The most straightforward solution comes if we are using a cloud DBaaS solution. In the example of MongoDB Inc's own MongoDB Atlas, we can manage backups from the GUI.

If we host MongoDB in our own servers, we can then use MongoDB Inc's MongoDB Cloud Manager (former MMS tool). Cloud Manager is a SaaS that we can point to our own servers to monitor and backup our data. It uses the same oplog that replication uses and can backup both replica sets and sharded clusters.

If we don't want (or can't for security reasons) to point our servers to an external SaaS service, we can use Cloud Manager's functionality on-premises using MongoDB Ops Manager. To get MongoDB Ops Manager we need to get a subscription to the Enterprise Advanced Edition of MongoDB for our cluster.