Check mysql domain that is using resources
You could check your slow query log. If it's CPU intensive, it may be some heavy hitting queries that take a while to process. Check to make sure your slow query threshold is set to a reasonable amount of time and then look at your log.

When your server is in the middle of a CPU spike, log in and do show full processlist to look at the queries that are running at that moment. Is there a higher number of queries than normal? Is there a high number of slow queries than normal?

You could use show open tables which will show you what's in the table cache, but it doesn't necessarily tell you what is using up all the resources, but rather which databases/tables are the most active.