you can use  the test for amylase production gene by PCR

The test very best for gene detection , you will found gene in bacteria . It's ability starch hydrolysis  

There are several Xanthomonas species responsible for tomato and pepper bacterial spot, some hydrolyzing starch and some not. The best way of achieving a reliable diagnostic would be to PCR amplify several housekeeping genes and have these double strand Sanger sequenced. For more info you can read :

Hamza, A. A., Robène-Soustrade, I., Jouen, E., Lefeuvre, P., Chiroleu, F., Fischer-Le Saux, M., Gagnevin, L., and Pruvost, O. 2012. Multilocus sequence analysis- and amplified fragment length polymorphism-based characterization of xanthomonads associated with bacterial spot of tomato and pepper and their relatedness to Xanthomonas species. Syst. Appl. Microbiol. 35:183-190.

Serap,  look at original paper Jones, Jeffrey B., et al. "Reclassification of the xanthomonads associated with bacterial spot disease of tomato and pepper." Systematic and applied microbiology 27.6 (2004): 755-762. -

in general: Xanthomonas vesicatoria, X. perforans, X. arboricola  and X. raphani (last two are rare but present in some regions) can utilize starch, X. euvesicatoria and X. gardneri - cannot. To know the taxonomic position of your strains you can use MLST as Oliver said. 

thank you very much for your suggesting. I rewieved all the articles. I suppose, as you said, the best way of the diagnostic, sequencing.

If you need some guidance or if you want to compare your sequences to those currently in our database, you are welcome. Let me know.