Thank you for your query.
It is very surprising to find E. Histolytica in a 5 month child. This can be due to unhygienic feeding and/or water and this can be the main reason why the diarrhoea
is not getting controlled. Though the medicines are appropriate but proper hygiene is more important.
As you are saying the that child has depressed fontanelle and sunken eyes, I will suggest that you get him re-evaluated by your doctor and, if required, get him admitted for proper care.
I hope I have responded to your query satisfactorily.
Wishing your baby an early recovery.