Research Associate - School of Biosciences - 97294 - Grade 6

Research Associate in Mathematical Modelling of Antimicrobial Resistance

School of Biosciences

Location: University of Birmingham, Edgbaston, Birmingham UK

Full time starting salary is normally in the range £27,511 to £30,046, with potential progression once in post to £33,797.

Grade 6

Full Time/FTC for 27 months

Closing date: 17th May 2021

This is an exciting opportunity for a 27-month post funded by the UK-India NERC project AMRflows: antimicrobials and resistance from manufacturing flows to people: Joined up experiments, mathematical modelling and risk analysis.

See amrflows.org for more details.

AMRflows will combine field sampling, mesocosm and laboratory studies, and mathematical modelling to quantify resistance gene and plasmid transfer dynamics in antimicrobial resistance (AMR) bacteria in Indian rivers receiving wastes from pharmaceutical facilities. The project's goal is to perform quantitative risk analysis to develop optimal intervention strategies.

The main duty of the post holder will be to undertake and coordinate mathematical modelling as part of AMRflows.

The post-holder will help develop, analyse and calibrate a model of AMR dynamics in river environments. This will include competition between sensitive and resistant bacteria, their growth by nutrient consumption, the transfer of resistance plasmids and degradation of antibiotics. The post-holder will interface this small-scale model with large-scale hydrological models of water flow that are being developed by other team members. Together, this will predict fate and transport of AMR in Indian river environments. The post-holder will therefore have a central role in coordinating the mathematical modelling effort of the project, in partnership with the lead PI of the project who is an AMR modeller (Jan Kreft) and a hydrologist as co-supervisor (Josh Larsen).

AMRflows includes 12 co-investigators from 3 institutions in the UK and 3 in India, therefore evident ability to collaborate and learn across social contexts and other disciplines is essential. Frequent communication with other team members will be an important part of the endeavour.

Role Summary

• Work within a large international team to accomplish the tasks set out in the AMRflows project
• Develop mathematical models and statistical methods to advance our understanding of AMR dynamics
• Analyse and interpret research findings and results
• Communicate results effectively with supervisors and the wider team
• Ensure that other team members supply the required information to understand the data including reliability of the data
• Lead and contribute to timely publication of the results
• Engage with stakeholders
• Contribute to public understanding of AMR

Main Duties

• Modelling work as appropriate on the project:
o Development of deterministic and stochastic differential equation and individual-based models for spread of antimicrobial resistance under selective pressure and varied environmental conditions
o Calibration of models by fitting to data derived from a variety of sources such as measurements of water quality, antibiotic and metal concentrations, bacterial counts, qPCR and metagenomics, resistance phenotypes etc.
o Model simulations using appropriate computer software, e.g. Matlab, R, Python, Java
o Interpretation and visualization of model results
• Support the Bayesian Belief Network based quantitative risk analysis conducted by other team members by ensuring modelling outcomes can feed into the Bayesian Network
• Supervision of related project students and staff:
o To provide technical support on methodologies and advice for UG and PG-students and staff working on the project
• Communication of results and coordination of work within our research team:
o Consulting with team members and training them as required
o Making sure that the work of other team members is understandable
o Preparation of reports, tutorials etc
o Presentations in group meetings
o Contribute to writing research grant proposals
• Communication of results beyond the research team:
o Writing papers for publication in top international journals
o Presenting work at conferences
o Engage with stakeholders
o Contribute to public outreach
• Deal with problems that may affect the achievement of research objectives and deadlines
• Carry out administrative tasks related directly to the delivery of the research
• Promote equality and diversity, acting as a role model and fostering an inclusive working culture

Person Specification

Essential requirements:

o BSc (hons) or equivalent degree in a relevant mathematical, physical, engineering or biological subject

o PhD in mathematical, computational or statistical modelling applied to a relevant scientific area in the biological or environmental sciences, or near completion or equivalent proven knowledge, skills and experience

o Experience in development and analysis of differential equation models (deterministic or stochastic)

o Experience or training in statistical approaches applied to relevant scientific data, including Bayesian statistics and relevant computational methods, e.g. MCMC

o Programming skills in relevant languages, e.g. C/C++/Java, Matlab, R, Python

o Proven track record of research ambition as evidenced by timely publication of research, coupled with a commitment to the research in this project as part of on-going career development

o Ability to design, execute and write up work independently and to troubleshoot failed modelling approaches

o Evidence of the ability to prioritise and balance a range of activities

o Ability to work and communicate effectively with supervisors and team members across a wide range of disciplines

o Willingness to travel to India to work with other team members, as needed

o Good planning, organisational, data curation and time management skills

o An understanding of the issues of confidentiality and to conduct themselves in a manner that protects any confidential information in their possession

Desired requirements:

o Broad appreciation of wider relevant disciplines, including microbiology, environmental sciences and chemistry

o Excellent oral and written English language skills

o Willingness to communicate

o Excellent interpersonal skills to build trust with collaborating groups

o Research experience with agent-based models

o Understanding or experience with hydrodynamics, hydrology or hydraulics

o Research experience of modelling or data analysis in antimicrobial resistance

o Research experience in bioinformatics applied to genomics or metagenomics

o Research experience or knowledge in chemistry, analytical chemistry or water quality analysis

o Development or use of risk models to inform policy or practice

o Demonstrable success working with stakeholders on politically sensitive or emotive subjects

o Demonstrable success managing own contribution to complex research projects

Informal enquiries please contact j.kreft@bham.ac.uk

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