EVAL-FARMS: Evaluating the Threat of Antimicrobial Resistance in Agricultural Manures and Slurries

Today NERC announced that our £1.5M AMR grant has been funded. We are very excited!

First thing to say is that it was a total team effort. I am embarrassed by the fact that only my name is listed on the announcement – it really would have been impossible without the expertise, intelligence, energy, commitment and open spirit of collaboration of my totally awesome colleagues: Jon Hobman, Rachel Gomes, Helen West, Sujatha Raman, Jan Kreft, Stephen Ramsden, Christine Dodd, Chris Thomas, Mike Jones, Andrew Millard, Richard Emes, David Barrett,  Carol Morris, Theodore Kypraios and Chris Hudson. And then the support we received: pump priming  for research from the schools of Biosciences, Pharmacy and Engineering, and for a grant-writing retreat from the University of Nottingham; writing support from Emma Allaway, Chris Satterley, Zoe Wilson and especially Diane Levine; and the enthusiasm of an array of external stakeholders from industry and policy, including NFU, BCVA, Velcourt, Lindhurst Engineering, DEFRA (VMD and APHA), FSA, JHI amd Severn Trent Water.

Project details (summarized from the Case for Support)

Our vision is to establish a strategic research programme in antimicrobial resistance (AMR) in waste from agricultural farm environments. Our aim is to quantify and mitigate the risks of emergence of resistant pathogens and AMR gene reservoirs associated with mixing antimicrobials with waste matter in these environments.

The project is focussed on the University of Nottingham’s (UoN) dairy and arable farm, which is typical of high performance UK dairy production, with ~200 high yielding cows. Slurry is stored in a 3M L slurry tank and subsequently spread on surrounding fields. We hypothesise that conditions in the slurry tank environment drive the evolution and acquisition of antimicrobial resistance, and the slurry acts as a reservoir for AMR that is regularly distributed into the environment

The project consists of six integrated Research Questions:

RQ1: What are the levels and nature of antimicrobial and virulence genes present in the slurry tank, their prevalence, carriage, and bacterial hosts?

RQ2: What are the chemical agents in the tank? What is their persistence?

RQ3: To what extent is resistance maintained after slurry application to soil?

RQ4: How can we elicit culturally embedded ways in which scientists and stakeholders know AMR risks? How can we use narrative and visual methods of engaging across these ways of knowing to develop resources for deliberation on AMR risk management?

RQ5: To what extent can we reduce resistance profiles through changes in slurry tank composition?

RQ6: Can we quantify the risk of emergence of AMR pathogens and what factors are predicted to control this risk best?

The first three posts will be advertised shortly. These will be 24 month post-docs in microbiology (supervised by Jon Hobman and Christine Dodd), pharmaceutical analysis (supervised by Rachel Gomes and David Barrett) and a 36 month 60% post-doc in cultural research (supervised by Sujatha Raman and Carol Morris). In practise, these posts will work across the different Research Questions in the grant, so the postdocs will interact with the full team. Technician posts to follow a little after, and a modelling postdoc will start in January 2018. There will also be three associated PhD studentships (pharmaceutical analysis, social research, mathematical modelling) to start in September 2017.

We have also developed an infographic to help explain how conditions in slurry could lead to emergence and selection for AMR bacteria. Here it is:





New publication:So why have you added me? Adolescent girls’ technology-mediated attachments and relationships.

Work from Di’s PhD has just been published! This is very much Di’s work. My contribution was making the figures in R. Very proud of Di! This is my first social research article – my publication record becomes increasingly eclectic.

Levine DT and Stekel DJ 2016. So why have you added me? Adolescent girls’ technology-mediated attachments and relationships. Computers in Human Behaviour 63:25-34.


  • Adolescent girls can develop attachment with others through, and with, technology.
  • Adolescent girls use technology to meet others and mediate relationships.
  • Facets of relationships can be understood as functions of secure relationships.
  • Functions include proximity-seeking, trust, exploration and return to secure base.
  • Technology use can amplify girls’ secure relationships with peers and parents.


Technology plays an almost ubiquitous role in contemporary British society. Despite this, we do not have a well-theorised understanding of the ways adolescent girls use digital devices in the context of their developing secure relationships with their families and friends. This study aims to address this gap in understanding. Fifteen young women based in the Midlands and from across the socio-economic spectrum participated between 2012 and 2013. Participants completed three research tools exploring technology-mediated attachment and relationships, and participated in a face-to-face interview. The findings suggest that it is possible for girls to develop attachments with others through, and with, technology; technology use brings people together and mediates relationships in a range of ways encapsulated by attachment functions. The study highlights the ongoing importance of parental and peer relationships by suggesting that technology can act as a means by which the positive and negative attributes of existing relationships can be amplified.

