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FoodBioSystems DTP - Tackling antimicrobial resistance in dairy production: using microfluidics and smartphone technology to monitor resistance genes alongside functional antibiotic sensitivity testing


Project Description

Research Group: FOODBIOSYSTEMS BBSRC DTP

PROBLEM - Dairy farming is a socially and economically important sector of agriculture, and also illustrates the importance of a ‘one health’ approach that addresses both human and animal health. Antibiotics are used extensively to treat important infections in agriculture, including mastitis – a bacterial infection of the udder – which can infect 1 in 5 cows every year even in modern farms with extensive infection control measures. Mastitis not only causes animal suffering, but significantly reduces milk production. Antimicrobial resistance (AMR) is common in bacterial mastitis making it harder to treat. Agricultural antibiotic use (including treating mastitis in dairy farming) contributes to the rise and spread of AMR, which is a major global public health risk, as bacterial infections become ever-harder to treat. It has become clear that industrial antibiotic use (e.g. in dairy production) is one driver for a rise in ‘superbugs’ spreading across the world, which are resistant to multiple antibiotics. A major route of AMR from farm to human is through food production- in the case of dairy, through milk and cheese products. As well as becoming a serious threat to human health and public safety, treatment of our animals – not just dairy cattle but also companion animals – becomes ever-harder as antibiotics become less effective. Preliminary research by our groups suggests that not only is AMR common in mastitis, but antibiotic resistance can be detected in a range of dairy foods. A ‘one health’ approach, where food producing animal and human health are addressed hand-in-hand, is now vital to tackle the global threat of AMR.

SOLUTION - Conventional AMR tests (e.g. using agar plates) are very slow and can only be conducted in labs. As a result, vets must administer antibiotics without knowing which antibiotic will effectively treat an infection or what AMR genes are present. This project combines several cutting edge tools for the first time, to create powerful yet simple new methods for faster AMR testing outside a laboratory. At Reading, we have focused on functional cellular assays that measure bacterial growth or killing when combined with antibiotics, using lowcost microcapillary devices read by smartphone cameras. At Surrey, the latest DNA techniques including isothermal amplification and whole genome sequence analysis, has made it possible to both rapidly detect specific AMR genes, and survey genomes of resistant organisms. Crucially, we will develop methods that combine these complementary technologies to both detect AMR genes, and measure functional antibiotic sensitivity; by combining these tools we will be able to gain unique insights into rise and spread of AMR. Ultimately, if we can rapidly test for antibiotic resistance on the farm, we can make sure that animals with mastitis are treated with safe and effective medication.

TOOLS and TECHNOLOGY - Microfluidics, the science of miniaturization, allows laboratory analysis to be taken outside the lab and can give more rapid results than conventional bioanalytical methods. At the same time, global demand for high quality smartphone cameras has made high performance digital imaging portable and affordable. Our research teams at Reading and Surrey have developed rapid and portable testing technology for both functional bacterial assays including antibiotic sensitivity measurement, and genetic detection for example for AMR genes. This PhD project will focus on combining these analytical tools to allow us to track both genetic and phenotypic AMR, and then applying the technology developed to tackling the problem of AMR in dairy production and dairy food manufacture.

TEAM - This project brings together three complementary research groups: the leading veterinary and ‘one health’ microbiology team at Surrey ; CEDAR- the University of Reading’s excellent centre for dairy research established >25 years ago within the School of Agriculture; brought together by the Biomedical Technology Laboratory within the School of Chemistry, Food and Pharmacy. This will allow the student access to state-ofthe-art microbiology and microbial genetics facility at Surrey, in addition to the 600-cow commercial farm plus bioengineering facilities at Reading.

Training opportunities: The project combines an opportunity to develop new methods and technology, with field visits highly relevant to both food safety and animal health. Method and technology development will utilize the latest life sciences (e.g. next-generation sequencing and genomics) and bioengineering tools (microfluidics, 3D printing, open source robotics). To apply new technology to ‘one health’ problems where animal welfare meets human food safety, you will undertake visits to local dairy farms and dairy production facilities. Finally, you will work within an entrepreneurial and innovation environment and learn about research commercialization and technology transfer.

Student profile: This exciting cross-disciplinary project will suit an enthusiastic student from any relevant background who has an appetite to learn how to develop new technology to apply to vital challenges in public health, animal health and food safety. Suitable degrees would include biology, microbiology, veterinary science and medicine, agriculture, food science or any related science. We would also welcome applications from students from a bioengineering, biotechnology or biochemical engineering background with an appetite to gain life science research expertise. An ambition to use the latest science and technology to solve real-world problems, and/or an entrepreneurial outlook would also be beneficial.

Funding Notes

This project is part of the FoodBioSystems BBSRC Doctoral Training Partnership (DTP), it will be funded subject to a competition to identify the strongest applicants. Due to restrictions on the funding, this studentship is only open to UK students and EU students who have lived in the UK for the past three years.

The FoodBioSystems DTP is a collaboration between the University of Reading, Cranfield University, Queen’s University Belfast, Aberystwyth University, Surrey University and Brunel University London. Our vision is to develop the next generation of highly skilled UK Agri-Food bioscientists with expertise spanning the entire food value chain. We have over 60 Associate and Affiliate partners. To find out more about us and the training programme we offer all our postgraduate researchers please visit View Website.

References

https://doi.org/10.1371/journal.pone.0224878
https://doi.org/10.1093/jac/dky037
https://doi.org/10.1016/j.mcp.2016.08.001

How good is research at University of Reading in Allied Health Professions, Dentistry, Nursing and Pharmacy?

FTE Category A staff submitted: 23.20

Research output data provided by the Research Excellence Framework (REF)

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