Identification and analysis of genomic islands in Burkholderia cenocepacia AU 1054 with emphasis on pathogenicity islands

Abstract

BackgroundGenomic islands (GIs) are genomic regions that reveal evidence of horizontal DNA transfer. They can code for many functions and may augment a bacterium’s adaptation to its host or environment. GIs have been identified in strain J2315 of Burkholderia cenocepacia, whereas in strain AU 1054 there has been no published works on such regions according to our text mining and keyword search in Medline.ResultsIn this study, we identified 21 GIs in AU 1054 by combining two computational tools. Feature analyses suggested that the predictions are highly reliable and hence illustrated the advantage of joint predictions by two independent methods. Based on putative virulence factors, four GIs were further identified as pathogenicity islands (PAIs). Through experiments of gene deletion mutants in live bacteria, two putative PAIs were confirmed, and the virulence factors involved were identified as lipA and copR. The importance of the genes lipA (from PAI 1) and copR (from PAI 2) for bacterial invasion and replication indicates that they are required for the invasive properties of B. cenocepacia and may function as virulence determinants for bacterial pathogenesis and host infection.ConclusionsThis approach of in silico prediction of GIs and subsequent identification of potential virulence factors in the putative island regions with final validation using wet experiments could be used as an effective strategy to rapidly discover novel virulence factors in other bacterial species and strains.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-017-0986-6) contains supplementary material, which is available to authorized users.

Comparative Evolutionary Patterns of Burkholderia cenocepacia and B. multivorans During Chronic Co-infection of a Cystic Fibrosis Patient Lung

“…The presence of Putative GIs was also predicted using IslandViewer 4 ( Bertelli et al, 2017 ), unique GIs were manually confirmed and curated in the genome sequences of B. cenocepacia IST439 and B. multivorans IST419. For this confirmation, it was considered that they are unique continuous DNA regions absent in the available genome sequences of the published epidemic clones and longer than 10 kbp, flanked, at both sides, by homologous regions (especially those inserted immediately downstream of tRNA), and have lower (or higher) GC content compared with the rest of the genome ( Guo et al, 2017 ; Nunvar et al, 2017 ). The absence of DNA regions homologous to these unique GIs in the genomes of epidemic clones – B. cenocepacia ET12 and ST32 ( Holden et al, 2009 ; Nunvar et al, 2017 ) and B. multivorans ATCC_17616 and ATCC_BAA-247 ( Komatsu et al, 2003 ; Johnson et al, 2015 ; Johnson et al, 2016 ) – was confirmed and visualized by Progressive MAUVE whole genome pairwise alignment and ACT/Artemis ( Carver et al, 2005 ; Darling et al, 2010 ).…”

Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status

“…3 and 5). Specifically, BCC08 and BCC05 should represent B. cenocepacia genomovars IIIA and IIIB, respectively [23,56,57]. The dDDH and Fig.…”

Trehalose 6‐phosphate phosphatases ofPseudomonas aeruginosa

“…are opportunistic bacteria and include the human pathogens Burkholderia cepacia (causing pulmonary infections) and Burkholderia pseudomallei (causing melioidosis). Intriguingly, both genera make use of genomic islands for pathogenicity (67), are susceptible to the same phage-transfer mechanisms (68), and are each capable of influencing gene expression in the other (69,70). Moreover, Burkholderia spp.…”