I think whenever you apply any chemical compounds to plant leaves or to the soil, the effect on different organisms is going to be a mixed bag. Some may be inhibited, some may be increased, and for some there may be no significant effect. I haven't seen any evidence that Neem Oil could be called an actual bactericide although some products sold for human use may claim that is effective against some pathogenic bacteria.
I wouldn't be concerned with it in the mix with Actinovate. Serious bactericides like Copper based products, Bleach or Hydrogen Peroxide would be bad.
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