Genomic epidemiology of human bacterial pathogens reconstructed from metagenomic data

Eötvös Loránd Tudományegyetem

Biológia Doktori Iskola

Ari Eszter

biológiai tudományok

This project will develop and apply metagenomic pipelines to recover strain‑ and sequence type-level resolution for Escherichia coli across human and environmental niches. By comparing strain repertoires from gut, urinary tract, hospital surfaces, wastewater, and farm animals, it will quantify niche diversity, persistence, and overlap that underpin transmission. Phylogenomic analyses from metagenomic reads and metagenome‑assembled genomes will resolve within‑lineage relationships and detect outbreak‑linked clones without requiring culture. Concurrent resistome profiling will map antibiotic resistance genes, plasmids, and mobile elements to their E. coli hosts to identify drivers and routes of AMR spread. Together, these analyses will deliver a genomic epidemiology framework that integrates metagenomes with any available isolates to inform surveillance, infection control, and targeted interventions.

1 fő

ELTE Eötvös Loránd University, Faculty of Science, Institute of Biology, Department of Genetics

2026-05-31

English

General knowledge of bioinformatics, programming in Python and/or R languages, knowledge of OMICS data analysis (genomics, metagenomics), and understanding of molecular phylogenetics methods.