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Baker M, Williams AD, Hooton SPT, Helliwell R, King E, Dodsworth T, María Baena-Nogueras R, Warry A, Ortori CA, Todman H, Gray-Hammerton CJ, Pritchard ACW, Iles E, Cook R, Emes RD, Jones MA, Kypraios T, West H, Barrett DA, Ramsden SJ, Gomes RL, Hudson C, Millard AD, Raman S, Morris C, Dodd CER, Kreft JU, Hobman JL, Stekel DJ. Antimicrobial resistance in dairy slurry tanks: A critical point for measurement and control. Environ Int 2022; 169:107516. [PMID: 36122459 DOI: 10.1016/j.envint.2022.107516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 06/15/2023]
Abstract
Waste from dairy production is one of the largest sources of contamination from antimicrobial resistant bacteria (ARB) and genes (ARGs) in many parts of the world. However, studies to date do not provide necessary evidence to inform antimicrobial resistance (AMR) countermeasures. We undertook a detailed, interdisciplinary, longitudinal analysis of dairy slurry waste. The slurry contained a population of ARB and ARGs, with resistances to current, historical and never-used on-farm antibiotics; resistances were associated with Gram-negative and Gram-positive bacteria and mobile elements (ISEcp1, Tn916, Tn21-family transposons). Modelling and experimental work suggested that these populations are in dynamic equilibrium, with microbial death balanced by fresh input. Consequently, storing slurry without further waste input for at least 60 days was predicted to reduce ARB spread onto land, with > 99 % reduction in cephalosporin resistant Escherichia coli. The model also indicated that for farms with low antibiotic use, further reductions are unlikely to reduce AMR further. We conclude that the slurry tank is a critical point for measurement and control of AMR, and that actions to limit the spread of AMR from dairy waste should combine responsible antibiotic use, including low total quantity, avoidance of human critical antibiotics, and choosing antibiotics with shorter half-lives, coupled with appropriate slurry storage.
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Affiliation(s)
- Michelle Baker
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Alexander D Williams
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Steven P T Hooton
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; (a)Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Richard Helliwell
- School of Sociology and Social Policy, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK; School of Geography, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK; Ruralis, University Centre Dragvoll, N-7491 Trondheim, Norway
| | - Elizabeth King
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Thomas Dodsworth
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; ResChem Analytical Ltd, 8 Jubilee Parkway, Jubilee Business Park, Stores Road, Derby DE21 4BJ, UK
| | - Rosa María Baena-Nogueras
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Andrew Warry
- Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Catherine A Ortori
- School of Pharmacy, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Henry Todman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; School of Mathematical Sciences, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Charlotte J Gray-Hammerton
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Alexander C W Pritchard
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Ethan Iles
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Ryan Cook
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Michael A Jones
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Theodore Kypraios
- School of Mathematical Sciences, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Helen West
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - David A Barrett
- School of Pharmacy, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Stephen J Ramsden
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Rachel L Gomes
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Chris Hudson
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Andrew D Millard
- (a)Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Sujatha Raman
- School of Sociology and Social Policy, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK; Centre for Public Awareness of Science, Australian National University, Linnaeus Way, Acton ACT 2601, Canberra, Australia
| | - Carol Morris
- School of Geography, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Christine E R Dodd
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Jan-Ulrich Kreft
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT
| | - Jon L Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Dov J Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; Department of Mathematics and Applied Mathematics, University of Johannesburg, Auckland Park Kingsway Campus, Rossmore, Johannesburg, South Africa.
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Alcock TD, Salt DE, Wilson P, Ramsden SJ. More sustainable vegetable oil: Balancing productivity with carbon storage opportunities. Sci Total Environ 2022; 829:154539. [PMID: 35302036 DOI: 10.1016/j.scitotenv.2022.154539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/08/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Intensive cultivation and post-harvest vegetable oil production stages are major sources of greenhouse gas (GHG) emissions. Variation between production systems and reporting disparity have resulted in discordance in previous emissions estimates. The aim of this study was to assess global systems-wide variation in GHG emissions resulting from palm, soybean, rapeseed and sunflower oil production. Such an analysis is critical to understand the implications of meeting increasing edible oil demand. To achieve this, we performed a unified re-analysis of life cycle input data from diverse palm, soybean, rapeseed, and sunflower oil production systems, from a saturating search of published literature. The resulting dataset reflects almost 6000 producers in 38 countries, and is representative of over 71% of global vegetable oil production. Across all oil crop systems, median GHG emissions were 3.81 kg CO2e per kg refined oil. Crop specific median emissions ranged from 2.49 kg CO2e for rapeseed oil to 4.25 kg CO2e for soybean oil per kg refined oil. Determination of the carbon cost of agricultural land occupation revealed that carbon storage potential in native compared to agricultural land cover drives variation in production GHG emissions, and indicates that expansion of production in low carbon storage potential land, whilst reforesting areas of high carbon storage potential, could reduce net GHG emissions whilst boosting productivity. Nevertheless, there remains considerable scope to improve sustainability within current production systems, including through increasing yields whilst limiting application of inputs with high carbon footprints, and in the case of palm oil through more widespread adoption of methane capture technologies in processing stages.
