New publication: Human dissemination of genes and microorganisms in Earth’s Critical Zone

Delighted that our second review on AMR in the environment is now available on Global Change Biology. This is as much longer article than the piece we wrote for Science. It was nice to have the opportunity to express my opinions about the challenges of modelling in AMR: complexities associated with the wide range of actors; wide range of temporal and spatial scales; and the challenge of calibrating models against empirical data.

Citation and abstract are:

Zhu Y-G, Gillings M, Simonet P, Stekel DJ, Banwart S and Penuelas J. 2018. Human dissemination of genes and microorganisms in Earth’s Critical Zone. Global Change Biology: doi:10.1111/gcb.14003.

Abstract

Earth’s Critical Zone sustains terrestrial life and consists of the thin planetary sur- face layer between unaltered rock and the atmospheric boundary. Within this zone, flows of energy and materials are mediated by physical processes and by the actions of diverse organisms. Human activities significantly influence these physical and bio- logical processes, affecting the atmosphere, shallow lithosphere, hydrosphere, and biosphere. The role of organisms includes an additional class of biogeochemical cycling, this being the flow and transformation of genetic information. This is partic- ularly the case for the microorganisms that govern carbon and nitrogen cycling. These biological processes are mediated by the expression of functional genes and their translation into enzymes that catalyze geochemical reactions. Understanding human effects on microbial activity, fitness and distribution is an important compo- nent of Critical Zone science, but is highly challenging to investigate across the enormous physical scales of impact ranging from individual organisms to the planet. One arena where this might be tractable is by studying the dynamics and dissemina- tion of genes for antibiotic resistance and the organisms that carry such genes. Here we explore the transport and transformation of microbial genes and cells through Earth’s Critical Zone. We do so by examining the origins and rise of antibiotic resis- tance genes, their subsequent dissemination, and the ongoing colonization of diverse ecosystems by resistant organisms.

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MRF National PhD Programme in Antimicrobial Resistance – projects at Nottingham

The Medical Research FoundationMedical Research Foundation has funded a national PhD training programme in antimicrobial resistance. With £2.85M of funding, this will support 18 four year PhD scholarships (full fees and enhanced stipend) in 15 different institutions. Applications are now open with deadline 31st January and applicants have a choice of 54 projects.

The University of Nottingham will host one PhD student; applications are being taken for three projects, and the best student will get the scholarship. Our projects (for full details please follow the links) are:

The different projects will welcome applicants from a range of backgrounds, including microbiology, biotechnology, economics or maths. Please apply using the University of Nottingham postgraduate application page, stating the project, supervisor, and that you are applying for the MRF scholarship.

 

 

Medical Research Foundation funds £2.8M PhD programme in antimicrobial resistance

The Medical Research Foundation has announced a £2.8M PhD programme in antimicrobial resistance. Led by Matthew Avison at Bristol, this will bring 18 fully funded PhD students to support ongoing AMR projects. One of the students will be at Nottingham in association with the EVAL-FARMS project. We will be advertising three projects as part of the programme; these will be led by team members who don’t have any direct resource from the existing EVAL-FARMS funding – and are likely to be in the areas of phage-mediated spread of resistance, use of anaerobic digestion to mitigate resistance, and farm systems economic models to identify factors to best mitigate the impact of agri-AMR on human health.

Nottingham has also posted a Blog on the funding and I reproduce the text below:

New funding for Antimicrobial Resistance research

Research into new ways to tackle antimicrobial resistance has been given a boost as the University of Nottingham is one of the universities set to benefit from a £2.85m investment from the Medical Research Foundation.

New scientists will explore ways to tackle antimicrobial resistance through a new PhD training programme by the Medical Research Foundation, the charitable foundation of the Medical Research Council (MRC).

Fully funded

The first intake of the Antimicrobial Resistance PhD Training Programme will fully fund 18 students for four years, and the University of Nottingham is one of the 16 participating universities across the UK.

Dr Dov Stekel is leading the University of Nottingham programme and will be looking to recruit students later this year ready to start in 2018. Dr Stekel says: “This funding allows us to broaden our research with a PhD student working with team members who have not yet had access to resources from our other antimicrobial resistance research grants. Antimicrobial Resistance is a major global challenge and it will be very exciting to see the type of projects that are put forward and how they will help us progress our understanding of this problem.”

Antibiotics transformed healthcare in the 20th Century and are considered one of the greatest medical achievements of the era. Today, we still rely on antibiotics to treat everything from minor cuts to life-threatening bacterial infections, and to prevent infection after surgery. These drugs have drastically improved our quality of life and increased our lifespan.

