PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking.

Background: Food contamination by pathogens poses a global health threat, affecting an estimated 600 million people annually. During a foodborne outbreak investigation, microbiological analysis of food vehicles detects responsible pathogens and traces contamination sources. Metagenomic approaches offer a comprehensive view of the genomic composition of microbial communities, facilitating the detection of potential pathogens in samples. Combined with sequencing techniques like Oxford Nanopore sequencing, such metagenomic approaches become faster and easier to apply. A key limitation of these approaches is the lack of accessible, easy-to-use, and openly available pipelines for pathogen identification and tracking from (meta)genomic data.

Findings: PathoGFAIR is a collection of Galaxy-based Findable, Accessible, Interoperable, and Reusable (FAIR) workflows employing state-of-the-art tools to detect and track pathogens from metagenomic Nanopore sequencing. Although initially developed to detect pathogens in food datasets, the workflows can be applied to other metagenomic Nanopore pathogenic data. PathoGFAIR incorporates visualizations and reports for comprehensive results. We tested PathoGFAIR on 130 samples containing different pathogens from multiple hosts under various experimental conditions. For all but 1 sample, workflows have successfully detected expected pathogens at least at the species rank. Further taxonomic ranks are detected for samples with sufficiently high colony-forming unit and low cycle threshold values.

Conclusions: PathoGFAIR detects the pathogens at species and subspecies taxonomic ranks in all but 1 tested sample, regardless of whether the pathogen is isolated or the sample is incubated before sequencing. Importantly, PathoGFAIR is easy to use and can be straightforwardly adapted and extended for other types of analysis and sequencing techniques, making it usable in various pathogen detection scenarios.