Did your little guy have a fever? I was just curious? Because they gave him antibiotics and that is for something bacterial. However, if this is a virus it will not have any affect . My Suzi use to have a cough that sounded likt she was choking. She does not hardly do that anymore, and it cleared up on its own. When he is have a coughing spell, rub his throat. This will sooth it, and maybe help .
If he still is not feeling better I'd defiantely talk to the vet again.