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Study of the effect of livestock industry biosecurity and hygiene measures on the occurrence and control of antimicrobial resistance - OZ0514

Resistance to therapeutic antimicrobial agents is a growing problem for both human and veterinary medicine, and is a current One Health policy priority and is highlighted in the National Action Plan (NAP) for Antimicrobial Resistance (AMR). Substantial progress has been made in reducing agricultural antimicrobial drug use in UK, particularly in the pig and poultry sector. However, evidence suggests that resistant pathogenic and commensal bacteria can persist and spread within and between livestock premises despite declining or zero antimicrobial use. Ineffective biosecurity has often been identified as a risk factor for AMR on farms, but there are large gaps in our understanding of the mechanisms behind such observations. This project will focus on the impact of farm biosecurity and hygiene interventions on dissemination and persistence of AMR bacteria, and will contribute to the delivery of UK NAP for AMR.
Conserving the effectiveness of existing antimicrobial drugs is an urgent priority, as the capacity to develop novel and affordable antibacterial drugs is in doubt. The World Health Organisation has highlighted AMR pathogens of particular concern. Escherichia coli Enterococcus faecium and livestock‚Äďassociated MRSA (LA-MRSA) will be studied in this project via a combination of laboratory models and field case studies, as well as investigating Salmonella strains with AMR and epidemic potential.
With respect to AMR among broiler-associated E. coli in vertically-integrated Western European production, imported elite breeding stock and of hatcheries can present risks for the introduction and maintenance/transmission of resistant bacteria. In pigs, LA-MRSA appears to transmit between tiers of the breeding pyramid, but also engages in local intra- and inter-species spread. In all these cases, external biosecurity and hygiene, including cleaning and disinfection (C&D) are of major importance for control. In this study we will investigate the routes for introduction, dissemination and persistence of AMR bacteria within the livestock industry and the infectivity of AMR organisms in environmental samples for chicks.
There is also a body of experimental data on AMR-related phenomena such as effects on bacterial fitness, induction of biocide resistance, co-resistance to antimicrobial drugs/biocides and horizontal transmission of resistance in the presence of antimicrobials or co-selecting substances,
such as heavy metals, in artificial laboratory models. In this project we will investigate the role of AMR in fitness and biofilm formation and the potential involvement of other inhibitory substances, such as heavy metals and biocides, in selection for AMR bacteria. mutants, pre-existing resistant strains and stimulating transfer of mobile resistance elements, particularly plasmids.
The elimination of any environmental bacterial population on livestock premises is challenging. There is a large data gap regarding the effective disinfection of bacteria exhibiting AMR, whether commensal or potential zoonotic pathogens. An assumption that antimicrobial-resistant bacteria are similar to their non-resistant counterparts in the face of C&D procedures may not be justified. This study will include investigations of the efficacy of disinfectants to eliminate resistant organisms in comparison with their sensitive counterparts in realistic laboratory simulations and field studies. In vivo challenge studies will also be used to assess the acquisition of AMR bacteria from contaminated environmental elements.
Faecal waste contains a wide variety of antimicrobial resistant bacteria, resistance genes and mobile genetic elements that can carry AMR, including phages. Such waste is used as fertiliser for pasture, arable crops and horticulture and run-off can leach into watercourses. The project will investigate the ability of different methods of waste management (e.g. composting, anaerobic digestion and larviculture) to minimise persistence of AMR.
This project will provide a platform for a multidisciplinary team of veterinarians, bacteriologists, AMR and molecular genetic specialists

1. Investigation of the dissemination of antimicrobial resistance in the livestock industry; this will address Section 2.3.4 of the UK 5-year National Action Plan (NAP) for AMR - to achieve a better understanding of how AMR spreads between and among humans, animals and the environment.
2. Investigation of biocide activity against antimicrobial resistant bacteria; this will address Section 2.4.1 of the NAP - to deepen understanding about AMR in the environment and how it can be controlled.
3. Molecular characterisation of antimicrobial resistant bacteria and the metagenome of farm waste; this will address Section 2.4 of the NAP, and also Section 3.4 of the NAP by using whole genome sequencing (WGS) and metagenomics to enhance detection of AMR and to identify transmission pathways. Metagenomics studies will also deliver to section 2.5.1 of the NAP, by strengthening the evidence base for AMR and food safety.
4. Bacterial survival studies to address section 2.4 of the NAP
5. Bioassay studies to address Section 2.4 of the NAP to minimise spread of AMR through the environment, as well as section 2.3.4 by providing information on how AMR spreads.
Time-Scale and Cost
From: 2021

To: 2025

Cost: £1,082,152
Contractor / Funded Organisations
APHA (Animal and Plant Health Agency)
Public Health              
Fields of Study
Animal Health