Monitoring the Global Spread of Antimicrobial Resistance.

Antimicrobial resistance (AMR) is increasingly being recognized as a cross-cutting threat to global health and it threatens to undermine decades of progress in treatment of infectious diseases [1,2]. AMR is a complex problem with multiple, interconnected drivers. A reliable base of evidence that accurately describes and characterizes the global burden and transmission of AMR is essential to address this challenge and will determine global and national priority setting, public health actions, and treatment decisions.

Current surveillance of AMR is mainly based on passive reporting of clinical diagnoses and phenotypic laboratory results for specific pathogens. This procedure leads to significant time-delays and a narrow pathogen spectrum not capturing all relevant AMR genes, where the bulk may be present in the commensal bacterial flora.

From a surveillance point of view, sewage is an attractive matrix because it combines material from a large and mostly healthy population, which would otherwise not be feasible to monitor. Utilizing metagenomic sequencing (high-throughput sequencing of all genetic material simultaneously) and quantifying all AMR genes will provide a much broader resolution than offered by current methodologies.

Microbial next generation sequencing (NGS) based diagnostics provide both cost-efficient sample analysis and rapid turnaround. Metagenomics benefit from the ability to quantify thousands of targets in a sample without requiring a priori knowledge of which genes are present, including additional features of interest, such as pathogens and virulence genes. Lately, an online method for identifying all known resistance genes was developed allowing to quantify AMR genes from sequencing data [3]. Such complex data have to be further analysed by statistical modelling and associated to explanatory epidemiological information, especially if collected from global sources, to provide meaningful data for interventions.

The overall objective of this project is to identify key factors explaining differences in composition of AMR genes across the world and test hypothesis on how AMR genes spread around the world.

A 3 year PhD position is available:

Epidemiological spread of resistance globally.
Supervisors: Prof. Mark Woolhouse & Dr Bram van Bunnik.
The aims of this project are:
• To identify epidemiological data that best predicts the occurrence of AMR genes across the world.
• To perform a spatial-temporal analysis on the distribution of AMR-genes around the world using the previously identified potential explanatory variables to inform potential surveillance systems.
• Develop a model for the prediction of the distribution of resistance genes in space and time.

The PhD project is in close collaboration with the Danish Technical University (DTU) and the successful candidate is expected to spend up to six months of the project at the DTU, where valuable knowledge of and insights into the sequencing of the samples will be gained.
The successful candidate will work in at the interface of epidemiology, evolutionary biology, statistics, and bio-informatics

The expected outcomes of the training programme are:
• Advanced mathematical and statistical model skills
• Quantitative genomics and genetics skills
• Handling of large volume of data (Big Data)


Requirements

The candidate needs to have a good undergraduate degree (equivalent to a 2.1 or above) in a relevant discipline and preferably a MSc degree (though this is not essential). A background on an epidemiological or bioinformatic related discipline and statistical/modelling skills are essential, hence the ideal candidate would be someone with such background wishing a career in epidemiology, public health, or bioinformatics related fields.

The candidate will also need to meet the requirements for the Global Health PhD programme described at:
http://www.ed.ac.uk/studying/postgraduate/degrees/index.php?r=site/view&id=698


Application procedure

Please provide a CV, a personal statement detailing your research interests and reasons for applying, degree certificate(s), marks for your degree(s) and 2 written academic references. All documents should be in electronic format and sent via e-mail to:
Bram van Bunnik ([Email Address Removed]) or
Kath Tracey ([Email Address Removed])

The closing date for applications is: Friday 27th of April 2018.

Following interview, the selected candidate will need to apply and be accepted for a place on the Usher Institute Global Health PhD programme. Details about the PhD programme can be found here: http://www.ed.ac.uk/studying/postgraduate/degrees/index.php?r=site/view&id=698