Are you using this plugin: https://github.com/sebest/collectd-mongodb
Looking at the code, it doesn't seems to be possible to monitor more
than one database. Which is strange, because it's implemented as an
object, so it would be trivial to create one instance per database, but
the config code doesn't do that. I'd suggest filing a ticket on their
github page.
Until that's fixed you could use a bad workaround:
Create a few copies of that Python file with different names and load
and configure every file individually. Not great, but it should work.
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