a couple of thoughts (for what they are worth)
> you show some beneficial e-coli, which is good. benefical e-coli (remember there are 1000's of species of ecoli - many of them are good - ) but beneficial ecoli is sort of the master species of bacteria colonizing the gut. According to many it holds the framework for population of other beneficial pro biotic species. It also has some killing ability of bad bacteria.
> e histolytica is a nasty little protozoa.
protozoas (e.g. histolytica) like to eat bacteria in the gut, so I would think that clearing the histolytica would be primary before introducting any probiotic into the system. You may be forced to do some rx's designed for eradication These are typically short term (Flagyl is used for 7-10days).
As far as negatives on the other parasites, this could be a false negative. In that stool sampling is hit or miss when diagnosing parasites. But I would go off the testing and treat the protozoa infection first then go after the nasty bacteria. The bacteria could be killed off using some very good probiotics like Ohhira's or Jordan Rubins -- I would also take a look at Jarrow EPS. Adding some fresh garlic w/ enteric coated Oil of Oregano might work good and adding some Neem would be an extra kick.
You could also try some tonifying herbals or programs to strengthen the intestinal environment. Colostrum comes to mind as one option.