Intended and unintended consequences of the ZnO ban from pig diets on antimicrobial resistance, post-weaning diarrhoea and the microbiome.

In most countries, farmed pigs are typically weaned at around four weeks of age. Young pigs are especially vulnerable to gut problems due to their immature digestive system and are particularly susceptible to a condition known as post-weaning diarrhoea. Post-weaning diarrhoea results in distress and discomfort in affected animals, and can lead to death. Recovered piglets often have poorer health and reduced growth, affecting welfare and farm productivity. Gastro-intestinal disease is currently the single most significant challenge to the sustainability of UK and global pig systems and affects more than half of pig farmers worldwide, at significant cost to the industry.

Until recently, post-weaning diarrhoea was controlled by the addition of Zinc Oxide (ZnO) to feed after weaning, which reduced disease and improved piglet outcomes. However, due to concerns that ZnO contributes to the development of antibiotic resistance, prophylactic use of ZnO has recently been banned in both the EU and UK. At present, there is no direct replacement for ZnO, but rather a range of practices. These include a variety of nutritional and management changes, that may be variously applied according to the circumstances of each farm. This is prompting concern that by withdrawing ZnO, post-weaning diarrhoea may become more difficult to manage, with adverse consequences on piglet health and welfare. Despite the sector's best efforts, treatment will more likely need to rely on antibiotics to treat disease and manage diarrhoea. This, therefore, presents us with a conundrum: banning ZnO may possibly increase antibiotic resistance on farms, because farmers may need to use more antibiotics in practice, to treat sick piglets after weaning. These intended and unintended consequences of ZnO withdrawal are the focus of this proposal.

In this study, we will work closely with producers over the withdrawal period to investigate the impact of ZnO withdrawal on piglet health and to identify measures that may help. In particular we are interested in the consequences of ZnO withdrawal on the levels of disease-causing bugs on farms and any changes in carriage of antibiotic resistance by pigs. We will do so by collecting dung samples from a small number of commercial herds across the UK and comparing samples from before and after the ZnO ban. We have already collected pre-ban samples from a number of UK commercial herds, in a precursor pilot project to this proposed study. Laboratory analysis of these dung samples will show which disease-causing bugs are present, and allow us to look for changes in the characteristics of these bugs and their association with disease, before and after the ZnO ban. Using genome sequencing technologies, we will look for antibiotic resistance markers, to see whether these all change after ZnO is withdrawn. Our findings will provide a 'barometer' of piglet health across UK farms during the transitional withdrawal period. We will also examine what differences are seen in the healthy gut microflora in pigs in the presence of ZnO and whether particular beneficial bacteria can be identified. We will investigate how we can exploit these differences to develop alternative feed supplements, such as "friendly bug" supplements that may help in the control of disease and improve piglet health.

By providing evidence-based information, this project will help offset existing uncertainties and inform wider discussion as the sector adjusts to 'zero zinc.' This in turn would be expected to lead to the development of pig production systems that deal sustainably with the challenge of managing the post-weaned piglet.

Post-weaning diarrhoea (PWD) is the most significant challenge to pig rearing throughout the industry, affecting health, welfare and production. Zinc oxide (ZnO) is added to weaner diet at high levels to control disease, however this practice is now banned in the EU, due to associations with antimicrobial resistance (AMR). In the UK, ZnO will be prohibited by June 2024 and it is expected that PWD, and consequent use of antimicrobials for treatment, will increase.

We will conduct a longitudinal study, re-visiting farms from a pre-ZnO ban survey, to evaluate the impact of the ban on PWD and prevalence of causative pathogens, enterotoxigenic Escherichia coli (ETEC) and rotavirus. We will collect faecal samples from pens, record changes in antibiotic usage and identify any shifts in AMR diversity, following ZnO removal. Genomic analysis using long and short read sequencing will enable tracking of AMR genes and multiple drug resistance, comparing across age groups on farm, with and without ZnO. Associations and putative genetic linkage between ARGs, mobile elements, heavy metals, and biocide resistance will be identified. Through phylogenetic analysis, we will examine whether the ZnO ban results in change to the predominate ETEC circulating clones in the UK.

Alternative strategies are urgently required to manage PWD. By means of a highly-powered trial, we will identify differences in structural and functional microbial communities within the intestine that are associated with ZnO supplementation. Through metagenomic sequencing, we will characterise the local microbiota and identify which consortia are associated with reduced PWD and better growth. Using a novel, culturomics approach, we will isolate beneficial microbes from ZnO-supplemented groups, to identify microbiota-based solutions which may be exploited to enhance resilience during weaning. Findings from this study will be shared with the farming industry and stakeholders through knowledge exchange events.