Drush custom command not found in context of running --root option Drush 8. Have the custom module with the custom command.

Call drush custom-command works as expected.

Call drush --root=sites/subsite custom-command thiggers the error:

The drush command 'custom-command' could not be found.

How to call the drush command in the context of the subsite?
To call a command on a certain instance of a multisite you are supposed to pass the -l option. Also be sure that the custom module that provides the custom command is enabled on the multisite instance you are trying to call that command on.

$ drush custom-command -l subsite