Authorship networks as an alternative to authorship lists

I am starting to think about different barriers to multidisciplinary research. One of the barriers is the traditional list of authors on journal research articles. The problem is that one has a linear list – and as a consequence the position on that list becomes hierarchical. Typically in our field, that means that being the first or final author on the list is over-valued, while other authorship locations are less valued. This then has an impact on jobs, promotions, etc.

Where research is genuinely multidisciplinary, this then becomes very problematic. Journals have tried to respond to this in various ways, including having joint first (or last) authorships and lists of author contributions (usually an afterthought at the end of the paper).

I propose here a radical alternative to an author list: an authorship network. This would replace the list of authors with a network (or graph) showing how the people have contributed to the work. Nodes on the graph could represent people, activities or grant codes. Edges could connect people to activities, people to grants (either as authors of the grant, or employed by the grant), people to each other (e.g. supervision relationships).

I have had a go at representing my most complex paper in this way. Here it is. Rectangular nodes are the authors. Rounded rectangles are the grants. Ovals are activities. Arrows between people link who is supervised by whom. Edges between people and grants represent grant authorship (blue) or employment (arrows). Edges from people to activities show who has done what, with thicker edges for the main contributors (i.e. Hiroki doing most of the modelling and Taku doing most of the experiments).

takahashi_et_alCompare the graph with the list of authors:

Hiroki Takahashi, Taku Oshima, Jon L. Hobman, Neil Doherty, Selina R. Clayton, Mudassar Iqbal, Philip J. Hill, Toru Tobe, Naotake Ogasawara, Shigehiko Kanaya, Dov J. Stekel.
I think the graph is far more informative. It is immediately clear that there are two main activities in experiments and modelling. It is clear that the BBSRC/JST is the central grant, while there is a contribution from the other BBSRC grant. Jon Hobman’s centrality to the research is also much clearer from the graphical view than appears from his position as third author on the list.
I’d appreciate some feedback and ideas.


The demise of May Fest: has the measurable defeated the important?

For the past 7 years, the University of Nottingham has run a fabulous event called May Fest. May Fest was the University’s main community engagement activity. Hundreds of staff and students ran interactive activities, events and stands, aimed at people of all ages. Thousands of people would attend – mainly families, and others too. The highlights for our own family have been the amazing engineering room with interactive dam-building, the bucky balls in the chemistry stand, and the opportunity for our girls to see real women scientists talking excitedly about science.

For the last two years I was involved in our own stands: two years ago I arranged for a glow-in-the-dark bacteria activity, with children entering a black out tent to see them. And last year an antimicrobial resistance in slurry activity: read about it here. Both events went down really well.

This year, sadly, there is no May Fest.

I do not know why this decision was made, and I very much hope that it will run in 2017. My hypothesis: in a society and sector obsessed with the measurable, important and exciting activities, such as May Fest, that do not meet measurable outcomes, are devalued and potentially lost.

I am led to this hypothesis is what I hear about REF and Workload Planning. In the last REF, one of our departments received a clean sweep of 4* Impact Case Studies. It turns out that as part of their (highly succesful) process, a potential impact case study that focussed on a May Fest activity was excluded as not submissible: despite considerable public engagement, there was no clearly measurable ‘impact’ as defined by REF. The implication was clear: if contributing to May Fest does not count as potentially REF-able activity, why would individual academics or heads of schools support such contribution? But surely there must be some latitute to do important and exciting activities that are not REF-able?

Enter Workload Planning. Friends at many British universities have told me about the workload planning models (WLPs) that have been brought in.The problem is, of course, that only some activities count towards it, and how they count is usually impossible to capture in any fair way. The result? Academic staff start only doing activities that count and stop doing activities that don’t count. I have now experienced several occasions where people have said “I’m not doing that: it’s not on the WLP model”. Is contributing to May Fest on the WLP model? Of course not – and it shouldn’t be – staff should not be pressurized into giving up their Saturdays for university activity.

So what happens? May Fest does not fit into any measurement model. Because you cannot really measure the delight of a small child as they fish a cuddly fluorescent green bacterium out of a ball pit “slurry tank”. In our measurement-obsessessed management models, academic staff and middle management are disincentivised from supporting May Fest. The activities are devalued. Perhaps this is why it was cancelled.

I very much hope that May Fest will run in 2017. It showcases the best of the University of Nottingham: the intelligence, ingenuity, energy and passion of its staff and students, which is shared freely and willingly with the wider community in Nottingham and beyond.