Evaluating antimicrobial resistance in dairy farming: Understanding real world interactions
Lead Research Organisation:
University of Nottingham
Department Name: Sch of Biosciences
Abstract
Aims
Antimicrobial resistance (AMR) continues to be a growing global issue. Modern farming practices require the use of antibiotics, biocides and metals such as copper to ensure low disease occurrence and high production output (1,2,3). AMR genes are often located on mobile genetic elements such as plasmids, transposons and integrons therefore allowing horizontal exchange between bacteria. The aim was to examine the acquisition of resistance genes on large self-transmissible plasmids (4,5).
Methods and results
Surveillance of a 3 million litre slurry tank from a UK dairy farm with specific focus on Escherichia coli, identified isolates that displayed resistance to all major classes of antibiotics used in agricultural, medical, and veterinary science. Sequence analysis of whole genome and plasmid sequences for isolates E. coli BCC2, BS7, BCE3, and A2.5 revealed several large transmissible plasmids encoding novel traits, virulence factors, resistance genes including extended-spectrum beta-lactamases, metal resistance for mercury, toxin systems capable of acting as addiction modules and transfer genes. This detailed analysis of the sequence data has given insight into the complexity of the transferable resistance present within a single slurry tank.
Conclusions
Poor absorption of antibiotics within animal guts results in the excretion of antibiotics within their faeces (6, 7). When slurry is spread onto agricultural land, trace amounts of antibiotics or metals can result in the selection and incorporation of resistance genes onto large mobile genetic elements (4, 8). Even at low levels (previously thought insignificant) antibiotic resistance can be selected for (9).
Significance of study
The spreading of slurry and the use of antibiotics, metals and biocides looks to remain a stable part of farming practice. Therefore it is vitally important to gain a greater understanding of how mobile genetic elements such as plasmids, transposons and integrons are exchanged and maintained within the environment, the selective pressures driving them and the anthropogenic activities influencing them.
References
(1) Joy, S.R., Bartelt-Hunt, S.L., Snow, D.D., Gilley, J.E., Woodbury, B.L., Parker, D.B., Marx, D.B., et al. (2013). "Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry". Environmental Science and Technology, Vol. 47 No. 21, pp. 12081-12088
(2) McLaughlin, D. and Kinzelbach, W. (2015). "Food security and sustainable resource management". Water Resources Research, Vol. 51 No. 7, pp. 4966-4985
(3) Woolhouse, M., Ward, M., van Bunnik, B. and Farrar, J. (2015). "Antimicrobial resistance in humans, livestock and the wider environment". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, Vol. 370 No. 1670, p. 20140083
(4) Heuer, H., Schmitt, H. and Smalla, K. (2011). "Antibiotic resistance gene spread due to manure application on agricultural fields". Current Opinion in Microbiology, Vol. 14 No. 3, pp. 236-243
(5) Ho, W.S., Yap, K.-P., Yeo, C.C., Rajasekaram, G. and Thong, K.L. (2015). "The complete sequence and comparative analysis of a multidrug-resistance and virulence multireplicon IncFII plasmid pEC302/04 from an extraintestinal pathogenic Escherichia coli EC302/04 indicate extensive diversity of IncFII plasmids". Frontiers in Microbiology, Frontiers Media SA, Vol. 6, p. 1547
(6) Boxall, A.B.., Fogg, L.., Blackwell, P.., Kay, P., Pemberton, E.. and Croxford, A. (2004). "Veterinary medicines in the environment". Reviews of Environmental Contamination and Toxicology, Vol. 180, pp. 1-91
(7) Chee-Sanford, J.C., Mackie, R.I., Koike, S., Krapac, I.G., Lin, Y.-F., Yannarell, A.C., Maxwell, S., et al. (2009). "Fate and transport of antibiotic residues and antibiotic resistance genes following land application of manure waste". Journal of Environment Quality, Vol. 38 No. 3, p. 1086
Antimicrobial resistance (AMR) continues to be a growing global issue. Modern farming practices require the use of antibiotics, biocides and metals such as copper to ensure low disease occurrence and high production output (1,2,3). AMR genes are often located on mobile genetic elements such as plasmids, transposons and integrons therefore allowing horizontal exchange between bacteria. The aim was to examine the acquisition of resistance genes on large self-transmissible plasmids (4,5).
Methods and results
Surveillance of a 3 million litre slurry tank from a UK dairy farm with specific focus on Escherichia coli, identified isolates that displayed resistance to all major classes of antibiotics used in agricultural, medical, and veterinary science. Sequence analysis of whole genome and plasmid sequences for isolates E. coli BCC2, BS7, BCE3, and A2.5 revealed several large transmissible plasmids encoding novel traits, virulence factors, resistance genes including extended-spectrum beta-lactamases, metal resistance for mercury, toxin systems capable of acting as addiction modules and transfer genes. This detailed analysis of the sequence data has given insight into the complexity of the transferable resistance present within a single slurry tank.
