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Project title

Nationwide analysis of Antimicrobial Resistance in soil environments to bridge the current data knowledge gaps

Primary Funding Agency

Environmental Protection Agency

Co-Funding Organisation(s)

Department of Agriculture, Food and Marine (DAFM)

Lead Organisation

Maynooth University (MU)

Lead Applicant

Fiona Walsh

Project Abstract

The World Health Organisation identified the development of antimicrobial resistance (AMR) as one of the major global threats to human society and recommends intensive monitoring for the identification and surveillance of critical hot spots, with the aim of reducing the spread of resistance. Critical hot spots are present in the environment, humans, animals and transmission routes between them. The data from national and EU surveillance of AMR in animal and human pathogens occurs annually and is openly available. These data are vital for the development of local, national and EU government policies and measures to tackle AMR. No such surveillance exists in the environment. Therefore, we do not know the levels of AMR in our environments. Data on AMR in soils in Ireland and the EU has been provided by research projects analysing a small number of soils, mainly in relation to the impact of manure application on the soil AMR levels. This project aims to provide a nationwide survey of AMR across 10,000 soil samples collected as part of the DAFM Farm Environmental Study Programme. Department of Agriculture Food and the Marine (DAFM) is currently collecting thousands of soils from Irish farms. This provides a unique and timely opportunity to utilise these samplese for the first national soil AMR survey. The DAFM programme has and will screen the soil for one specific type of AMR bacteria (ESBL Escherichia coli). These bacteria are recommended as the indicator of AMR to be compared across environmental, animal, and human samples. We will characterise the genomes of these bacteria and compare them with each other to identify the diversity of the bacteria and their AMR genes across Ireland. From the 10,000 samples we will extract DNA and form a national biobank of the soil and extracted DNA, a great resource for other scientists. We will screen all extracted DNA for the presence of the most relevant clinical AMR genes using a high throughput robotic liquid handler and machine-readable detection method. Where AMR genes are present, we will measure the relative abundances across soils to identify variations. The soil microbial biodiversity impacts plant growth, food production and is thought to impact AMR. Within a subset of soils (n = 200) we will analyse the total bacterial and fungal biodiversity. This will firstly provide a detailed picture of soil biodiversity across Ireland and secondly enable the correlation of the biodiversity data with the soil characteristics and AMR data. The final component of this project is the statistical and data analysis. The wealth of data collected by the DAFM programme will provide additional data e.g., soil carbon, nitrogen and phosphorous levels and farm type, these will be statistically analysed with the AMR data, the genome data, and the microbial biodiversity data to enable the identification of the parameters contributing to soils with the highest and lowest levels of AMR. These statistical analyses will be used to rank the risk of the soils as locations for AMR. This project will bridge the data gap on AMR in soils.

Grant Approved

�498,850.50

Research Hub

Healthy Environment

Research Theme

n/a

Start Date

03/01/2023

Initial Projected Completion Date

02/01/2027