The GenomeTrakr Validation Strain Set

Why confidence and consistency matter in WGS data

Unlike traditional typing methods, WGS involves complex, multistep laboratory and bioinformatics processes. Variability in sample preparation, sequencing platforms, analytical pipelines, and data interpretation can influence results, making it challenging to ensure consistency across laboratories. For global food safety surveillance, such variability can undermine the ability to reliably compare genomic data generated in different settings, directly impacting outbreak detection, source attribution, and regulatory response.

Standardizing WGS workflows for foodborne pathogen surveillance

To address the need for consistency and comparability in WGS-based foodborne pathogen surveillance, the GenomeTrakr network, a US Food and Drug Administration (FDA)-led global consortium of public health, regulatory, academic, and international laboratories that use WGS to investigate foodborne disease outbreaks, developed the GenomeTrakr Validation Strain Set (GTVSS). This strain set comprises a carefully curated collection of 32 well-characterized bacterial strains representing major foodborne pathogens that span a broad range of genomic diversity, antimicrobial resistance profiles, and key sequence features. By using this common, well-defined strain set, laboratories can more effectively assess sequencing accuracy, reproducibility, and overall workflow performance across platforms, reagents, and bioinformatics tools.

Authenticated reference materials and high-quality genomic benchmarks

To support broader access and long-term stewardship of these validation materials, the GenomeTrakr Validation Strain Set has been made available through ATCC as a panel of all 32 strains (ATCC® MP-44™) or as six-vial packs of individual strains (ATCC® BAA-3401-NGS-PACK – BAA-3432-NGS-PACK™). Each strain is authenticated using a polyphasic approach that evaluates materials for purity, identity, and functional activity. 

The GenomeTrakr Validation Strain Set has also been characterized using both short-read and long-read sequencing technologies, generating high-quality reference datasets. The resulting fully annotated, batch-specific complete genomes for all 32 isolates are available through the ATCC Genome Portal, a publicly accessible database of reference genomes with biological provenance. These data provide laboratories with transparent, reliable benchmarks for evaluating critical components of the WGS workflows, including genome coverage, assembly accuracy, detection of antimicrobial resistance genes, and SNP-based phylogenetic analysis. 

Supporting FDA-recommended validation and ongoing quality assurance

Recommended in FDA guidance for next-generation sequencing validation, the GenomeTrakr Validation Strain Set (ATCC® MP-44™) can be used for routine performance verification, initial method validation, interlaboratory comparability studies, and ongoing quality assurance. By establishing a shared foundation for evaluating WGS workflows, this strain set helps laboratories generate accurate, reproducible, and defensible genomic data, strengthening foodborne pathogen surveillance and supporting public health protection worldwide.

Did you know?

The GenomeTrakr Validation Strain Set enables benchmarking of SNP recovery, plasmid and toxin detection, AMR analysis, GC‑content performance, and organism‑diversity workflows.

Order now