Hi I'm not sure using acetonitrile would be great. If you are looking to see if your sample is releasing a water soluble bactericidal substance you could try using the zone of inhibition test:
Or if you are looking at anti-adhesion properties see: Yuehuei H An, Richard J Friedman Laboratory methods for studies of bacterial adhesion Journal of Microbiological Methods, Volume 30, Issue 2, 1 August 1997, Pages 141-152
Try different solvents, and make sure they do not interfere with bacterial growth. Diluted DMSO (5-10%) does not inhibit most bacterial strains I tested. If your compound is solubilized by DMSO then you can dilute with water and see if the compound is still in solution.
We usually prepare 100-fold higher concentration in solvent and then we dilute it 1:100 in cultivation medium (or other suitable diluent harmless to the organism tested) so that you get 1% of the solvent in final solution. You can try higher solvent concentration if the solubility is pure but you should check the antimicrobial effect of the solvent at the concentration used to avoid false positive results.
If the compound s soluble in acetonitrile then dissolve it in acetonitrile and do the well diffusion. Put acetonitrile as a control on another well and incubaye. After incubation measure the zone of clearence for both acetonitrile and acetonitrile+ compound. Minus the zone of clearence of acetonitrile from the mixture zone and if this compound has any antibacterial activity u will get a positive number. Since well diffusion is a qualitative test dont worry for the numerical values of zone size.
you can re diluted with acetonitrile then take your concentration and inoculated into sterile disc and then perform antimicrobial tests. try with disc diffusion method.