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Affiliation(s)
- Thomas D Alcock
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK; Crop Physiology, School of Life Sciences - Weihenstephan, Technical University of Munich, 85354 Freising, Germany.
| | - David E Salt
- Future Food Beacon of Excellence, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK; School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
| | - Paul Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
| | - Stephen J Ramsden
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
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Townsend TJ, Ramsden SJ, Wilson P. Analysing reduced tillage practices within a bio-economic modelling framework. Agric Syst 2016; 146:91-102. [PMID: 27375318 PMCID: PMC4913617 DOI: 10.1016/j.agsy.2016.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 04/15/2016] [Accepted: 04/18/2016] [Indexed: 05/27/2023]
Abstract
Sustainable intensification of agricultural production systems will require changes in farm practice. Within arable cropping systems, reducing the intensity of tillage practices (e.g. reduced tillage) potentially offers one such sustainable intensification approach. Previous researchers have tended to examine the impact of reduced tillage on specific factors such as yield or weed burden, whilst, by definition, sustainable intensification necessitates a system-based analysis approach. Drawing upon a bio-economic optimisation model, 'MEETA', we quantify trade-off implications between potential yield reductions, reduced cultivation costs and increased crop protection costs. We extend the MEETA model to quantify farm-level net margin, in addition to quantifying farm-level gross margin, net energy, and greenhouse gas emissions. For the lowest intensity tillage system, zero tillage, results demonstrate financial benefits over a conventional tillage system even when the zero tillage system includes yield penalties of 0-14.2% (across all crops). Average yield reductions from zero tillage literature range from 0 to 8.5%, demonstrating that reduced tillage offers a realistic and attainable sustainable intensification intervention, given the financial and environmental benefits, albeit that yield reductions will require more land to compensate for loss of calories produced, negating environmental benefits observed at farm-level. However, increasing uptake of reduced tillage from current levels will probably require policy intervention; an extension of the recent changes to the CAP ('Greening') provides an opportunity to do this.
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Key Words
- Bio-economic modelling
- CAP, Common agricultural policy
- CT, conventional tillage
- DRT, deep reduced tillage
- GHG, greenhouse gas
- GM, gross margin
- NE, net energy
- NM, net margin
- RP, rotational ploughing
- RT, reduced tillage
- Reduced tillage
- SB, spring barley
- SI, sustainable intensification
- SRT1, shallow reduced tillage 1
- SRT2, shallow reduced tillage 2
- Sustainable intensification
- WB, winter barley
- WFB, winter field beans
- WOSR, oilseed rape
- WW, winter wheat
- ZT, zero tillage
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Baker M, Hobman JL, Dodd CER, Ramsden SJ, Stekel DJ. Mathematical modelling of antimicrobial resistance in agricultural waste highlights importance of gene transfer rate. FEMS Microbiol Ecol 2016; 92:fiw040. [PMID: 26906100 DOI: 10.1093/femsec/fiw040] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2016] [Indexed: 01/19/2023] Open
Abstract
Antimicrobial resistance is of global concern. Most antimicrobial use is in agriculture; manures and slurry are especially important because they contain a mix of bacteria, including potential pathogens, antimicrobial resistance genes and antimicrobials. In many countries, manures and slurry are stored, especially over winter, before spreading onto fields as organic fertilizer. Thus, these are a potential location for gene exchange and selection for resistance. We develop and analyse a mathematical model to quantify the spread of antimicrobial resistance in stored agricultural waste. We use parameters from a slurry tank on a UK dairy farm as an exemplar. We show that the spread of resistance depends in a subtle way on the rates of gene transfer and antibiotic inflow. If the gene transfer rate is high, then its reduction controls resistance, while cutting antibiotic inflow has little impact. If the gene transfer rate is low, then reducing antibiotic inflow controls resistance. Reducing length of storage can also control spread of resistance. Bacterial growth rate, fitness costs of carrying antimicrobial resistance and proportion of resistant bacteria in animal faeces have little impact on spread of resistance. Therefore, effective treatment strategies depend critically on knowledge of gene transfer rates.
