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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Meat Safety and Quality » Research » Publications at this Location » Publication #430260
Research Project: Holistic Tactics to Advance the Microbiological Safety and Quality of the Red Meat Continuum

Location: Meat Safety and Quality

Title: The gene taxonomic prevalence (GeTPrev) pipeline for scalable gene prevalence estimation across bacterial taxa

Author
item WU, WEIFAN - University Of Florida
item Dickey, Aaron
item VIPHAM, JESSIE - Kansas State University
item ARTHUR, TERRANCE - Fremonta Corporation
item Schmidt, John

Submitted to: Journal of Food Protection
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/19/2026
Publication Date: 5/26/2026
Citation: Wu, W., Dickey, A.M., Vipham, J.L., Arthur, T.M., Schmidt, J.W. 2026. The gene taxonomic prevalence (GeTPrev) pipeline for scalable gene prevalence estimation across bacterial taxa. Journal of Food Protection. 89(7). Article 100819. https://doi.org/10.1016/j.jfp.2026.100819.
DOI: https://doi.org/10.1016/j.jfp.2026.100819

Interpretive Summary: Millions of bacterial genome sequences are publicly available but tools to determine gene prevalences in specific bacterial classifications were lacking. We developed a bioinformatics tool to fill this gap (GeTPrev) that leverages high-performance computing systems to perform analysis of large projects with minimal user interaction. GeTPrev offers a practical solution for gene-centric analyses for various food safety applications . The automated GeTPrev tool leverages the existing pathogen sequence databases designed to determine relatedness for outbreak traceback to enable identification of prevalences of specific genes that reduces time needed to develop new specific assays to detect traits of interest such as virulence. GeTPrev should assist the development of new food safety diagnostic tools and can be applied beyond food safety. GeTPrev is publicly available and free to use.

Technical Abstract: National Center for Biotechnology Information (NCBI) stores over 1 million bacterial genome sequences with no tools capable of estimating the prevalence of specific nucleotide sequences within or across taxa. To address this gap, we developed the Gene Taxonomic Prevalence (GeTPrev) pipeline. GeTPrev estimates the presence of user-specified genes in bacterial genome collections across taxa. Implemented in Bash, GeTPrev integrates BLAST-based sequence alignment with two operational modes tailored to different analytical needs. The default mode performs a one-pass search against curated complete genome databases formatted for BLAST. A “Heavy” mode expands the search to include both complete and draft genomes for a broader representation of genomic diversity. GeTPrev is managed through a Conda environment and designed for compatibility with high-performance computing (HPC) systems, enabling efficient batch analysis of large genome datasets. GeTPrev supports the construction of user-defined gene taxonomic targets. However, pre-built complete genome databases of seven Enterobacteriaceae genera are included with the pipeline to support rapid analysis. GeTPrev functionality and flexibility was demonstrated by eight example applications. GeTPrev offers a practical solution for gene-centric analysis in microbial genomics, molecular epidemiology, and food safety surveillance.