With PHP and MySQL, if the MySQL is upgraded you may end up with this error on every request to the database from PHP. This error means the MySQL library in PHP is not compatible with the version of MySQL it is connecting to. So, the solution is that you have to upgrade your PHP version that is compatible with the MySQL client library version.
There is another method (not tested) for resolving this issue. Pull the mysqli.so file from a server with PHP compiled with MySQL 5.5 and replace it in the /usr/lib/php5/ directory. Now it should be able to connect to the MySQL.