Harmonization of multi-platform NGS workflows for bacterial pathogens

Next-generation sequencing (NGS) is now central to genomic surveillance of foodborne bacterial pathogens, but results generated on different sequencing platforms are not always directly comparable. This project aims at developing a standardized bioinformatic framework for comparative genomic analysis of Listeria monocytogenes, Campylobacter jejuni, Salmonella spp. and Escherichia coli, using data from Illumina, Ion Torrent, Oxford Nanopore and PacBio platforms. The framework targets both the congruency of genomic results across technologies and their downstream use in phylogenetic inference and AI/ML-based surveillance, so that outbreak investigations stay reliable regardless of which sequencer a laboratory uses.