If you plan to do it for RNA-seq, and know the bacterial genome, no worries - extract everything and your bioinformaticians will map the reads to both, the bacteria and the host genome, perhaps "subtracting" and "overlapping" the alignment sets. I happened to do it for small parazites of animals' intestines... 

If you ask for a lab technique.. may be hard, I guess :|

That’s true, the RNA splicing and modification is somewhat unique for eukaryotes. So don’t worry extract total RNA by using TRI reagent or any other reagent and proceed for further step. Using Bioinformatics tools and PCR u can amplify and quantify your desired gene of interest.

Thank you all!!