Could be any protozoa, there are many pathogenic ones and there are genotypes of each which means these are mutant strains, this is well known in the b. hominis strain.
Some of these will be quite resistant to Flagyl etc. The difficult strains will require a combination as listed on badbugs.org. Typically you will need a triple cocktail that includes lumicidal drugs such as Diloxinide Furoate etc. in combination with Secnidazole and either Nitazoxanide or Bactrim (2 Antibiotics ).
Proper testing can help identify what species you have so the correct protocol can be given.