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

Abstract

Pathogenicity is a complex multifactorial process confounded by the concerted activity of genetic regions associated with virulence and/or resistance determinants. Pathogenicity islands (PAIs) and resistance islands (REIs) are key to the evolution of pathogens and appear to play complimentary roles in the process of bacterial infection. While PAIs promote disease development, REIs give a fitness advantage to the host against multiple antimicrobial agents. The Pathogenicity Island Database (PAIDB, http://www.paidb.re.kr) has been the only database dedicated to providing comprehensive information on all reported PAIs and candidate PAIs in prokaryotic genomes. In this study, we present PAIDB v2.0, whose functionality is extended to incorporate REIs. PAIDB v2.0 contains 223 types of PAIs with 1331 accessions, and 88 types of REIs with 108 accessions. With an improved detection scheme, 2673 prokaryotic genomes were analyzed to locate candidate PAIs and REIs. With additional quantitative and qualitative advancements in database content and detection accuracy, PAIDB will continue to facilitate pathogenomic studies of both pathogenic and nonpathogenic organisms.