Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens.

ABSTRACT: Different laboratories employ different Whole-Genome Sequencing (WGS) pipelines for Food and Waterborne disease (FWD) surveillance, casting doubt on the comparability of their results and hindering optimal communication at intersectoral and international levels. Through a collaborative effort involving eleven European institutes spanning the food, animal, and human health sectors, we aimed to assess the inter-pipeline clustering congruence across all resolution levels and perform an in-depth comparative analysis of cluster composition at outbreak level for four important foodborne pathogens: Listeria monocytogenes, Salmonella enterica, Escherichia coli, and Campylobacter jejuni. We found a general concordance between allele-based pipelines for all species, except for C. jejuni, where the d

SUBMITTER: Mixao V 

PROVIDER: S-EPMC12038046 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature