Persistent Connections have been a mixed bag. They can give you a significant performance boost by caching (pooling) connections although MySQL is already comparatively fast at establishing connections. However,connections are stored "as-is" in the cache. They are not "cleaned up".

The ext/mysqli driver takes care of this and a few other problems surrounding the persistent connections by cleaning up things like rolling back active transactions, unlocking tables, closing prepared statements and closing handlers. The trick is in a call to the C-API function mysql_change_user() (= COM_CHANGE_USER).