Postdoc in Pathogen Genomics and Antimicrobial Resistance

We are seeking a highly motivated post-doctoral student 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. 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 - Supervision of the PhD student(s) recruited to this project You will work closely work with other researchers and technicians in an interdisciplinary group as well as PhD students who are working in the field of clinical microbiology and infection control. The work will be done in close collaboration with international partners.

We are looking for a candidate with a PhD in molecular microbiology, with broad experience in laboratory work including next-generation sequencing and a strong interest in using bioinformatics for identification of bacteria and yeasts, and their potential antimicrobial resistance markers and mechanisms. Required Expertise

PhD 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 - Experience in own and innovative, question-driven experimental design - 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 a non-specialist audience

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 - Exprience in international collaboration or a time spent abroad - Previous experience with supervision of technicians, master students, and PhD students Grant writing