PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species

Abstract

5Funded by the National Institute of Allergy and Infectious Diseases, the Pathosystems Resource Integration Center (PATRIC) is a genomics-centric relational database and bioinformatics resource designed to assist scientists in infectious-disease research. Specifically, PATRIC provides scientists with (i) a comprehensive bacterial genomics database, (ii) a plethora of associated data relevant to genomic analysis, and (iii) an extensive suite of computational tools and platforms for bioinformatics analysis. While the primary aim of PATRIC is to advance the knowledge underlying the biology of human pathogens, all publicly available genome-scale data for bacteria are compiled and continually updated, thereby enabling comparative analyses to reveal the basis for differences between infectious free-living and commensal species. Herein we summarize the major features available at PATRIC, dividing the resources into two major categories: (i) organisms, genomes, and comparative genomics and (ii) recurrent integration of community-derived associated data. Additionally, we present two experimental designs typical of bacterial genomics research and report on the execution of both projects using only PATRIC data and tools. These applications encompass a broad range of the data and analysis tools available, illustrating practical uses of PATRIC for the biologist. Finally, a summary of PATRIC's outreach activities, collaborative endeavors, and future research directions is provided.

Paralogous Outer Membrane Proteins Mediate Uptake of Different Forms of Iron and Synergistically Govern Virulence in Francisella tularensis tularensis

“…tularensis Schu S4 has a relatively small genome of 1.89 Mb and 2097 CDS as most recently catalogued by the Pathosystems Resource Integration center (PATRIC) database (49). Sixteen F. tularensis and eight F. novicida genomes have been analyzed at PATRIC.…”

The PhoP/PhoQ System and Its Role in Serratia marcescens Pathogenesis

“…S. marcescens PhoP exhibits 82% identity and 95% homology, while PhoQ exhibits 62% identity and 80% homology, to the Salmonella enterica PhoP and PhoQ proteins, respectively. Compared with Yersinia pestis, an enterobacterium phylogenetically more closely related to S. marcescens (25), PhoP displays 90% identity and 94% homology, and PhoQ shows 80% identity and 90% homology. This analysis allowed us to predict a highly conserved function for the PhoP/PhoQ system in Serratia.…”

Francisella guangzhouensis sp. nov., isolated from air-conditioning systems

“…A phylogenetic tree of sequences from whole genomes from members of the genus Francisella was generated using concatenated housekeeping gene sequences [dnaK, gyrB, rpoA, rpoB, groEL, mdh (first 472 nt only), recA, rpoD, rpoH and sdhA] as well as genes encoding the small and large rRNA subunits. Gene sequences were downloaded from whole genomes at PATRIC (http:// patricbrc.vbi.vt.edu/; Gillespie et al 2011) and aligned using Sequencher 5.01 (Gene Codes). The total length of the concatenated sequences was 21 633 nt, including gaps, for the alignment of the 20 genomes containing all of these genes.…”