We have all had to answer questions about why, if God's so good, there's harmful x, y, and z. We have to acknowledge first that what God created was good, that humans and every other thing on earth and in the sky were to live in a symbiotic relationship. Second, we have to point to our rebellion that caused the fall of everything, including the amoebas, ticks, and roaches.
Please take a moment and view the picture of entamoeba histolytica at the link above. Then thank God for His creation and giving us the ability to see microbes like entamoeba histolytica. Finally, pray that researchers come up with medication to ameliorate said entamoeba histolytica.