibiotic resistance genes within different farming systems is very simplistic. We do not know how management decisions on farm impact on the diversity of the commensal and environmental bacteria on the farm and how this relates to the 'quantity' of antibiotic resistance genes in this system. We also do not understand what happens to these resistance genes in the face of different antibiotic treatment protocols, whether some protocols are 'worse' than others at selecting for resistance and whether the levels of resistance genes decay when antibiotic treatment is stopped. We therefore do not have a clear evidence base as to the most effective way to reduce and refine antibiotic use on farms to minimise selecting for antibiotic resistance genes.The aim of this work is therefore to demonstrate that changes in the diversity of bacteria and 'quantity' of antimicrobial resistance genes within pig faeces and their environment can be measured and related to one another, antibiotic use and management changes on the farm. The application of this work will be to develop a framework with which changes to both management practices and antibiotic use on farms can be proposed that minimise the selection for antibiotic resistance. This will benefit farmers by reducing the likelihood of selecting for resistant bacteria that infect farm animals and society more generally by reducing the likelihood that antibiotic resistant infections in humans will develop as a consequence of antibiotic use in farm animals.