A computational approach for identifying pathogenicity islands in prokaryotic genomes

Abstract

Background: Pathogenicity islands (PAIs), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup of genomic islands (GIs) that have been acquired by horizontal gene transfer event. Up to now, computational approaches for identifying PAIs have been focused on the detection of genomic regions which only differ from the rest of the genome in their base composition and codon usage. These approaches often lead to the identification of genomic islands, rather than PAIs.

Results: We present a computational method for detecting potential PAIs in complete prokaryotic genomes by combining sequence similarities and abnormalities in genomic composition. We first collected 207 GenBank accessions containing either part or all of the reported PAI loci. In sequenced genomes, strips of PAI-homologs were defined based on the proximity of the homologs of genes in the same PAI accession. An algorithm reminiscent of sequence-assembly procedure was then devised to merge overlapping or adjacent genomic strips into a large genomic region. Among the defined genomic regions, PAI-like regions were identified by the presence of homolog(s) of virulence genes. Also, GIs were postulated by calculating G+C content anomalies and codon usage bias. Of 148 prokaryotic genomes examined, 23 pathogenic and 6 non-pathogenic bacteria contained 77 candidate PAIs that partly or entirely overlap GIs.

Conclusion: Supporting the validity of our method, included in the list of candidate PAIs were thirty four PAIs previously identified from genome sequencing papers. Furthermore, in some instances, our method was able to detect entire PAIs for those only partial sequences are available. Our method was proven to be an efficient method for demarcating the potential PAIs in our study. Also, the function(s) and origin(s) of a candidate PAI can be inferred by investigating the PAI queries comprising it. Identification and analysis of potential PAIs in prokaryotic genomes will broaden our knowledge on the structure and properties of PAIs and the evolution of bacterial pathogenesis.

Figure 1

Flow chart of the algorithm.

Figure 2

Projection of PAI-like regions in their G+C contents and length-proportion of horizontally transferred genes. Projection of PAI-like regions which overlap genomic islands (cPAI) and those which do not overlap genomic islands (nPAI) in their G+C contents (X axis) and length-proportion of horizontally transferred genes (Y axis). Each symbols denotes follows; cPAI (plus sign), nPAI (minus sign), cPAI and nPAI matching to a PAI identified from the genome sequencing paper (circle and triangle, respectively)

Figure 3

Example of a PAI-like region and a cPAI in genome sequences. 48.5-kb of PAI I_CFT073 from E. coli CFT073 was detected by merging genomic strips similar to known PAI loci (yellow strip) including partial sequence of PAI I_CFT073. The genomic region contains homologs of the virulence genes on the known PAIs (red arrow) and genomic island (grey bar). Therefore, this PAI-like region is considered as a cPAI. Red and orange arrows in yellow strips denote virulence and putative virulence gene, respectively. Numbers on the yellow strips indicate parts of the PAI loci homologous to the genomic strips: 1. PAI I₅₃₆ (accession number: AJ488511, host strain: E. coli 536); 2. PAI II₅₃₆ (AJ494981, E. coli 536); 3. PAI III₅₃₆ (X16664, E. coli 536); 4. LEE (AJ278144, E. coli 4797/97); 5 and 6. LEE (AF071034, E. coli O157:H7 EDL933); 7 and 8. PAI II_CFT073 (AF447814, E. coli CFT073); 9. PAI I_CFT073 (AF081284, E. coli CFT073); 10. PAI I_CFT073 (AF081285, E. coli CFT073). Note that accessions of PAI II_CFT073 that were included in the query set are partial sequence of the PAI. Some boxes are joined by a line for saving the space of the figure.

Figure 4

Distribution of genomic regions homologous to the PAIs from enteropathogenic bacteria. According to each PAI, left bar denotes the number of genomes containing at least one cPAI. Right hatched bar delineates the number of genomes containing at least one PAI-like region. Different colors represent the number of genomes of different taxon – Enterobacteriales (black), Proteobacteria except Enterobacteriales (red), and phylums except Proteobacteria (green). The demonstrated PAIs are PAI I,II,III₅₃₆ in uropathogenic E. coli 536, PAI II_CFT073 in uropathogenic E. coli CFT073, LEE in enterohemorrhagic E. coli O157, SPI-2 in S. typhimurium, SHI-2 and SRL in S. flexneri, HPI in Y. enterocolitica, and TTSS locus in Photorhabdus lumniescens.