Congratulations to Sankalp Arya: International Research Collaboration Award

Congratulations to Sankalp who has received a £2300 International Research Collaboration Award from the University of Nottingham. Sankalp will spend two months (September and October) in Barth Smets’s laboratory at the Technical University of Denmark. This is a really fantastic opportunity for Sankalp to work in one of the leading environmental microbiology groups in the world. His work will focus on developing the iDynomics platform for individual based modelling of microbial interactions to model antimicrobial resistance. Well done Sankalp! And I look forward to visiting Barth’s lab too as part of the project.

 

Alan Perelson’s 70th Birthday Conference: Viral Dynamics: Past, Present and Future

Sankalp and I have just returned from a weekend trip to Santa Fe for the Viral Dynamics conference in honour of Alan Perelson’s 70th birthday.

The conference itself was very high quality – excellent talks throughout from some extremely eminent people in virus research. I particularly appreciated David Ho’s opening talk and Alan Perelson’s closing keynote; David’s talk on HIV dynamics reminding me just how good Alan and Avidan Neumann’s modelling contribution was: it wasn’t about developing big complex models, or doing very fancy mathematics; it was about doing the right simple model to make the most use of the data. Alan’s talk focussed on his earlier work in theoretical immunology – very many interesting examples showing how much you can learn by thinking in mathematical/computational ways.

The best part of the conference was meeting up with people – whether old friends from the short time I spent in LANL (Alan, Jack) and my PhD days (Ruy, Sebastian) – or brilliant people I hadn’t met before with whom I had some very stimulating conversations.

What was also evident was the warmth felt by so many people towards Alan. I only spent 3 months in the lab in 1994 – in between my degree and PhD – and went back for another month in the summer of 1995 – and yet when Ruy Ribeiro sent the invitation I immediately felt that this was a meeting I couldn’t miss. Many people there had collaborated with Alan for many years. And while Alan’s contribution to science is enormous, the plaque that the organizers made for him was for friendship, collaboration and mentorship, with a network graph of his collaborative research outputs. In this, Alan is a positive example for us all.

We went with a poster:

poster

which was Sankalp’s first conference poster presentation! I thought that this would be a good opportunity for him; although Sankalp’s model is about bacteriophage in the context of AMR, while the conference focussed on human disease viruses, the conference attendees mainly worked in mathematical models of virus dynamics. This meant that Sankalp was among people who understood what he was doing and why he was doing it, speaking the same language. Sankalp was busy – he had people speaking with him for the full 2 hours of the poster session – and we received many interesting ideas and suggestions from these conversations.

Nearly new publication: Metal Resistance and Its Association With Antibiotic Resistance. Advances in Microbial Physiology

Last month the review that Sankalp and I contributed to was published on line by Advances in Microbial Physiology. This review was led by Jon Hobman, with considerable writing by Chandan Pal. It is a real honour to have co-authored with the amazing Joakim Larsson. My own contribution was small: Sankalp contributed some review material on modelling, and I got stuck in with Joakim and Jon in the editing phase to ensure we had a coherent story. Overall, this is a very nice and timely review, and we have had a lot of interest in it already. Citation and abstract:

Pal C, Asiani K, Arya S, Rensing C, Stekel DJ, Larsson DGJ and Hobman JL 2017. Metal Resistance and Its Association With Antibiotic Resistance. Advances in Microbial Physiology. DOI: https://doi.org/10.1016/bs.ampbs.2017.02.001.

Abstract

Antibiotic resistance is recognised as a major global threat to public health by the World Health Organization. Currently, several hundred thousand deaths yearly can be attributed to infections with antibiotic-resistant bacteria. The major driver for the development of antibiotic resistance is considered to be the use, misuse and overuse of antibiotics in humans and animals. Nonantibiotic compounds, such as antibacterial biocides and metals, may also contribute to the promotion of antibiotic resistance through co-selection. This may occur when resistance genes to both antibiotics and metals/biocides are co-located together in the same cell (co-resistance), or a single resistance mechanism (e.g. an efflux pump) confers resistance to both antibiotics and biocides/metals (cross-resistance), leading to co-selection of bacterial strains, or mobile genetic elements that they carry. Here, we review antimicrobial metal resistance in the context of the antibiotic resistance problem, discuss co-selection, and highlight critical knowledge gaps in our understanding.

Congratulations to Hannah Williams and Laurence Shaw

Congratulations to both Hannah Williams and Laurence Shaw who have both now left the lab (after short positions) to new roles. Hannah is now working at Public Health England as a mathematical modeller. Laurence is now working for Nottingham Trent University as a lecturer in statistics. Wishing both Hannah and Laurence all the best in what I am sure will be fabulous careers. Both are on fixed term contracts so if you are reading this and looking to recruit an excellent mathematician/statistician then both Hannah and Laurence have my highest recommendation!

On AMR Panel with Lord Jim O’Neill at University of Nottingham Chancellor’s Lecture

Last night I had the enormous privilege of being on a panel following Lord Jim O’Neill’s lecture on AMR as part of the University of Nottingham’s Chancellor’s Lecture series.

oneillpanel

It was a real coup for the university to have Jim O’Neill speak. It was a great event – well attended by alumni and many other’s. The lecture was brilliant: O’Neill is a very engaging speaker and spoke with confidence and passion on the findings of his report. He mainly focussed on the ten point plan:

 

10-point-plan_white

It was especially interesting seeing AMR from the perspective of an economist: not just in quantifying the problem in monetary terms (his argument that $40B spend will save $100T costs is compelling) but also how he breaks down the solutions into ‘supply’ and ‘demand’ side solutions and especially his emphasis on the importance of reducing demand for antibiotics through 6 of his points. (I’m not sure where our emphasis on waste management fits into that – but that is another matter – and actually having an economist (Steve Ramsden) on our project also helps framing it).

