Occurrence and horizontal gene transfer of carbapenemase and ESBL genes in soil microbiomes

This project aims to understand the potential of environmental reservoirs and transmission of AMR in members of autochthonous soil microbiomes and between transient allochthonous human and animal pathogens entering the environment, for example from faecal agricultural wastes or domesticated or wild animal and bird faecal ingress. It also seeks to understand if horizontal gene transfer occurs successfully between potential pathogens in the various soil microbiomes and complex matrices encompassing clay, loam and sandy soils. The work will utilize modern molecular biology and genomics to screen microbiome populations and defined third generation ESBL and fourth generation carbapenemase E. coli and Klebsiella pneumoniae donor strains, with an E. coli sensitive strain as the recipient.

The University of Southampton team comprises an established scientific group with expertise in survival of faecal pathogens in soil and water, and HGT of ESBL and carbapenemase resistance genes between different species, in collaboration with an Early Career Researcher with expertise in soil microbiology and processes, and stable isotope probing (SIP) to understand community viability, metabolic turnover and gene acquisition. Previous work for UKWIR and Defra/FSA has developed grassed soil microcosms of clay, loam and sandy soils and demonstrated survival of zoonotic pathogens therein for several weeks following faecal waste irrigation. These pathogens were subsequently released from the complex soil matrices using a novel, gentle pulsification procedure followed by membrane filtration and quantitative resuscitation on appropriate selective agar media.

This proposal will help identify the specific environmental drivers of the HGT and beta lactamase selection processes, including implications for both anthropogenic (animal husbandry, human wastewater disposal) and non-anthropogenic (wild animal and bird faecal ingress) drivers. The work will also include identifying the implications for pathogens of clinical and/or veterinary importance such Klebsiella pneumonia and E. coli. The research will be able to help inform AMR policy and management strategies, and will form the basis of a subsequent large research proposal to address these policies and strategies more fully.

The approaches and methodologies to be developed in this proposal could be translated to other environments, antibacterials or other bacterial communities of interest to the AMR funding bodies.

The project will investigate the potential of environmental reservoirs and transmission of AMR in members of authochthonous soil microbiomes and between transient allochthonous human and animal pathogens entering the environment, for example from human wastewater, faecal agricultural wastes or domesticated or wild animal and bird faecal ingress. It also seeks to understand if horizontal gene transfer occurs successfully between potential pathogens in the various soil microbiomes and complex matrices encompassing clay, loam and sandy soils.

Thus, the project provides a major opportunity for UK PLC, firstly through improved management of agricultural land to avoid infection of grazing animals from faecally contaminated land, potentially reducing their health status and a source of food poisoning, but also protect humans from handling or consuming crops grown on the land. Thus industry will benefit from improved animal health and providing high quality, safe food to the public. Secondly, benefits to the wider industry from this research in terms of reduced chemical use when faecal wastes are managed properly.

Immediate beneficiaries will include all fresh produce suppliers and retail outlets in the UK and internationally. The producers will better comply with international sanitary standards for the sale of fresh produce and protect their workers from exposure to AMR pathogens; the retailers will benefit from improved customer confidence and sales. The consumer will benefit since it is critical to establish the safest means of animal husbandry and fresh produce production from the farm to the fork to protect the public health, improve their diet, and maintain consumer confidence following the regular reports of food-borne disease outbreaks. Thus, directly impacting on the nation's health, wealth and culture.