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If whooping cough is suggested as a diagnosis it is natural to ask how it can be proved or disproved.

There are now several ways, but which is best depends on where you live, because different laboratories are likely to do different tests. If you live in the United Kingdom a saliva test can now be done by the NHS.

The best, but most difficult way is to try to detect the causative organism (Bordetella pertussis) in the back of the nose. This usually involves passing a swab on a wire through a nostril to the back of the throat and sending it to a medical lab to culture the material. This may take 5 to 7 days.  If Bordetella pertussis or parapertussis grows this is usually taken as proof that it is whooping cough. Parapertussis also causes whooping cough. It is much less common, I would guess less than 1 in 100 cases. It may be less severe because it does not produce pertussis toxin I am told. Most blood tests look for pertussis toxin antibodies so presumably will not detect Bordetella parapertussis.

Unfortunately the organisms is delicate, killed easily by many antibiotics and has often been eliminated from the body by natural defences by the time the diagnosis is suspected. It is easiest to find it in the first 2 weeks but very unlikely after 3 weeks. But the patient has often had it for 3 weeks before whooping cough is suspected.  So it is unusual to get a positive culture in whooping cough. In other words, if a swab is negative, the patient can still have whooping cough.

A better and more modern way of detecting the organism is by detecting its unique DNA pattern by means of polymerase chain reaction (PCR). This also involves getting secretions from the back of the nose and specialist laboratory testing.  A result can be obtained in 24 to 48 hours.

The test depends on the organism being present, which it may no longer be, but since it detects minute quantities of genetic material it is more likely to be positive than culture in cases of whooping cough.

Antibody tests are done by some laboratories on blood samples taken after several weeks of illness. By looking at IgG and IgA antibodies to fimbria, pertussis toxin and filamentous haemagglutinin, it is possible to say whether it is likely the patient has had whooping cough.  It is a highly specialized test and you may have difficulty finding a lab able to do it. There are several variations on this theme. Sometimes one specimen about 2 weeks into the illness is required, sometimes two specimens some weeks apart. Some labs do less satisfactory immunological tests.  These tests are not always accurate. They sometimes say the patient has had whooping cough when they haven't, and sometimes the other way round. You need to know the reliability of a test before accepting the answer as true.

In the United Kingdom since 2002, NHS labs (via the PHLS) can do anti-pertussis toxin ELISA IgG on a single sample at least 2 weeks into the illness and give a highly reliable diagnostic result. They can also arrange PCR in special (usually hospitalised) cases. A big step forward was made in 2007 when the Health Protection Agency made oral fluid antibody testing available. The test is based on measuring anti-pertussis toxin IgG levels like the blood test. It can be done as soon as 2 weeks into the coughing illness. The purpose of the test is to provide verification of notified whooping cough. The kits for testing are the same as used for measles and rubella and will be supplied by any NHS laboratory. It will confirm about 80% of cases. The test cannot measure immunity and is invalid if the person has had immunization within the previous year

The bottom line is that in practice the diagnosis has usually to be made on symptoms and course of the illness alone, unless blood or oral fluid antibody tests can be done. 

Todar's online bacteriology chapter on pertussis

Link to information about oral fluid testing in the United Kingdom