PhD student in Pathogen Genomics and Antimicrobial Resistance

20 Jan 2024
Job Information

Organisation/Company

University Medical Centre Groningen (UMCG)

Research Field

Medical sciences

Researcher Profile

Recognised Researcher (R2)
First Stage Researcher (R1)

Country

Netherlands

Application Deadline

4 Feb 2024 - 23:00 (UTC)

Type of Contract

Temporary

Job Status

Not Applicable

Hours Per Week

36.0

Is the job funded through the EU Research Framework Programme?

Not funded by an EU programme

Is the Job related to staff position within a Research Infrastructure?

No

Offer Description

We are seeking a highly motivated PhD candidate to join our dynamic research team, which is at the forefront of developing cutting-edge solutions for the diagnosis and management of bloodstream infections (BSI). The successful applicant will play a pivotal role in the implementation and enhancement of genome-based diagnostics for antimicrobial resistance (AMR). The position will be embedded in a team within a large international consortium, funded by the Horizon Europe program and is based at the University Medical Center Groningen, The Netherlands: DRAIGON (Diagnosing Infections with Multi-Drug Resistant Microorganisms using AI-powered Genomic Antibiotic Susceptibility Prediction from Long-Read Sequencing Data). The Department of Medical Microbiology and Infection Prevention is responsible for patient-specific laboratory diagnostics, clinical consulting, teaching, and research in infection prevention & control, virology, bacteriology, mycology, and parasitology.

Project aim
The DRAIGON consortium is committed to develop an innovative in vitro diagnostic device (IVD) that integrates whole-genome sequencing (WGS) and artificial intelligence (AI) for the rapid and accurate diagnosis of patients infected with multi-drug resistant (MDR) microorganisms. Subsequently, the goal is to validate the device and to demonstrate the clinical efficacy focusing on blood and joint infections.

Work package and key responsibilities
- Design and establish patient inclusion criteria and determine relevant outcome parameters for data collection
- Conduct comparative analysis of AMR prediction results using both short-read and long-read sequencing technologies
- Develop and standardize a comprehensive end-to-end workflow for profiling pathogens and detecting AMR from pre-enriched cultures derived from BSI patients.
- Collect and integrate clinical data as specified, alongside standard-of-care diagnostics and sequencing data
- Perform in-depth data analysis to compare the efficacy of sequence-based diagnostics with conventional standard-of-care methods
- Identify and evaluate critical steps within the diagnostic process that affect the time-to-result, the availability of on-demand access, and the identification of reliable stopping points in the workflow

Requirements
Specific Requirements

Required Expertise
- Master’s degree in Biomedical Sciences, Molecular Biology, or a related field
- Demonstrable experience or a strong interest in molecular microbiology and laboratory techniques, including next-generation sequencing
- A collaborative spirit to work effectively within an interdisciplinary team and with clinical partners
- Excellent organizational skills to manage complex workflows and data collection processes
- Strong communication skills, both written and verbal, with the capability to present research findings to both a specialist and non-specialist audience
- Team player with excellent communication and collaborative skills

Additional experience in the following areas is highly desirable
- Proficiency in bioinformatics, with a focus on bacterial and yeast identification, as well as the detection of AMR markers and mechanisms
- Skilled in data analysis and interpretation, with the ability to compare and contrast different diagnostic approaches

The UMCG has a preventive Hepatitis B policy. The UMCG can provide you with the vaccination, should it be required for your position. In case of specific professions a ‘Certificate of Good Conduct’ is required.

Additional Information
Benefits

The PhD student position is for a duration of four years, with an initial contract of one year followed by an extension, based on performance. The candidate will be provided with a stimulating work environment and opportunities for professional development within the field of infectious disease diagnostics. Your salary will be a minimum of € 2.901,- gross per month in the first year and a maximum of € 3.677,- gross per month (scale PRO) in the final (4th) year, based on a full-time appointment. In addition, the UMCG will offer you 8% holiday pay, and 8.3% end-of-year bonus.
The conditions of employment comply with the Collective Labour Agreement for Medical Centres (CAO-UMC).

To apply, kindly utilize the digital application form located at the bottom of this page. Only submissions made through this form will be considered. Applications will be accepted until January 31, 2024, or until the position is filled. To ensure full consideration, please submit a complete application consisting of a cover letter, curriculum vitae, and the contact details of two professional references.

We are looking forward to your application and the possibility of you joining our team to contribute to this groundbreaking research endeavor.

Selection process

Prof. John Rossen, [email protected]
Prof. Bhanu Sinha MD PhD, [email protected]

Additional comments

Prof. John Rossen
[email protected]

Prof. Bhanu Sinha MD PhD
[email protected]

Website for additional job details

https://www.academictransfer.com/336815/

Work Location(s)

Number of offers available

1

Company/Institute

University Medical Center Groningen (UMCG)

Country

Netherlands

City

Groningen

Postal Code

9713 GZ

Street

Hanzeplein 1

Geofield

Where to apply

Website

https://www.academictransfer.com/en/336815/phd-student-in-pathogen-genomics-and…

Contact

City

Groningen

Website

http://www.werken.umcg.nl/

Street

Hanzeplein 1

Postal Code

9713 GZ

STATUS: EXPIRED