Global change and antibiotic resistance gene dissemination through horizontal gene transfer

Background

Global change (i.e. climate change and anthropogenic pollution) exposes environmental bacteria to multiple physical (temperature, UV, pH) and chemical stresses (antibiotics and non-antibiotic pollutants) that can impose a selective pressure and promote the selection, maintenance and dissemination of antibiotic resistance genes (ARGs) in the environment. Freshwater ecosystems are both a receiver of pollution from anthropogenic sources, a natural reservoir of antibiotic resistance and a contact point between the environmental and the human microbiome. There is a growing concern that aquatic ecosystems increasingly exposed to global change may promote ARG maintenance and spread across bacterial populations and their dissemination from the aquatic microbiome to human pathogens. This phenomenon is a major global public health threat that deserves urgent attention to avoid entering a post-antibiotic era where antibiotic therapy will no longer be effective against bacterial infections. However, the magnitude of this increased dissemination risk and the mechanisms involved remain unknown. We have two full-time MSc thesis project positions opening in September 2026 to work on global change-driven antibiotic resistance gene dissemination across bacterial populations through horizontal gene transfer.

Objectives

Project 1: Horizontal gene transfer of antibiotic resistance genes from environmental bacteria to human pathogens in European aquatic ecosystems

In this project you will determine the frequency of horizontal gene transfer of ARGs (ARG-HGT) from aquatic microbiomes to human pathogens and establish dose-response relationships between global change stress (physical and chemical stresses) and ARG-HGT. You will use a combination of flow cytometry, phenotypical antibiotic resistance testing, genomic sequencing, qPCR and metatranscriptomics to quantify ARG acquisition by human pathogens in aquatic ecosystems and identify the involved mechanisms.

Project 2: Non-antibiotic pollutants as drivers of ARG maintenance and dissemination at environmentally-relevant concentrations

In this project you will determine the role of non-antibiotic pollutants (microplastics, drugs, metals, biocides) on promoting ARG maintenance and dissemination at residual doses found in environmental settings. You will carry out evolutionary experiments using a combination of culture, flow cytometry, phenotypical antibiotic resistance testing, qPCR/RT-qPCR, genomics and transcriptomics to quantify the contribution of non-antibiotic pollutants, alone and in combination, to the maintenance and expression of plasmid-encoded ARGs, as well as their dissemination through vertical and horizontal gene transfer.

Tasks

Bacterial culture, in vitro/microcosm exposure experiments, FACS sorting and antibiotic resistance testing

• DNA/RNA extraction, qPCR/RT-qPCR
• Genome and transcriptome sequencing and analysis (quality control, assembly, genome reconstruction, comparative genomics, functional annotation, differential expression/abundance analysis)
• Statistical analyses and establishment of dose-response relationships

Skills involved

• Bacterial culture, microcosm and in vitro experiments
• Flow cytometry quantification and FACS sorting
• Phenotypical antibiotic resistance testing
• DNA/RNA extraction
• qPCR/RT-qPCR
• Genome and transcriptome sequencing
• Bioinformatics
• Statistics

Duration of the projects

Full-time MSc thesis projects

Contact

Please send your CV and motivation letter to:

Concepción Sánchez-Cid Torres
concepcion.sanchez-cid@bio.ku.dk

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