I think you can just use the TIMEDIFF function. From the manual
TIMEDIFF(expr,expr2)
TIMEDIFF() returns the time between the start time expr and the end time expr2. expr and expr2 are time or date-and-time expressions, but both must be of the same type.
mysql> SELECT TIMEDIFF('2000:01:01 00:00:00',
-> '2000:01:01 00:00:00.000001');
-> '-00:00:00.000001'
mysql> SELECT TIMEDIFF('1997-12-31 23:59:59.000001',
-> '1997-12-30 01:01:01.000002');
-> '46:58:57.999999'