Research Scientist (Microbial Genomic Epidemiology)
Post Details
Job Title
Research Scientist (Microbial Genomic Epidemiology)
Post Number
1003660
Closing Date
23 Apr 2019
Grade
SC6
Starting Salary
£31,250 - £38,100
Hours per week
37
Project Title
Drivers and dynamics of antimicrobial resistance and Salmonella in Brazilian pig and poultry production
Expected/Ideal Start Date
13 May 2019
Months Duration
24

Job Description

Main Purpose of the Job

Join a project in Dr Alison Mather’s group at the Quadram Institute Bioscience (QIB) based in Norwich UK, focusing on the drivers and dynamics of antimicrobial resistance (AMR) in Salmonella in Brazilian pig and poultry production. Brazil is the world’s largest exporter of chicken meat and the fourth largest producer of pigs, and with an increasing demand for animal protein, antimicrobial consumption in livestock is expected to nearly double in Brazil by 2030. This project involves a combination of approaches, including short- and long-read whole genome sequencing, bioinformatics analyses of large datasets and statistical modelling to identify factors associated with AMR in this setting. The work is in collaboration with researchers at the University of São Paulo and will involve analysis of both existing genomes and those that will be generated in the project. These genomic data, along with the associated epidemiological metadata, provides an incredible opportunity to address key questions in this field, such as the relative importance of horizontal gene transfer, the impact of antimicrobial use on AMR, and the dynamics of Salmonella and AMR within these production systems.

Key Relationships

Internal: With the line manager, Dr Alison Mather, group members and, as necessary, other researchers, research support staff and students across the Institute.
External: Collaborators at University of Sao Pãulo

Main Activities & Responsibilities

Percentage
Bioinformatics/genomic epidemiology analysis of AMR and bacteria in pigs and poultry in Brazil using whole genome sequences
60
Long-read sequencing and bioinformatics of bacterial isolates using the Oxford Nanopore MinION technology; some laboratory method development
10
Preparation of manuscripts and seminars
10
Present research findings at project meetings, scientific conferences and outreach/translation events
5
Contribute to laboratory management, group meetings and interactions with collaborators
5
As agreed with the line manager, any other duties commensurate with the nature of the post

Person Profile

Education & Qualifications

Requirement
Importance
An awarded PhD in a relevant subject (e.g. Computational Biology, Microbiology, Molecular Genetics, Bioinformatics, Epidemiology or related discipline)
Essential

Specialist Knowledge & Skills

Requirement
Importance
Understanding of high-throughput sequencing and microbial genomics
Essential
Bioinformatics skills
Essential
Proficiency in working in the Linux environment
Essential
Good publication record in peer-reviewed scientific journals commensurate with experience
Desirable

Relevant Experience

Requirement
Importance
Experience of oral research presentations
Essential
Proven record in scientific writing commensurate with experience
Essential
Hands-on experience with microbial genome sequencing and analysis
Essential
Experience in microbiology and molecular laboratory work
Desirable
Experience with large sequence datasets
Desirable
Experience with command-line and cloud-computing environment
Desirable

Interpersonal & Communication Skills

Requirement
Importance
Excellent time management and organisational skills
Essential
Ability to prioritise
Essential
Demonstrated ability to work independently, using initiative and applying problem solving skills
Essential
Excellent communication skills, both written and oral, including the ability to present complex information with clarity
Essential
Ability to collaborate with internal and external stakeholders
Essential
Good interpersonal skills, able to work as part of a team
Essential
Accurate record keeping
Essential
Ability to think creatively, contribute new ideas, troubleshoot
Desirable

Additional Requirements

Requirement
Importance
Promotes equality and values diversity
Essential
Ability to undertake occasional travel (national/international) related to collaborations and/or seminars
Essential
Willingness to undertake any necessary training for the role
Essential
Ability to maintain confidentiality and security of information where appropriate
Essential
Willingness to embrace the expected values and behaviours of all staff at the Institute, ensuring it is a great place to work
Essential
Willingness to work outside standard working hours when required
Essential
Able to present a positive image of self and the Institute, promoting both the international reputation and public engagement aims of the Institute
Essential
Attention to detail
Essential

Who We Are

Quadram Institute Bioscience

The Quadram Institute is at the forefront of a new interface between food science, gut biology and health, developing solutions to worldwide challenges in food-related disease and human health.

