There is video evidence of the "indecent assault" that he is being charged with. If he tests positive for the STD and she now has it, yes there's a defense argument that could be made, but barring any evidence of a prior relationship between her and the janitor (which seems unlikely at this point), it would fail and he would also be convicted of the aggravated assault with a deadly weapon.
Genome evidence probably not necessary with evidence or with a distinct lack of evidence of a prior relationship between the two.
Further, it probably doesn't matter if she got the STD from him or not. There is clear evidence that "aggravated assault with a deadly weapon" occurred, as having video that shows he put his STD-infected genitals in contact with her water bottle is already proof that the assault with a deadly weapon occurred, whether or not the assault was successful.
If I attack you with a knife but don't manage to cut you, did assault with a deadly weapon not occur?
The prosecution rests, your honor.