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Affiliation(s)
- Michelle Baker
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Jon L Hobman
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Christine E R Dodd
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Stephen J Ramsden
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Dov J Stekel
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
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Ibrahim DR, Dodd CER, Stekel DJ, Ramsden SJ, Hobman JL. Multidrug resistant, extended spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from a dairy farm. FEMS Microbiol Ecol 2016; 92:fiw013. [PMID: 26850161 DOI: 10.1093/femsec/fiw013] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2016] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli strains were isolated from a single dairy farm as a sentinel organism for the persistence of antibiotic resistance genes in the farm environment. Selective microbiological media were used to obtain 126 E. coli isolates from slurry and faeces samples from different farm areas. Antibiotic resistance profiling for 17 antibiotics (seven antibiotic classes) showed 57.9% of the isolates were resistant to between 3 and 15 antibiotics. The highest frequency of resistance was to ampicillin (56.3%), and the lowest to imipenem (1.6%), which appeared to be an unstable phenotype and was subsequently lost. Extended spectrum β-lactamase (ESBL) resistance was detected in 53 isolates and blaCTX-M, blaTEM and blaOXA genes were detected by PCR in 12, 4 and 2 strains, respectively. Phenotypically most isolates showing resistance to cephalosporins were AmpC rather than ESBL, a number of isolates having both activities. Phenotypic resistance patterns suggested co-acquisition of some resistance genes within subsets of the isolates. Genotyping using ERIC-PCR demonstrated these were not clonal, and therefore co-resistance may be associated with mobile genetic elements. These data show a snapshot of diverse resistance genes present in the E. coli population reservoir, including resistance to historically used antibiotics as well as cephalosporins in contemporary use.
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Affiliation(s)
- Delveen R Ibrahim
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough, Leicestershire LE12 5RD, UK
| | - Christine E R Dodd
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough, Leicestershire LE12 5RD, UK
| | - Dov J Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough, Leicestershire LE12 5RD, UK
| | - Stephen J Ramsden
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough, Leicestershire LE12 5RD, UK
| | - Jon L Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough, Leicestershire LE12 5RD, UK
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Glithero NJ, Wilson P, Ramsden SJ. Prospects for arable farm uptake of Short Rotation Coppice willow and miscanthus in England. Appl Energy 2013; 107:209-218. [PMID: 23825896 PMCID: PMC3688319 DOI: 10.1016/j.apenergy.2013.02.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 01/18/2013] [Accepted: 02/08/2013] [Indexed: 05/09/2023]
Abstract
Biomass will play a role in the UK meeting EU targets on renewable energy use. Short Rotation Coppice (SRC) and miscanthus are potential biomass feedstocks; however, supply will rely on farmer willingness to grow these crops. Despite attractive crop establishment grants for dedicated energy crops (DECs) in the UK, uptake remains low. Drawing on results from an on-farm survey with 244 English arable farmers, 81.6% (87.7%) of farmers would not consider growing miscanthus (SRC), while respectively, 17.2% (11.9%) would consider growing and 1.2% (0.4%) were currently growing these crops. Farmer age, location, land ownership, farm type, farm size and farmer education level were not significant factors in determining acceptance of DECs. The main reasons cited for not growing DECs were impacts on land quality, lack of appropriate machinery, commitment of land for a long period of time, time to financial return and profitability. Reasons cited for willingness to grow DECs included land quality, ease of crop management, commitment of land for a long period of time, and profitability. Farmers cited a range of 'moral' (e.g. should not be using land for energy crops when there is a shortage of food), land quality, knowledge, profit and current farming practice comments as reasons for not growing DECs, while those willing to grow DECs cited interest in renewable energy, willingness to consider new crops, and low labour needs as rationale for their interest. Farm business objectives indicated that maximising profit and quality of life were most frequently cited as very important objectives. Previous research in the UK indicates that farmers in arable areas are unlikely to convert large areas of land to DECs, even where these farmers have an interest and willingness to grow them. Assuming that those farmers interested in growing DECs converted 9.29% (average percentage of arable land set-aside between 1996 and 2005) of their utilised agricultural area to these crops, 50,700 ha and 89,900 ha of SRC and miscanthus would, respectively, be grown on English arable farms. While farm business objectives were not identified as key determinants of DEC acceptance, enhanced information exchange through extension agents, providing market security and considering land reversion grants post-production are potential policy considerations.
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