db={CollectionA:[{"_id":1,"operation":"SEC","name":"x"},{"_id":2,"operation":"SEC","name":"y"},{"_id":3,"operation":"SEC","name":"z"}],CollectionB:[{"_id":1,"operation":"SEC","name":"x"},{"_id":2,"operation":"SEC","name":"y"},]}

db.CollectionA.aggregate([{$lookup:{from:"CollectionB",let:{root:"$$ROOT"},pipeline:[{$match:{$expr:{$eq:["$$ROOT","$$root"]}}}],as:"collectionB"}},{$match:{"collectionB.0":{$exists:false}}},{$unset:"collectionB"}])