Antimicrobial resistance (AMR) is one of the most pressing global health challenges, with projections estimating up to 10 million annual deaths by 2050. Advances in next-generation sequencing (NGS) have enabled large-scale detection of antimicrobial resistance genes (ARGs), yet there remains a need for robust computational frameworks that integrate environmental resistomes with clinical and epidemiological data.
This PhD project will develop scalable bioinformatics workflows for tracking the spread of pathogens and antibiotic resistance genes in hospitals and associated environments. The research will focus on metagenomic analysis, including functional annotation of ARGs, virulence factors, and mobile genetic elements, as well as reconstruction of metagenome-assembled genomes (MAGs).
Using large-scale datasets generated at the Małopolska Centre of Biotechnology (www.mcb.uj.edu.pl) and through the International MetaSUB Consortium (www.metasub.org), the candidate will integrate environmental, clinical, and epidemiological data to investigate how resistance determinants circulate between hospital environments and human pathogens. The project will also explore links between ARG prevalence, antibiotic consumption patterns, and regional epidemiological trends using advanced statistical and machine-learning approaches.
The ultimate goal is to develop predictive models and analytical tools that improve our understanding of AMR transmission dynamics and support future surveillance strategies.
Read more here: science.phd.uj.edu.pl/join/biomedical/topic/-/journal_content/56_INSTANCE_ayWUsfnIfuWH/142594442/160782909
Required professional qualifications
The candidate appointed to the position of Ph.D. researcher should:
- hold a Master's (M.Sc.) degree in the Life Science discipline
- have a solid understanding of microbiology and genetics
- have a programming experience
- have a data science experience
- have a good knowledge of (written and spoken) English
Desirable professional qualifications
The ideal candidate appointed to the position of Ph.D. researcher should:
- be familiar with pipeline development using tools like Nextflow, Snakemake, or Docker/Singularity
- be experienced in high-performance computing (HPC) or cloud environments
- be familiar with resistance development and spread
- be prepared to learn new scientific techniques and protocols
- be creative with a responsible attitude, and have good communication skills and willingness to work as part of a dynamic team
Application deadline: June 8th
science.phd.uj.edu.pl/en_GB/join/biomedical
- Check the admissions schedule.
- Read the rules and detailed conditions of admission.
- Find a potential supervisor.
- Collect the required documents.
- Apply in the Online Application System (IRK).
-- see instructions on how to apply in IRK (irk.uj.edu.pl/en-gb/home/SD_PC_26/)
-- please note: in the IRK system, admission to this programme may not be visible until applications open in IRK
- Take the exam.
- Wait for the announcement of the results.
- Make an enrolment in the Doctoral School.