What Causes Whooping Cough?

I have a daughter who is down syndrome. She has had alot of colds in the past and her airways shut down due to mucus plugging. She had whooping cough at around 14yrs old. She is now 25yrs old. 2 weeks ago she came down with cold like symptoms (mild fever, runny nose) they put her on antibiotic to stop her getting a chest infection. We have finished the antibiotics 5 days ago, but the mucas has built up again and she has a very croupy cough with lots of phlegm which is thick. It reminds me of when she had whooping cough. The doctor had taken a swab from the nose and has just told me its not whooping cough and it is probably a post viral cough. Can the results be wrong due to the time it was take. As my son had it when he was 5yrs old and my niece at the same time, my niece results came back a definite yes but my sons came back negative, but he did have it and it was more serve than my niece. So my question is can the results vary as to at what stage of the cough the test is taken to determine if it is whooping cough and can whooping cough reoccur Thanks Marie