It sounds as if your microbes are culturable. If so, perhaps the easiest screen will be to grow them in replica 96-well plates, and challenge one or more replicates with a nitro-prodrug antibiotic such as metronidazole, to identify sensitive strains that can activate metronidazole by nitro-reduction. Preliminary tests should help you identify the ideal concentration for use - I'd suggest trying three replicates, one unchallenged, one challenged with about 75 uM metronidazole, and one challenged with 750 uM metronidazole.

Hope this helps - David