Professor Liz Sockett kindly asked me to serve on the panel (along side Dr Mat Diggle from EmPath) – this was a new experience for me – I was a little nervous – but the questions were good and interesting. The first couple of questions were more clinically focussed and answered by Liz and Mat. A question came up about how we prevent rapid spread of resistance to any new antibiotics we might discover. Mat gave a good answer from a clinical perspective, and I was able to add that there would need to be very wise use (if at all) of any new clinically important antibiotics in veterinary use. (To be fair, that point is  made in the O’Neill report anyway!) And then got a question direct to me about agricultural waste  management practises in developing countries. This was a nice one – as I have recently visited China and then had visitors from South Africa. So I was able to speak about the challenges of AMR from pig farming in China – the Chinese government are very committed to environmental research and China has a very well-funded research programme; South Africa is also very interesting because there is a mix of modern farming where the challenge of reducing antibiotic use is similar to in the UK, and then traditional subsistence farming, where nutrition is the biggest challenge, and the antibiotic challenge is more about access to antibiotics rather than use reduction.

After the talk, many interesting people came to speak with me, which was really nice, while Professor Christine Dodd looked after our stand and she also received many questions.

Official photographs will follow. The photograph at the top is thanks to Adam Roberts (from his twitter feed).

 

 

 

 

Job Opportunity – Research Technician for EVAL-FARMS project

We are advertising for the second research technician post for the EVAL-FARMS project. The post-holder will be responsible for sampling from the slurry tank, with a particular focus on measuring water quality and preparation of samples for pharmaceutical analysis. The post-holder will work very closely with other team members.

Research Technician

Reference
SCI307616X1
Closing Date
Monday, 6th February 2017
Job Type
Technical Services
Department
School of Biosciences – Technical Services
Salary
£22494 to £26829 per annum, depending on skills and experience. Salary progression beyond this scale is subject to performance

Applications are invited for the above full-time post based within the School of Biosciences at the Sutton Bonington Campus.

The post is to provide technical support on a NERC funded research project “Evaluating the Threat of Antimicrobial Resistance in Agricultural Manures and Slurries”.

The role holder will assist with the collection of wastewater slurry and soil samples & sample processing for water quality parameters and sample preparation/wet chemistry ready for LC-MS and ICP/AAS analysis. The role will require working off-site.

Duties will include:

  • Processing samples for water quality indicators (e.g. DO, TSS, COD, TOC) including spectrophotometer use.
  • Sample preparation of environmental samples for antibiotic drugs and metals suitable for LC-MS and ICP/AAS analysis.
  • Ensuring stocks & equipment in own areas of responsibility are maintained & available for use.
  • Maintaining a safe working environment in accordance with statutory & University Health & Safety procedures.

Full details can be found in the job description.

Candidates must have a HNC in a relevant subject or equivalent qualifications plus considerable relevant technical/scientific experience OR substantial work experience in a relevant technical or scientific role.

Candidates should have proven technical and/or experimental expertise in techniques for characterising environmental samples for water quality parameters e.g. DO, TSS, TDS, COD, TOC etc.

This full-time post is available as soon as possible on a fixed-term contract for a period of 15 months.

Informal enquiries may be addressed to: Dov Stekel tel: 0115 9516294 Or email dov.stekel@nottingham.ac.uk. Please note that applications sent directly to this email address will not be accepted.

The University of Nottingham is an equal opportunities employer and welcomes applications from all sections of the community.

Visualizing complex data in geographical space using PCA colouring

I have recently had some very interesting dicussions with scientists in China about visualizing complex AMR data (e.g. patterns of gene abundance or bacterial taxa) in geographical space to show if data from nearby locations are similar or different from each other. Our collaborators had already shown that PCA was successful at separating the data, so the idea I had was to use the PCA scores to colour points which could then be plotted on a map at the locations from which the data were derived. Nearby points with similar data should then have similar colours, while nearby points with different data should have different colours.

To test the idea, I used a built in data set in R (state.x77 in the datasets package). This has demographic data about states in the USA, as well as longitude/latitude coordinates for the centres of the states. In the analysis I have:

1. Run a PCA on the demographic data
2. Normalized the first three PCA scores to be between 0 and 1 (since this is what the rgb() function in R requires to define colours)
3. Used a simple map library to plot a map of the USA including state boundaries
4. Plotted the points into the centres of the states using the rgb() defined colours

What you can see in the map (below) is that generally nearby states are similar to each other in that they have similar colours – but there are some exceptions where the colours are very different.

statemap

The code is:

require(maps) # Simple R interface for maps
require(datasets) # Contains some example data

# This function converts a range into the range [0,1) which we need for the rgb colour map
normalize = function(x,eps=1e-3) { # eps is a small number to ensure the outputs are all <1 as rgb doesn't like values of 1
    xnorm = as.numeric((x-min(x))/(max(x)-min(x)+eps))
    return(xnorm)
}

spc = princomp(state.x77[,3:6]) # this is some demographic data about states in the USA - it is just an example
sred = normalize(spc[[6]][,1])
sgreen = normalize(spc[[6]][,3]) # this order, i.e. using blue on the 2nd PC, is to help red-green colour blind people
sblue = normalize(spc[[6]][,2])

map('usa') # draws a simple map of USA
map('state',add=T) # adds state boundaries
points(state.center$x,state.center$y,pch=19,col=rgb(red=sred,green=sgreen,blue=sblue)) # puts coloured points into the centre of each state. An alternative could be to fill the states