Conclusions
Poor absorption of antibiotics within animal guts results in the excretion of antibiotics within their faeces (6, 7). When slurry is spread onto agricultural land, trace amounts of antibiotics or metals can result in the selection and incorporation of resistance genes onto large mobile genetic elements (4, 8). Even at low levels (previously thought insignificant) antibiotic resistance can be selected for (9).
Significance of study
The spreading of slurry and the use of antibiotics, metals and biocides looks to remain a stable part of farming practice. Therefore it is vitally important to gain a greater understanding of how mobile genetic elements such as plasmids, transposons and integrons are exchanged and maintained within the environment, the selective pressures driving them and the anthropogenic activities influencing them.
References
(1) Joy, S.R., Bartelt-Hunt, S.L., Snow, D.D., Gilley, J.E., Woodbury, B.L., Parker, D.B., Marx, D.B., et al. (2013). "Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry". Environmental Science and Technology, Vol. 47 No. 21, pp. 12081-12088
(2) McLaughlin, D. and Kinzelbach, W. (2015). "Food security and sustainable resource management". Water Resources Research, Vol. 51 No. 7, pp. 4966-4985
(3) Woolhouse, M., Ward, M., van Bunnik, B. and Farrar, J. (2015). "Antimicrobial resistance in humans, livestock and the wider environment". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, Vol. 370 No. 1670, p. 20140083
(4) Heuer, H., Schmitt, H. and Smalla, K. (2011). "Antibiotic resistance gene spread due to manure application on agricultural fields". Current Opinion in Microbiology, Vol. 14 No. 3, pp. 236-243
(5) Ho, W.S., Yap, K.-P., Yeo, C.C., Rajasekaram, G. and Thong, K.L. (2015). "The complete sequence and comparative analysis of a multidrug-resistance and virulence multireplicon IncFII plasmid pEC302/04 from an extraintestinal pathogenic Escherichia coli EC302/04 indicate extensive diversity of IncFII plasmids". Frontiers in Microbiology, Frontiers Media SA, Vol. 6, p. 1547
(6) Boxall, A.B.., Fogg, L.., Blackwell, P.., Kay, P., Pemberton, E.. and Croxford, A. (2004). "Veterinary medicines in the environment". Reviews of Environmental Contamination and Toxicology, Vol. 180, pp. 1-91
(7) Chee-Sanford, J.C., Mackie, R.I., Koike, S., Krapac, I.G., Lin, Y.-F., Yannarell, A.C., Maxwell, S., et al. (2009). "Fate and transport of antibiotic residues and antibiotic resistance genes following land application of manure waste". Journal of Environment Quality, Vol. 38 No. 3, p. 1086
Organisations
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M008770/1 | 01/10/2015 | 31/10/2024 | |||
| 1645076 | Studentship | BB/M008770/1 | 01/10/2015 | 30/09/2019 |
| Description | The carriage of resistance within the dairy farm environment has changed over the last 4 years. For example large self transmissible plasmids are not being isolated as much as they were in 2014. Many of the resistances seen are now more frequently found to be chromosomally encoded. Further work is now being conducted using PacBio sequencing to help me understand how the population of bacteria has changed since the last set of isolates was sequenced in 2014. In the past year a lot has been discovered in relation to how the population of E. coli within the dairy farm has changed. For example 10 ESBL carrying E. coli have been sequenced and found to be clonal. These 10 sequenced isolates are also all carrying an element with the ability to horizontally transfer an ESBL determinant. Transposition assays have shown this element is able to mobilise by utilising resident plasmids and can be enhanced to mobilise in the presence of antibiotics commonly used within dairy farming. I have also noted that although many of my isolates carry plasmids, these are cryptic and contain no resistance genes (antibiotic or metal). However transposition assays have shown plasmids are vital for the successful transfer of other mobile elements such as transposons. Further discoveries have shown that similar phenotypic resistance profiles may be due to more than one mechanism. Many of the isolates I have studied show a very similar resistance profile within disc diffusion assays, but further analysis revealed different mechanisms. |
| Exploitation Route | The dairy farm is an ever changing bacterial ecosystem that is influenced by a number of factors including antibiotic usage and human behaviour. Further research could look to continue the monitoring and understanding of how bacteria change in response to those factors. |
| Sectors | Agriculture, Food and Drink,Healthcare |