I’m not too sure if it covers table changes but MySQL comes with a slow log tool which tells you what queries are causing performance issues and if need be help optimize query requests itself, indexing even though is painstaking is perhaps the best way to fix the issue in the long run but to track down the slow queries in the first place and mitigate against them individually I’d use slow log.
https://dev.mysql.com/doc/refman/5.7/en/slow-query-log.html