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After some more debugging I think it isn't tied to prepared statements but to connection pool. Looks like connections that overflow the pool are not closed properly and mysql logs it as aborted connection.
On second execution of a prepared statement the connection gets aborted, mysql increases 'Aborted clients' status variable and logs:
180816 13:39:30 [Warning] Aborted connection 3434103 to db: 'xxx' user: 'xxx' host: 'x.x.x.x' (Got an error reading communication packets).
Tested on MariaDB 5.5 and latest 10.3
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