Elastic APM does not instrument the MongoDB process directly, instead queries are traced from within the application they are made. So if you're running a Node.js application that is talking to your MongoDB database, you install the Elastic APM Node.js Agent into your Node.js app.
That being said, you should also consider collecting the metrics from MongoDB using the MongoDB Metricbeat module and its logs using either Filebeat or Logstash. But ingesting metrics and logs is not a replacement for APM data, it's just a compliment. Together Metrics, Logs, and APM data gives the full picture.
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