Global threat

In the 21st Century, antibiotic overuse and misuse has led to antibiotics rapidly becoming ineffective. Antimicrobial resistance, specifically antibiotic resistance, now poses a global threat to human life. We need urgent action to halt resistance and to speed up new treatments for bacterial infection. The Medical Research Foundations PhD Training Programme in AMR has been designed in response.

Working with the MRC, the Medical Research Foundation spotted a gap in funding for PhD studentships in this field of research – currently there are few emerging researchers trained in the multidisciplinary approach required to tackle the antimicrobial resistance problem. The programme is designed to help build a strong, active network of new researchers to approach this global challenge in innovative ways.

The Medical Research Foundation’s Chair, Professor Nicholas Lemoine, said: “The Medical Research Foundation is delighted to be funding the UK’s only national PhD Training Programme in antimicrobial resistance research.  We believe this will help to strengthen the UK’s research capacity to respond to the global health challenge of antimicrobial resistance, including antibiotic resistance and drug-resistant infections.”

The Medical Research Foundation is continuing to seek funds from its supporters and other sources to fund two further cohorts of PhD students in antimicrobial resistance in the future.

 

Sankalp Arya will be speaking at EDAR 4

Sankalp is on a roll! More good news. His Abstract to the 4th International Symposium on the Environmental Dimension of Antibiotic Resistance has been accepted as an oral presentation. He’ll be giving a talk with title “Comparison of Different Modelling Approaches for Plasmid Transfer Dynamics” during Session 7 on Thursday 17th August. We have some interesting phage model results too so it is possible he may talk about both plasmid and phage mediated transfer.

When we submitted the abstract there was a “modelling” stream to submit to (which we dutifully did) – interestingly there is no modelling stream at the conference. There appear to be some bioinformatics talks, but it looks like Sankalp’s will be the only modelling talk. I am a bit surprised by this – there is a very clear need for models to be able to quantify spread of AMR, and make predictions about interventions. Perhaps on the other hand this is an opportunity for collaborations – we do modelling!

Congratulations again to Sankalp Arya

Congratulations again to Sankalp Arya for obtaining another scholarship. He has received a Travel Award to present his work at the 4th International Symposium on the Environmental Dimension of Antibiotic Resistance (EDAR4). EDAR3 was fantastic – and EDAR4 will no doubt be much more widely attended. This is going to be a great opportunity for Sankalp to present his work (we are not yet sure whether this will be oral or poster) and hear from the best in the field.

 

Now recruiting: Research Associate/Fellow in Antimicrobial Resistance Modelling

We are now recruiting the mathematical modelling post-doc for the EVAL-FARMS project. This post will work with me, Theo Kypraios in Maths, and the EVAL-FARMS team more generally, developing mathematical models for risk of emergence of AMR pathogens in agricultural waste, using all the exciting data that are being generated by the empirical researchers on the grant. Details of the advert, as well as links to it, are:

Research Associate/Fellow in Antimicrobial Resistance Modelling

Agricultural & Environmental Sciences

Location:  Sutton Bonington
Salary:  £26,052 to £38,183 per annum, depending on skills and experience (minimum £29301 with relevant PhD). Salary progression beyond this scale is subject to performance
Closing Date:  Wednesday 28 June 2017
Reference:  SCI158617

We are seeking an excellent researcher in modelling of antimicrobial resistance. The successful applicant will use mathematical and statistical models to make predictions on risk of emergence of antimicrobial resistant pathogens in a farm slurry system and slurry amended soil. The post is funded by NERC-led EVAL-FARMS project (Evaluating the Threat of Antimicrobial Resistance in Agricultural Manures and Slurries). Thus the role holder will work closely with an interdisciplinary team, including experimental researchers in microbiology and analytical chemistry, and social researchers in science and technology studies, in order to develop meaningful, data driven risk models that could inform policy and practise. The work will involve deterministic and stochastic models, Bayesian statistics, data analysis and presentation.

Applicants must have, or be very close to completing, a PhD in mathematical, computer or statistical models applied to a relevant area in the biological or environmental sciences. Research experience in applying such models in antimicrobial resistance, metagenomics, analytical chemistry and/or water quality would be desirable. Applicants must be able to demonstrate skills in Bayesian approaches, including relevant computational techniques such as MCMC, development and analysis of deterministic and stochastic models, programming in a relevant language (e.g. R, Python or Matlab) and a broader appreciation of science. Applicants must also be able to demonstrate research ambition through timely publication of research, coupled with commitment to the research project as part of their on-going career development. Excellent oral and written English language skills are essential.

The post is a joint appointment between the Schools of Biosciences and Mathematical Sciences. The post holder will normally work on the Sutton Bonington Campus, and will also have meetings on the University Park Campus with staff in the School of Mathematics and other collaborating schools.

Fixed term for 2 years from 1st September 2017

Applications can be made through the University of Nottingham web site. I am happy to receive informal enquiries.