AMRflows UK-India project: antimicrobials and resistance from manufacturing flows to people: joined up experiments, mathematical modelling and risk analysis
Author:Jan Kreft
Jan-Ulrich Kreft's brief research interests and biography
I am a microbiologist turned mathematical modeller. My research interests revolve around the interactions between microorganisms with each other, the environment and host organisms. I believe we need to use mathematical modelling to make quantitative predictions that can be challenged by data so we can test our understanding of nature. For example, I have applied mathematical modelling to understand the dynamics of resistance plasmids in the environment where spatial structure and a diversity of microbes are prevalent yet disregarded in laboratory experiments. Recently, I started modelling activated sludge to look at AMR dynamics in sewage treatment.
I studied biology at the Universities of Konstanz and Tübingen in Germany, then did my PhD with Professor Bernhard Schink at Konstanz, looking at the biochemistry of anaerobic degradation of plant compounds in the then newly discovered, weird anaerobe we later named Holophaga foetida. After this, I decided to go into mathematical modelling to be able to address fundamental questions. I obtained a DFG fellowship and went to Professor Julian Wimpenny at Cardiff University, where I started individual-based modelling of microbes. I then joined the Theoretical Biology group at the University of Bonn in Germany as a “Wissenschaftlicher Assistent”, where I broadened my research topics and mathematical methods. I joined the University of Birmingham in 2007 as a Lecturer in Computational Biology (Assistant Professor), now Senior Lecturer (Associate Professor) and took this opportunity to start my own wet lab to be better able to test and parameterize my mathematical models.
The second poster will be presenting the EMBRACE-WATERS reporting standards that a team of experts led by our collaborator Mical Paul in Haifa, Israel have published:
Hassoun-Kheir N, Stabholz Y, Kreft J-U, de la Cruz R, Dechesne A, Smets BF, Romalde JL, Lema A, Balboa S, García-Riestra C, Torres-Sangiao E, Neuberger A, Graham D, Quintela-Baluja M, Stekel DJ, Graham J, Pruden A, Nesme J, Sørensen SJ, Hough R, Paul M (2021). EMBRACE-WATERS statement: Recommendations for reporting of studies on antimicrobial resistance in wastewater and related aquatic environments. One Health13: 100339 https://doi.org/10.1016/j.onehlt.2021.100339
This poster will be presented by AMRFlows team member Cansu Uluseker, here the pdf:
The third poster reports on work at a Dairy farm near Nottingham, UK, by a large team in the EVAL-FARMS project led by Dov Stekel, which has just been published
Baker M, Williams AD, Hooton SPT, Helliwell R, King E, Dodsworth T, Baena-Nogueras RM, Warry A, Ortori CA, Todman H, Gray-Hammerton CJ, Pritchard ACW, Iles E, Cook R, Emes RD, Jones MA, Kypraios T, West H, Barrett DA, Ramsden SJ, Gomes RL, Hudson C, Millard AD, Raman S, Morris C, Dodd CER, Kreft J-U, Hobman JL, Stekel DJ (2022). Antimicrobial resistance in dairy slurry tanks: a critical point for measurement and control. Environment International 169: 107516 https://doi.org/10.1016/j.envint.2022.107516
This will be presented by Jan Kreft, here the pdf:
Research Associate “Mathematical modelling of Antimicrobial Resistance dynamics in rivers in India”
We are looking for a mathematical modeller with an interest in the dynamics of Antimicrobial Resistance (AMR) in the environment, especially rivers polluted with waste from antibiotic production and sewage yet used by people.
This position will be central to a larger UK-India project, so enthusiasm to work closely with other modellers and experimentalists will be vital.
Our project “AMRflows: antimicrobials and resistance from manufacturing flows to people: joined up experiments, mathematical modelling and risk analysis” uniquely combines field sampling, mesocosm and laboratory studies with mathematical modelling of the population dynamics of sensitive versus resistant bacteria, plasmid transfer and selection by antibiotics and metals and mathematical modelling of water transport through the environment. This will lead to a quantitative risk analysis and identification of feasible and effective intervention strategies.
Strong experience with differential equation models will be essential. Experience with agent-based modelling and computer programming will be desirable, as is experience with population dynamics.
