:)Sorted! 
Step 1:
Create a system DSN on the target machine
Making sure you have changed the default database to your target
Make sure that authentication mode is integrated windows and your database is configured to use this authentication method
Step 2:
Edit your target Agent config file, adding the following
SubAgent = odbcquery.nsm
*ODBC
Query = SQL.MySQLQuery:YOURDSNNAME:SELECT Count(*) FROM YourTable:60
Step 3:
Push the config to the agent
Check that ODBC.* data collection items are now available
Step 4:
Set up a Data Collection Item for the target machine of type ODBC.QueryResult where the parameter is the name you used above. In my case SQL.MySQLQuery
If you get problems try the ODBC.QueryStatusText as this should return a string telling what your problem might be.
Note: I tried to get SQLServer authentication working by defining the DSN explicitly in the YOURDSNNAME section but could not get this to work. It should be possible to use something like DRIVER={SQL Server};SERVER=hrserver;UID=Smith;PWD=Sesame so that an explicit DSN on the target should not be required.
If anyone gets this working please, please, please let me know.