OMG, mgt-commerce??
i would not be so sure that they know something about system management or even magento optimization,
they are not installed security patches to the shops of its customers, for God's sake, they have not even installed security patches to their own shop.
probably busy counting your money...
you better check your shop now, and scan for any malware.
what about mysql - we have to see your mysql config file and memory available for the database and database size,
you also have to monitor queries with mytop.
cache, load balance or RDS will not help. but what you need to check if you have installed "Asynchronous Re-Index" extension, this is 95% solution to all mysql issues in magento.
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