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PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands

Sung Ho Yoon1, Young-Kyu Park2, Jihyun F Kim3

  • 1Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea Bio-Medical Science Co., Ltd., Daejeon 305-301, Republic of Korea moncher@kribb.re.kr.

Nucleic Acids Research
|October 23, 2014
PubMed

Insights

The Pathogenicity Island Database (PAIDB) now includes resistance islands (REIs), enhancing its utility for studying bacterial pathogens. This updated database aids in understanding bacterial infection and antimicrobial resistance evolution.

Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Pathogenicity islands (PAIs) and resistance islands (REIs) are crucial genetic elements in bacterial pathogenesis and antimicrobial resistance.
  • PAIs contribute to disease development, while REIs confer a survival advantage against antibiotics.
  • The Pathogenicity Island Database (PAIDB) was the primary resource for PAI information.

Purpose of the Study:

  • To present PAIDB v2.0, an expanded version of the Pathogenicity Island Database.
  • To incorporate resistance islands (REIs) into the PAIDB resource.
  • To enhance the study of pathogenomics by integrating PAI and REI data.

Main Methods:

  • Developed an improved detection scheme for identifying PAIs and REIs.
  • Analyzed 2673 prokaryotic genomes to locate candidate PAIs and REIs.
  • Updated the database with quantitative and qualitative advancements.

Main Results:

  • PAIDB v2.0 now includes 223 types of PAIs (1331 accessions) and 88 types of REIs (108 accessions).
  • The improved detection scheme successfully identified numerous candidate PAIs and REIs across prokaryotic genomes.
  • The database offers enhanced content and improved detection accuracy.

Conclusions:

  • PAIDB v2.0 is a comprehensive resource for studying both pathogenicity islands and resistance islands.
  • The integrated database facilitates pathogenomic research on pathogenic and non-pathogenic organisms.
  • Advancements in PAIDB will continue to support studies on bacterial evolution and infection mechanisms.

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