You can get a reference to the MongoClient instance that is created by Meteor’s mongo package and then call the transaction functions (e.g., startSession and commitTransaction) using this client:
import { MongoInternals } from "meteor/mongo";
const { client } = MongoInternals.defaultRemoteCollectionDriver().mongo;
const session = client.startSession();
...
I don’t have a complete example at the moment but you could check out this test case, which updates two documents atomically using the transaction APIs.