We are engaged in fundamental and translational food and health research, alongside clinical studies, endoscopy and industry, working together to become a leading international hub for food and health research, combining scientific excellence and clinical expertise, delivering impacts on patient care and accelerating innovation.

For more information about working at Quadram Institute Bioscience, please click here.

Department

Microbes in the Food Chain

Group Details

Our work aims to understand the evolution, origins and transmission of bacteria between different host populations, with a focus on bacteria that are resistant to antimicrobial drugs. We are particularly interested in understanding the relative contributions of animals, humans, the environment and food to the overall burden of disease caused by pathogenic bacteria and antimicrobial resistance (AMR). We also want to understand the importance of non-pathogenic bacteria, including those in the microbiome, as reservoirs of AMR genes. By defining and quantifying the importance of different sources of bacteria and AMR, we aim to address gaps in our knowledge, identify points where interventions may be most effectively applied, improve food safety, and inform policy and surveillance.

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Research Scientist

Applications are invited for a Research Scientist to join the Laboratory of Dr Alison Mather in the Microbes in the Food Chain Programme at Quadram Institute Bioscience (QIB), based in Norwich, UK.

Background:

The post holder will join a project to identify and investigate the drivers and dynamics of antimicrobial resistance (AMR) in Salmonella in Brazilian pig and poultry production. This research is highly topical and relevant to both animal and human health. This project is a collaboration with researchers in São Paulo, Brazil, and will involve a combination of approaches, including short- and long-read whole genome sequencing, bioinformatics analyses of large datasets and statistical modelling. These genomic data, along with the associated epidemiological metadata, provides an incredible opportunity to address key questions in this field, such as the relative importance of horizontal gene transfer, the impact of antimicrobial use on AMR, and the dynamics of Salmonella and AMR within these production systems.

The role:

The successful post holder will analyse microbial whole-genome sequence data from both Illumina and Oxford Nanopore MinION technologies, of both existing genomes and those that will be generated in the project, using various bioinformatics approaches to address the project aims. Some method development of molecular biology techniques is also part of the project. The post holder will occasionally present research findings at project meetings, scientific conferences and outreach/training events. The position will involve visits to São Paulo to work with the Brazilian collaborators on epidemiological and bioinformatics analyses.

The ideal candidate:

Candidates should have a PhD in a relevant subject (e.g. Computational Biology, Microbiology, Molecular Genetics, Bioinformatics, Epidemiology or related discipline), and experience in analysing microbial sequencing data. They should also possess a proven record in scientific writing, and excellent communication and interpersonal skills.

Additional information:

Salary on appointment will be within the range £31,250 to £38,100 per annum depending on qualifications and experience. This is a full time contract until 30th April 2021.

We are committed to equal opportunities and welcome applications from all sectors of society. The Institute supports equality of opportunity within the workplace and expects all employees to share and display these values. To support our commitment, we have a range of family, faith and diversity friendly working arrangements to help all staff achieve excellence in their area of work.

As a Disability Confident employer, we guarantee to offer an interview to all disabled applicants who meet the essential criteria for this vacancy.

About the Quadram Institute:

The Quadram Institute is a new interdisciplinary research institute at the forefront of a new era in food and health research. Its mission is to understand how food and the gut microbiota are linked to the promotion of health and the prevention of disease. A partnership between Quadram Institute Bioscience, the University of East Anglia, the Norfolk and Norwich University Hospital and BBSRC, it brings together scientists and clinicians in a new state-of-the-art building. The Quadram Institute is based on the Norwich Research Park, one of Europe’s largest centres of life sciences and home of the John Innes Centre and The Earlham Institute. (https://quadram.ac.uk/).

The closing date for applications will be 23 April 2019.

The Quadram Institute Bioscience is a registered charity (No. 1058499) and is an Equal Opportunities Employer.