We setup APM agent in our nodejs application. It captures requests even made by other npm too (which is very good), but it does not capture any queries to mysql.
We are using squelize as ORM to mysql.
Thanks for trying out Elastic APM 
We don't directly instrument sequelize. Instead we instrument the specific database driver installed as a peer dependency to sequelize.
Are you using the mysql package or the mysql2 package?
You can also see a list of all the database modules we currently support here: https://www.elastic.co/guide/en/apm/agent/nodejs/current/compatibility.html#compatibility-tracing-and-instrumentation
Sequelize uses mysql2 npm.
We currently do not support automatic instrumentation of the mysql2 module. But we're actively working on it. You can follow the progress in PR#298. Once that's released, you should see mysql spans.
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