I had a similar error when using the MySQL node last year (2021).
Are you using the latest version as @dceejay has done a lot of work improving this node, in fact there was an update a week ago.
One of my problems was the number of dB connections. I found when I reduced the number of connections the node behaved much better.
I'm also using this flow to perform a 'keep database alive' every 15-minutes.
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