I read this from their site.
"
The first engine (E1) is a creation of Emsisoft’s, the second one (E2) has been in use since we released Emsisoft Anti-Malware 7.0 and Emergency Kit 3.0 and comes from BitDefender. BitDefender is known for its very good detection rate as well as displaying few false alerts, which is why we use this third-party engine "