Five postdocs in epidemiology and surveillance of antimicrobial resistance and infectious diseases

DTU Fødevareinstituttet
mandag 30 apr 18

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Frist 25. maj 2018
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The National Food Institute (DTU Food) seeks five postdocs for vacant positions in:

  • Mathematical simulation and epidemiology within surveillance of pathogens and antimicrobial resistance in food-producing animals and food products.
  • Quantitative epidemiology and prediction of antimicrobial resistance in Danish pig production.
  • Global surveillance of antimicrobial resistance.
  • Global surveillance and predictive epidemiological modelling of drivers for infectious diseases including antimicrobial resistance.
  • Epidemiology, surveillance and risk assessment of antimicrobial resistance in food producing animals and food products.

The postdocs will all be affiliated with the Research Group for Genomic Epidemiology, which has the primary task of conducting targeted research with the aim of predicting and preventing infectious diseases in humans and animals, and supporting detection, surveillance and control. The research group is an EU reference laboratory for antimicrobial resistance and WHO collaborating centre for antimicrobial resistance in foodborne pathogens and genomics. The research combines expertise in conventional and molecular microbiology with statistical modelling, epidemiology and bioinformatics.

The Research Group for Genomic Epidemiology is together with several partners nationally and globally attempting to establish local and global surveillance of infectious diseases and AMR to a large extent based on metagenomic sequencing and to understand drivers for emergence, selection and transmission. For more information see: (www.genomicepidemiology.org, www.globalmicrobialidentifier.org, www.compare-europe.eu).

Funded by the Novo Nordisk Foundation, The European Union and the Danish Government, we now offer a number of postdoc positions in epidemiology as specified below.

Position 1 – Mathematical simulation (Håkan Vigre)
The group is involved in a EU a project named “Novel approaches for design and evaluation of cost-effective surveillance across the food chain” (NOVA), where we strive to develop new surveillance tools and methods and to harmonise and optimise the use of existing surveillance system data. The main focus of the postdoc is to develop mathematical models of occurrence of human hazards in the farm-to-fork chain and combine these with models simulating different sampling schedules and use of different laboratory methods.

Position 2 – Quantitative epidemiology of AMR in Danish pigs (Håkan Vigre)
Funded by the Danish Government, we strive to develop mathematical models for predicting the change in AMR when the AMU in the pig production is altered. The project includes large observational studies performed in pig farms and use of metagenomics for measuring AMR, utilisation of national databases of animal demography and AMU. There is a close connection to the authorities, and it is expected that the output from the project should be applied in the regulatory work of authorities.

Position 3 – Global surveillance of AMR (Frank Aarestrup)
Mainly funded by The Novo Nordisk Foundation, we are trying to establish global surveillance of AMR based on metagenomic sequencing of sewage. As part of this global endeavour, we are also conducting a number of longitudinal projects in different countries. There is a need for a dedicated and organized person with a strong international profile to organise and execute these country projects in collaboration with external and internal collaborators. The postdoc’s main responsibility will be to organize the country-specific sampling and generation of results and assist the international partners in how to conduct the analyses and sharing of data.

Position 4 – Epidemiology of global drivers (Tine Hald, Frank Aarestrup)
Also funded by the Novo Nordisk Foundation and aiming at global surveillance we are seeking a postdoc to work on identifying global, publicly available data which can be drivers or explanatory variables for the observed occurrence of AMR. Possible explanatory variables may for instance include climate, demographic, socioeconomic and health-related factors collected at the local, regional or national level and (publicly) available through various databases and registries. The postdoc’s main responsibility will be to analyse and interpret data from such external data sources and investigate how they correlate with each other and with the surveillance data collected from sewage from major cities around the world.

Position 5 – Epidemiology, surveillance and risk assessment (Tine Hald, Frank Aarestrup)
Partly funded by the EU and partly by Novo Nordisk Foundation, we are seeking a postdoc to compare different methods for measuring AMR for surveillance purposes and design an improved surveillance program, which results also enables assessing the risk for human health.

It is expected that the outcomes of all projects will have practical and cost-saving impacts on AMR and infectious disease surveillance and control.

