PATRIC as a unique resource for studying antimicrobial resistance

Dionysios A. Antonopoulos, Rida Assaf, Ramy Karam Aziz, Thomas Brettin, Christopher Bun, Neal Conrad, James J. Davis, Emily M. Dietrich, Terry Disz, Svetlana Gerdes, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Daniel E. Murphy-Olson, Eric K. Nordberg, Gary J. Olsen, Robert Olson, Ross Overbeek, Bruce Parrello, Gordon D. PuschJohn Santerre, Maulik Shukla, Rick L. Stevens, Margo Vanoeffelen, Veronika Vonstein, Andrew S. Warren, Alice R. Wattam, Fangfang Xia, Hyunseung Yoo

Research output: Contribution to journalArticle

Abstract

The Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org) is designed to provide researchers with the tools and services that they need to perform genomic and other 'omic' data analyses. In response to mounting concern over antimicrobial resistance (AMR), the PATRIC team has been developing new tools that help researchers understand AMR and its genetic determinants. To support comparative analyses, we have added AMR phenotype data to over 15 000 genomes in the PATRIC database, often assembling genomes from reads in public archives and collecting their associated AMR panel data from the literature to augment the collection. We have also been using this collection of AMR metadata to build machine learning-based classifiers that can predict the AMR phenotypes and the genomic regions associated with resistance for genomes being submitted to the annotation service. Likewise, we have undertaken a large AMR protein annotation effort by manually curating data from the literature and public repositories. This collection of 7370 AMR reference proteins, which contains many protein annotations (functional roles) that are unique to PATRIC and RAST, has been manually curated so that it projects stably across genomes. The collection currently projects to 1 610 744 proteins in the PATRIC database. Finally, the PATRIC Web site has been expanded to enable AMR-based custom page views so that researchers can easily explore AMR data and design experiments based on whole genomes or individual genes.

Original languageEnglish (US)
Pages (from-to)1094-1102
Number of pages9
JournalBriefings in bioinformatics
Volume20
Issue number4
DOIs
StatePublished - Mar 27 2018

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Genes
Genome
Molecular Sequence Annotation
Proteins
Research Personnel
Databases
Phenotype
Metadata
Mountings
Learning systems
Websites
Classifiers
Experiments

Keywords

  • RAST
  • antibiotic
  • antimicrobial resistance (AMR)
  • genome annotation
  • minimum inhibitory concentration
  • the SEED

ASJC Scopus subject areas

  • Information Systems
  • Molecular Biology

Cite this

Antonopoulos, D. A., Assaf, R., Aziz, R. K., Brettin, T., Bun, C., Conrad, N., ... Yoo, H. (2018). PATRIC as a unique resource for studying antimicrobial resistance. Briefings in bioinformatics, 20(4), 1094-1102. https://doi.org/10.1093/bib/bbx083

PATRIC as a unique resource for studying antimicrobial resistance. / Antonopoulos, Dionysios A.; Assaf, Rida; Aziz, Ramy Karam; Brettin, Thomas; Bun, Christopher; Conrad, Neal; Davis, James J.; Dietrich, Emily M.; Disz, Terry; Gerdes, Svetlana; Kenyon, Ronald W.; Machi, Dustin; Mao, Chunhong; Murphy-Olson, Daniel E.; Nordberg, Eric K.; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Santerre, John; Shukla, Maulik; Stevens, Rick L.; Vanoeffelen, Margo; Vonstein, Veronika; Warren, Andrew S.; Wattam, Alice R.; Xia, Fangfang; Yoo, Hyunseung.

In: Briefings in bioinformatics, Vol. 20, No. 4, 27.03.2018, p. 1094-1102.

Research output: Contribution to journalArticle

Antonopoulos, DA, Assaf, R, Aziz, RK, Brettin, T, Bun, C, Conrad, N, Davis, JJ, Dietrich, EM, Disz, T, Gerdes, S, Kenyon, RW, Machi, D, Mao, C, Murphy-Olson, DE, Nordberg, EK, Olsen, GJ, Olson, R, Overbeek, R, Parrello, B, Pusch, GD, Santerre, J, Shukla, M, Stevens, RL, Vanoeffelen, M, Vonstein, V, Warren, AS, Wattam, AR, Xia, F & Yoo, H 2018, 'PATRIC as a unique resource for studying antimicrobial resistance', Briefings in bioinformatics, vol. 20, no. 4, pp. 1094-1102. https://doi.org/10.1093/bib/bbx083
Antonopoulos DA, Assaf R, Aziz RK, Brettin T, Bun C, Conrad N et al. PATRIC as a unique resource for studying antimicrobial resistance. Briefings in bioinformatics. 2018 Mar 27;20(4):1094-1102. https://doi.org/10.1093/bib/bbx083
Antonopoulos, Dionysios A. ; Assaf, Rida ; Aziz, Ramy Karam ; Brettin, Thomas ; Bun, Christopher ; Conrad, Neal ; Davis, James J. ; Dietrich, Emily M. ; Disz, Terry ; Gerdes, Svetlana ; Kenyon, Ronald W. ; Machi, Dustin ; Mao, Chunhong ; Murphy-Olson, Daniel E. ; Nordberg, Eric K. ; Olsen, Gary J. ; Olson, Robert ; Overbeek, Ross ; Parrello, Bruce ; Pusch, Gordon D. ; Santerre, John ; Shukla, Maulik ; Stevens, Rick L. ; Vanoeffelen, Margo ; Vonstein, Veronika ; Warren, Andrew S. ; Wattam, Alice R. ; Xia, Fangfang ; Yoo, Hyunseung. / PATRIC as a unique resource for studying antimicrobial resistance. In: Briefings in bioinformatics. 2018 ; Vol. 20, No. 4. pp. 1094-1102.
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