use of entityManager.createNativeQuery(query,foo.class)

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.

That doesn't work because the second parameter should be a mapped entity and of course Integer is not a persistent class (since it doesn't have the @Entity annotation on it).

for you you should do the following:

Query q = em.createNativeQuery("select id from users where username = :username");
q.setParameter("username", "lt");
List<BigDecimal> values = q.getResultList();

or if you want to use HQL you can do something like this:

Query q = em.createQuery("select new Integer(id) from users where username = :username");
q.setParameter("username", "lt");
List<Integer> values = q.getResultList();

Regards.