Here's another good rule about using MySQL in your application:
Never let your application access the MySQL server with a user that has SUPER privileges (at least unless there's a VERY good reason to do it).
There may be more reasons for that but one is that it might stop your root user from accessing the server if all allowed connections are being used (the "Too many connections" error).
Here's what the manual says:
"mysqld actually allows max_connections+1 clients to connect. The extra connection is reserved for use by accounts that have the SUPER privilege. By granting the SUPER privilege to administrators and not to normal users (who should not need it), an administrator can connect to the server and use SHOW PROCESSLIST to diagnose problems even if the maximum number of unprivileged clients are connected."
But if your application user also has SUPER privileges, this might have used that one extra connection that should be reserved for that purpose.