Review of Antibiotic Use in Crops, Associated Risk of Antimicrobial Resistance and Research Gaps Report to Department for Environment, Food and Rural Affairs (Defra) & The Food Standards Agency (FSA) March 2020 Dr Edward Haynes, Dr Carmel Ramwell, Dr Tom Griffiths, Mr Don Walker, Mr Julian Smith Fera Science Ltd. https://doi.org/10.46756/sci.fsa.vnq132 Contents Glossary ..................................................................................................................... 4 Executive Summary ................................................................................................... 5 Introduction ................................................................................................................ 6 Use of Antibiotics in Crops ......................................................................................... 8 Information Gathering ............................................................................................. 8 Summary of Responses .......................................................................................... 9 Regulation of Antibiotics ........................................................................................... 10 Antibiotics Used in Plant Agriculture......................................................................... 11 Data on Use .......................................................................................................... 12 Crops and Diseases .............................................................................................. 13 Farming Practice ................................................................................................... 14 Misuse .................................................................................................................. 20 Risks ..................................................................................................................... 21 Summary............................................................................................................... 22 Prevalence of Antibiotics and Antimicrobial Resistance Genes in Crops ................. 23 Antibiotics in Crops ............................................................................................... 23 Compound ............................................................................................................ 25 Plant Type ............................................................................................................. 26 Manure Type ......................................................................................................... 27 Exposure Duration ................................................................................................ 27 Irrigation Water ..................................................................................................... 28 Hydroponics .......................................................................................................... 32 Antimicrobial Resistance Genes in Crops ............................................................. 35 Summary............................................................................................................... 37 Selection Pressure for Antimicrobial Resistance from Non-Antibiotic Sources ........ 38 Metals ................................................................................................................... 38 Pesticides.............................................................................................................. 39 Pollutants .............................................................................................................. 42 Biocides ................................................................................................................ 42 Summary............................................................................................................... 42 Detection of Antibiotics ............................................................................................. 44 Methods of Analysis .............................................................................................. 44 Extraction and Sample Clean-up .......................................................................... 53 2 Determination of Veterinary Medicines ................................................................. 54 Summary............................................................................................................... 54 Detection of Antibiotic Resistance ............................................................................ 55 Detection of Phenotypic Antimicrobial Resistance and Susceptibility ................... 55 Targeted Molecular Detection ............................................................................... 56 Non-Targeted Molecular Detection ....................................................................... 57 Summary............................................................................................................... 58 Conclusions .............................................................................................................. 59 Research Gaps ........................................................................................................ 61 Technical Improvements ....................................................................................... 61 Antibiotics and AMR in the Crop Environment ...................................................... 61 Antibiotic Use ........................................................................................................ 62 Acknowledgments .................................................................................................... 64 Supplementary Materials 1: Questionnaire on Use of Antibiotics in Crop Production ................................................................................................................................. 65 References ............................................................................................................... 68 3 Glossary ARB- Antimicrobial Resistant Bacteria ARG- Antimicrobial Resistance Genes AMR- Antimicrobial Resistance FAO- Food and Agriculture Organisation of the United Nations IPPC- International Plant Protection Convention LMICs- Low- and Middle-Income Countries LOD- Limit of Detection LOQ- Limit of Quantification MGE- Mobile Genetic Element MIC- Minimum Inhibitory Concentration Suggested Citation: Haynes et al., Fera Science Ltd. 2020. Review of Antibiotic Use in Crops, Associated Risk of Antimicrobial Resistance and Research Gaps. Report to Department for Environment, Food and Rural Affairs (Defra) & The Food Standards Agency (FSA). https://doi.org/10.46756/sci.fsa.vnq132 4 Executive Summary • Relatively few countries have national legislation in place regulating the use of antibiotics in crop agriculture. Furthermore, in many countries the compounds and volumes applied are not well monitored. • Where antibiotic use is regulated, there are some specific antibiotics (such as streptomycin, oxytetracycline, and kasugamycin) and crops (such as pome fruit and citrus fruit) where use is repeatedly reported. In general, where information is available, antibiotic use in crop agriculture appears to be at a significantly lower level than in livestock agriculture. However, in many countries official information is unavailable, and use may be considerably higher. • Soil amendments may constitute a more important source of antibiotics than direct application, especially when these are of livestock (e.g. manure) or human (e.g. sewage sludge) origin. Soil amendments can also introduce antimicrobial resistant organisms or antimicrobial resistance (AMR) genes on to crops. • Uptake of antibiotics by crops differs widely according to many factors, including antibiotic class, crop type and variety, and soil type. • Methods exist for the detection of antibiotics in a range of crops, but are limited, certainly in comparison with methods for animal products. Multi-class, multi- residue methods to monitor for a range of residues are available, but further work is required to extend the range of compounds tested for. • Rapid methods have been developed to test for both AMR genes and phenotypic antimicrobial resistance in bacteria. High throughput sequencing-based techniques, including metagenomics, can be used to simultaneously test for multiple gene targets in multiple organisms and can provide data on the genomic and environmental context of the AMR genes detected. • The risk of AMR arising in crop agriculture in the UK is likely relatively low, given the lack of antibiotic use on crops in this country. The risk of AMR arising due to co-selection from other agrichemicals is difficult to assess due to a lack of information about the co-selection properties of most pesticides. Some agriculturally important chemicals, such as copper compounds, do co-select for AMR. The possibility of importing AMR bacteria or genes on crops or plant products treated with antibiotics in countries where they are either used or misused is likely higher. Without more quantitative information on antibiotic use in crop agriculture in countries from which the UK sources plant products, or testing of imported products, it is difficult to draw firmer conclusions. 5 Introduction Antimicrobial resistance (AMR) is an increasingly important global health problem, with the potential to render antibiotics unusable, and negate medical treatments such as chemotherapy and organ transplant