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 non-pathogenic organisms.
Highlights
Increased awareness of infectious diseases of humans, animals and plants caused by microbial pathogens has accelerated the genome-wide study of microbial pathogenicity, called pathogenomics (1–3)
1596 candidate PAI (cPAI) were detected in strains and 210 cREIs were found in 178 strains (Figure 2, Supplementary Table S4)
If the identity of the resulting hit was over 80% for a DNA sequence of a non-protein coding open reading frame (ORF), or 40% for a protein sequence, and the aligned region was both over 70% of the length of the query and the hit, the pair of sequences was considered as a homolog
Summary
Increased awareness of infectious diseases of humans, animals and plants caused by microbial pathogens has accelerated the genome-wide study of microbial pathogenicity, called pathogenomics (1–3). The genomes were analyzed to predict potential PAIs and REIs, producing 3579 regions that were PAI-like or REI-like in strains Of these regions, 1596 cPAIs were detected in strains and 210 cREIs were found in 178 strains (Figure 2, Supplementary Table S4). Small genomic regions below 8 kb in size were excluded (20) Of these regions, PAI-like or REI-like regions were identified by checking for the presence of at least one virulence or resistance gene homolog, respectively. The presence of virulence- or resistance-related genes is a crucial criterion to identify candidate regions in a genome (Figure 1). GenBank or UniProt website––2266 ea from VFDB, 1833 from CARD and 702 from BacMet. PAI/REI-like regions were identified by checking for the presence of at least one virulence/resistance gene homolog, as described above. Multithreading, multiprocessing and queuing were implemented to accommodate the volume of the database, the increased number of input sequences and multiple requests by users
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