It's likely that either your connection has been killed (e.g. by wait_timeout or another thread issuing a KILL command), the server has crashed or you've violated the mysql protocol in some way.
The latter is likely to be a bug in PDO, which is extremely likely if you're using server-side prepared statements or multi-results (hint: Don't)
A server crash will need to be investigated; look at the server logs.
If you still don't know what's going on, use a network packet dumper (e.g. tcpdump) to dump out the contents of the connection.
You can also enable the general query log - but do it very carefully in production.