The workflow of AMRflows
You will be based at the University of Birmingham, UK and supervised by Jan-Ulrich Kreft (School of Biosciences & Institute of Microbiology and Infection & Centre for Computational Biology) in partnership with Josh Larsen (School of Geography, Earth and Environmental Sciences, GEES). We hope it will soon be possible for the post holder to travel to our collaborators in India and stay there for several weeks.
If you want to make a difference to the AMR crisis and are keen to support other team members to achieve our aim of establishing the first predictive model of AMR selection and transport through the environment, please apply.
We will offer you the chance to excel as part of an international and interdisciplinary team, to develop your research skills and to educate your collaborators about your expertise and to communicate your results to scientific and lay audiences.
Although our web page is only a few days old and not quite there yet, I am posting our first blog because we are in the process of hiring staff for our project.
Currently open posts:
1. Postdoc position (Research Associate in Microbial Genetics within Water Systems) at Newcastle University…
You will develop novel microbial genetic approaches for detecting mobile genetic element (MGEs) in natural and engineered ecosystems using conventional culture methods, a range of advanced molecular techniques, and flow cytometry. The work will tag plasmids and donor bacteria to quantify AMR gene transfer and frequency under nutritional conditions relevant to Indian rivers. You will provide data to parameterise micro- and macro-scale numerical models developed by others within the project.
2. Technical Assistant at Indian Institute of Technology Hyderabad…
You will be detecting and measuring the concentrations of various antibiotics in environmental samples from Hyderabad and Chennai. Experience in analytical techniques such as LC-MS-MS, ICP MS and GC MS are desirable.
There will be more positions coming up such as a mathematical modeller at the University of Birmingham and a hydrologist at the Indian Institute of Technology Gandhinagar.
General description of the project and who we are looking for:
We are hiring postdoctoral and doctoral researchers in the UK and India to work together to tackle Antimicrobial Resistance (AMR) in the environment.
Our project “AMRflows: antimicrobials and resistance from manufacturing flows to people: joined up experiments, mathematical modelling and risk analysis” uniquely combines field sampling, mesocosm and laboratory studies with mathematical modelling of the population dynamics of sensitive versus resistant bacteria, plasmid transfer and selection by antibiotics and metals and mathematical modelling of water transport through the environment. This will lead to a quantitative risk analysis and identification of feasible and effective intervention strategies.
The Musi river carries a mixture of antibiotics, some of which at clinical concentrations.
The study sites are two river networks in South India, the Musi river near Hyderabad and the Adyar river near Chennai. The Musi area is heavily polluted by drug manufacturers whereas the Adyar area is our ‘control’. Both receive treated and untreated sewage. This creates a ‘perfect storm’ where antibiotics and other pharmaceuticals and metals select for bacteria with resistance under conditions of high concentrations of nutrients and mobile genetic elements from sewage.
The Adyar during the Chennai floods in 2015: spreading AMR onto land and into communities
Our team of 12 scientists is based at three institutions in India (Indian Institutes of Technology Hyderabad (IITH), Madras (IITM) and Gandhinagar (IITGn) and three institutions in the UK (University of Birmingham, Newcastle University and The James Hutton Institute in Aberdeen and Dundee).
We are microbiologists, environmental engineers, hydrologists and modellers.
We are seeking researchers who want to make a difference to the AMR crisis and are keen to support other team members to achieve our aim of establishing the first predictive model of AMR selection and transport through the environment.
Willingness to collaborate and learn about the other fields of science combined with strong competence in your own field of work are essential.
We offer the chance to excel as part of an international and interdisciplinary team, to develop your research skills and to educate your collaborators about your expertise and to communicate your results to scientific and lay audiences.
We value independence, creativity and critical thinking.
Finally, you will be careful to avoid the risk of COVID-19 infection yet undeterred by the pandemic.
Team: Jan-Ulrich Kreft (UK Lead, UoB), Joshua Larsen (UoB), Willem Van Schaik (UoB), David W Graham (NU), Rupert Hough (JHI), Shashidhar Thatikonda (India Lead, IITH), Aravind Kumar Rengan (IITH), Soumendra Nath Kuiry (IITM), Balaji Narasimhan (IITM), Indumathi M Nambi (IITM), Pranab Kumar Mohapatra (IITGn), Vimal Mishra (IITGn).
