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ARS Home » Northeast Area » Wyndmoor, Pennsylvania » Eastern Regional Research Center » Characterization and Interventions for Foodborne Pathogens » Research » Publications at this Location » Publication #368929
Research Project: Development of Portable Detection and Quantification Technologies for Foodborne Pathogens

Location: Characterization and Interventions for Foodborne Pathogens

Title: PRAP: Pan Resistome Analysis Pipeline

Author
item HE, YICHEN - Shanghai Jiaotong University
item ZHOU, XIUJUAN - Shanghai Jiaotong University
item CHEN, ZIYAN - Shanghai Jiaotong University
item Gehring, Andrew
item SHI, XIANMING - Shanghai Jiaotong University

Submitted to: BMC Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/23/2019
Publication Date: 1/15/2020
Citation: He, Y., Zhou, X., Chen, Z., Gehring, A.G., Shi, X. 2020. PRAP: Pan Resistome Analysis Pipeline. BMC Bioinformatics. (2020) 21:20. https://doi.org/10.1186/s12859-019-3335-y.
DOI: https://doi.org/10.1186/s12859-019-3335-y

Interpretive Summary: Genes that make pathogenic bacteria resistant to antibiotic drugs can be spread to other bacteria via sharing of DNA in a process known as "horizontal gene transfer." This sharing of genetic material process is different for bacteria even within the same species. Since these differences in the total collection of antibiotic resistance genes (the "resistome") are unique for even the bacteria within the same species, the entire collection of genes (the "pan-genome") should be separately analyzed in order to identify unique features of the antibiotic resistance genes present for each bacteria in mixed populations. Software tools have been developed for pan-genome analysis and identification of antibiotic resistance genes, however few are capable of combining both as was done for this study.

Technical Abstract: Antibiotic resistance genes can spread among pathogens via horizontal gene transfer, resulting in their divergent distribution even within the same species. This indicates that the resistome of even the same species should be analyzed separately as a “pan-genome” to identify unique features of the antibiotic resistance genes present in the population. Software tools have been developed for pan-genome analysis or identification of antibiotic resistance genes, but few combine both.