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Background  Genomic 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.    Results  In 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.    Conclusions  This 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 material  The online version of this article (doi:10.1186/s12866-017-0986-6) contains supplementary material, which is available to authorized users.

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