What you do is called a projection. That's when you return only a scalar value that belongs to one entity. You can do this with JPA. See scalar value.
I think in this case, omitting the entity type altogether is possible:
Query query = em.createNativeQuery( "select id from users where username = ?");
query.setParameter(1, "lt");
BigDecimal val = (BigDecimal) query.getSingleResult();
Example taken from here.