Example for searching just one user with a specific id, you should do:

$options = ['limit' => 1];
$filter = ['_id' => new \\MongoDB\\BSON\\ObjectID('578ff7c3648c940e008b457a')];
$query = new \\MongoDB\\Driver\\Query($filter, $options);

$cursor = $manager->executeQuery('database_name.collection_name', $query);
$cursorArray = $cursor->toArray();
if(isset($cursorArray[0])) {
    var_dump($cursorArray[0]);
}