Does a fly pick up most of his bacteria from things he lands on? Or is it a carryover from his maggot days?
IANAE* but I would imagine most flies go through their entire life cycle without picking up any harmful bacteria at all. Lifecycles are too short.
I would also guess that bacteria picked up in pupae (if that is the correct term) would harm the fly.
So, in my inexpert opinion, I think adult flies pick up their bacteria as they go about their short-lived daily business.
* I Am Not An Etymologist
Adult flies like spoiled food as much as maggots do. I doubt bacteria from whatever the maggot feasted on plays much of a role in a fly’s “vectoring” beyond the first couple of days after leaving the pupae. Admittedly that is a significant fraction of a fly’s life.
Or even an Entomologist? 
Both of them, of course, know how to tell the difference between a clover and a plover.
Oops! Maggots in my brain, I suppose.
There are more than 150,000 species in the the order Diptera (flies). So it would very much depend on what species of fly you were referring to.
‘Harmful’ in terms of bacteria is pretty much like ‘weed’ in terms of gardening. Flies have a microbiome - gut bacteria and such - those bacteria can be harmful to humans, for example if they get into the top end of our digestive system in significant population, or take hold in a wound, but that’s also true of the bacteria of our very own microbiome.
Black soldier flies are considered “clean” and the larvae feed on decaying food waste. These are the ones you want to see in your compost bin. They don’t show any interest in feces or like some house flies, or much interest in your current meal.
I have been looking into soldier flies larva as a stuffing for sausage that could be fed to pets