Responsibilities and tasks
Position 1 – Mathematical simulation
  • Your main responsibility will be to develop models for simulation and evaluation of strategies for surveillance of human hazards in the food production.
  • You will accomplish this by coding mathematical models describing the occurrence of different human hazards in food production and overlay these models with models mimicking surveillance programs, taking into account both sampling schedules and performance of different laboratory methods such as culturing, whole genome and metagenome sequencing.
  • In addition to coding, efforts will be on parameterizing the models using data collected in existing surveillance programs and research projects.
Position 2 – Quantitative epidemiology of AMR in Danish Pigs
  • Your main responsibility will be to generate quantitative estimates for how changes in usage of different antimicrobials influence the occurrence of antimicrobial resistance genes in batches of pigs.
  • You will accomplish this by conducting observational studies in pig farms, where the occurrence of resistance (measured by metagenomics) is compared with the exposure to different antimicrobials at different rearing periods. The comparison will be performed using advanced biostatical methods.
  • The research must integrate knowledge about metagenomics, including both sampling handling and bioinformatic pipelines, as well as utilisation of data from large national databases.
Position 3 - Global surveillance of AMR
  • Your main responsibility will be to initiate and organize country-specific projects in relation to the global surveillance of AMR.
  • You will accomplish this by working together with multiple international partners and keep all of them on track.
  • You will help partners in analysing their sequencing data in combination with different national and global epidemiological variables.
Position 4 – Epidemiology of global drivers
  • Your main responsibility will be to identify macro-epidemiological factors that can contribute to explaining the occurrence, trends and emergence of infectious diseases and AMR.
  • You will accomplish this by analysing and interpreting data representing a range of possible explanatory/predictor variables using quantitative epidemiological methods (e.g., correlation analysis, PCA, MCA, time-series analysis, spatial analysis, multivariable regression and/or Bayesian modelling).
Position 5 – Epidemiology, surveillance and risk assessment
  • Your main responsibility will be to compare different methods for measuring AMR for surveillance purposes and design an improved surveillance program.
  • You will accomplish this by comparing the surveillance outcomes of applying various sampling schedules and performance of different laboratory methods such as culturing, whole genome and metagenome sequencing in mathematical models.
  • You will also be developing risk assessment models for assessing the human health impact associated with the usage of antimicrobials in the food-animal production. Efforts will be on parameterizing such models using surveillance data as measured above.
For all positions
  • You will communicate research results by presenting data at project meetings and international conferences, and write reports and manuscripts for publication.
  • You will engage in the general work carried out by the research group, including discussions and planning of strategies and projects, drafting research grant proposals, etc.
  • If your interest lies here and time allows, you will also supervise students and contribute to the group’s teaching activities.
  • The day-to-day work will be performed in close collaboration with other researchers in the Research Group for Genomic Epidemiology group and with national and international partners.
  • Collaboration includes active participation in national and international meetings and conferences, sharing of models and results and contribution to joint publications.

Qualifications
Candidates should have a PhD degree or equivalent.

The ideal candidate:
  • Holds a PhD degree within one of the following areas: human or veterinary quantitative epidemiology, mathematical modelling, biostatistics, population dynamics, or eco-epidemiology.
  • Is able to work independently and able to plan and carry out complex tasks, while also having the ability to engage constructively and positively in a large, international and cross-disciplinary research group.
  • Has good English communication skills, oral and written.
  • Is ambitious and has a strong drive for obtaining high-quality results.

Specifically for the individual positions:

Position 1
  • Has documented experience with mathematical simulation methods, including utilisation of real data.
  • Has proficiency in mathematical programming in R, MATLAB or similar.
  • Preferably, has experience with the epidemiology of food-borne hazards.
Position 2
  • Has documented experience with descriptive and statistical analysis of data collected in observational studies of AMR in animal population.
  • Preferably, has experience with modern animal production.
Position 3
  • Has documented experience with combining data generation, preferably metagenomics with epidemiological analyses of data from various sources.
  • Has international experience.
  • Has proficiency in statistical programming in R, MATLAB or similar.
  • Preferably, has experience with infectious disease epidemiology and bioinformatics.
Position 4
  • Has documented experience with quantitative epidemiological methods, including temporal and spatial analytical methods, and with linking and analysing data from various sources.
  • Has proficiency in statistical programming in R, MATLAB or similar.
  • Preferably, has experience with infectious disease epidemiology and bioinformatics.
Position 5
  • Has documented experience with quantitative epidemiological methods and/or mathematical modelling.
  • Has proficiency in mathematical programming in R, MATLAB or similar.
  • Preferably, has experience with the surveillance and epidemiology of AMR bacteria and/or zoonotic bacteria.

We offer
DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and an academic freedom tempered by responsibility.

Salary and terms of employment
The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed with the relevant union.

The period of employment is 2 to 3 years depending on the individual candidate and position.

You can read more about career paths at DTU here.

Further information
Further information may be obtained from:

Associate Professor Håkan Vigre, hvig@food.dtu.dk, tel.: +45 4060 1303
Professor Frank M. Aarestrup, fmaa@food.dtu.dk, tel. +45 3588 6281
Professor Tine Hald, tiha@food.dtu.dk, tel. +45 3588 7094

You can read more about the Genomic Epidemiology Research Group at http://www.food.dtu.dk/english/Research/Genomic-Epidemiology

Application procedure
Please submit your online application no later than 25 May 2018 (local time).

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply online", fill in the online application form, and attach all your materials in English in one PDF file. The file must include:

  • Application (cover letter)
  • CV
  • Diploma (MSc/PhD)
  • List of publications

Applications and enclosures received after the deadline will not be considered.

In the field “Please indicate which position you are applying for”, please indicate which position you are applying for.

All interested candidates irrespective of age, gender, disability, race, religion or ethnic background are encouraged to apply.

DTU Food (The National Food Institute, Technical University of Denmark) works within six technical focus areas: Biotechnology, nutrition, food quality, food safety, food technology and environment & human health. Activities cover a wide range of food products throughout the entire food chain from farm to table, comprising both research activities and research-based consulting and teaching.

DTU is a technical university providing internationally leading research, education, innovation and scientific advice. Our staff of 6,000 advance science and technology to create innovative solutions that meet the demands of society, and our 11,200 students are being educated to address the technological challenges of the future. DTU is an independent academic university collaborating globally with business, industry, government and public agencies.