As mentioned before, whooping cough is a bacterial infection caused by Bordetella pertussis. Infection occurs in the lining of the airways, principally in the trachea (the windpipe) as well as the bronchi (airways that branch off from the trachea to the lungs.s mentioned before, whooping cough is a bacterial infection caused by Bordetella pertussis. Infection occurs in the lining of the airways, principally in the trachea (the windpipe) as well as the bronchi (airways that branch off from the trachea to the lungs.