The Luxembourg Institute of Science and Technology (LIST) offers an outstanding opportunity for joining the newly created Doctoral Training Unit (DTU) MICROH – Microbiomes in One-Health (microh.uni.lu; coordinated by the University of Luxembourg), including 17 PhD projects and two post-doctoral fellowships. The position will extend over a maximum duration of 4 years. The PhD candidate will be part of the Environmental Microbiology and Biotechnology research group at the Department of Environmental Research and Innovation (ERIN) at LIST. Furthermore, the PhD candidate will be affiliated to the University of Luxembourg. The project will moreover give opportunities for collaboration with other public research institutions and private/industrial partners at national and international level.

Description

The food- and waterborne pathogen Campylobacter jejuni is the world’s leading cause of bacterial gastroenteritis. The human incidence of C. jejuni in Luxembourg is among the highest in the EU. Multiple antimicrobial resistance (AMR) patterns in C. jejuni constitute a severe threat to human health worldwide. AMR evolution and transmission in C. jejuni are clearly embedded in a One-Health context. Implementation of highly sensitive, cost-effective and rapid MALDI-ToF MS workflows in clinical, veterinary and environmental laboratories is currently revolutionizing the domain of routine diagnostics, microbial identification and characterization. In this study, a One-Health collection of local epidemiologically relevant C. jejuni isolates will be screened at the subspecies level, and the diversity of AMR profiles will be assessed through the development of a MALDI-ToF MS approach and bioinformatics toolbox. Mass spectrometry-derived antimicrobial susceptibility/resistance profiles will be compared to classical screening techniques as well as to whole-genome sequencing data. Proteomic fingerprinting using a dual MS-MS MALDI-ToF approach for identification of biomarkers of interest, including AMR signatures, will additionally be performed. We will evidence that MALDI-TOF MS will play an utmost central and crucial role in the future of routine diagnostics of antibacterial susceptibilities, multidrug-resistance screening, epidemiological surveillance and healthcare quality improvement in general. The methods used include matrix-assisted laser desorption ionization – time of flight mass spectrometry (MALDI-ToF MS), whole-genome sequencing (Illumina technology), several bioinformatics pipelines (including BioNumerics and SeqSphere+) and proteomics (biomarker identification through dual MS-MS). The PhD candidate will have a strong background in microbiology and molecular biology, with experience in Maldi-ToF-MS characterization and whole-genome sequencing of pathogenic bacteria.

Profile

Education

• Master degree in microbiology and molecular biology

Competencies

• Experience in microbial cultures and molecular biology
• Skills in bacterial characterization and genotyping
• Background in Maldi-ToF-MS and proteomics applications in bacteriology
• Skills in bioinformatics analytical approaches for mass spectrometry and whole-genome sequence analysis

Language

• Fluent in English (written and spoken)
• French is an asset