You could do whole genome comparison to close relatives that are known to be non-pathogenic. Then concentrate on the regions and genes that differ.
(For example compare to as many close pathogenic and non-pathogenic relative strains as you can find and check which regions your strain shares with the pathogenic ones or no other strain. I have done this before, using Mauve.)
There are usually also some known pathways that influence pathogenicity. Check if they are complete (compared to bacteria that are known to have the genes and utilize the pathway) and functional.
Is your complete genome annotated? Else you should probably start with doing that.
In addition to the answers from skymningen and martinahansen, I think it would help you to specifically address the topic of pathogenicity and virulence as these are vague terms. A compound or protein that may infer pathogenicity in one organism may elicit a heightened immune response in another.
In other words, it's not strictly a homology issue, although this is an important part of it. I would use the comparative genomics and blat-based identification highlighted in other answers, but also you should consider gene expression, motifs in novel or putative pathogenicity genes, and promoters/enhancers to get at the complete picture.