Sandbox:Pertussis laboratory findings

# Overview
There are differences in the diagnostic needs of the clinical versus the public health setting. In the clinical setting, the goal is to optimize sensitivity while providing rapid results. This ensures rapid diagnosis and appropriate treatment to prevent further transmission. In the public health setting, a high degree of specificity is needed to avoid unnecessary and ineffective public health interventions.  Several types of laboratory tests are commonly used for the diagnosis of Bordetella pertussis. Culture is considered the gold standard because it is the only 100% specific method for identification. Other tests that can be performed include polymerase chain reaction (PCR) and serology.

# Laboratory Findings

## Nasopharyngeal Swab
Determining who has pertussis can be difficult. Whenever possible, a nasopharyngeal swab or aspirate should be obtained from all persons with suspected cases. A properly obtained nasopharyngeal swab or aspirate is essential for optimal results.
If culture is planned, once an nasopharyngeal swab has been collected it should be plated directly or placed into transport medium immediately. Nasopharyngeal aspirates should be dispensed and plated within 24 hours of collection. The same specimen can be used both for culture and polymerase chain reaction (PCR). With PCR, the most rapid test, the specimen should ideally be collected during the first three weeks of illness, but may provide accurate results for up to 4 weeks. Culture has better specificity, but takes up to seven days to get results back.

## Culture
Since culture has excellent specificity, it is particularly useful for confirming pertussis diagnosis when an outbreak is suspected. Many other respiratory pathogens have similar clinical symptoms to pertussis and co-infections do occur. Furthermore, obtaining isolates from culture allows for strain identification and antimicrobial resistance testing. Identifying which strains of Bordetella pertussis are causing disease is of public health importance. Culture is best done from nasopharyngeal specimens collected during the first 2 weeks of cough when viable bacteria are still present in the nasopharynx. The bacteria can be recovered from the patient only during the first three weeks of illness, rendering culturing useless after this period; therefore, sensitivity is decreased and the risk of false-negatives increases after the first 2 weeks.

## PCR
PCR is a rapid test and has excellent sensitivity. PCR tests vary in specificity, so obtaining culture confirmation of pertussis for at least one suspicious case is recommended any time there is suspicion of a pertussis outbreak. Results should be interpreted along with the clinical symptoms and epidemiological information. PCR should be tested from nasopharyngeal specimens taken at 0-3 weeks following cough onset, but may provide accurate results for up to 4 weeks. After the fourth week of cough, the amount of bacterial DNA rapidly diminishes, which increases the risk of obtaining falsely-negative results. PCR assay protocols that include multiple target sequences allow for speciation among Bordetella species. The high sensitivity of PCR increases the risk of false-positivity, but following some simple best practices can reduce the risk of obtaining inaccurate results.

## Serology
CDC and FDA have developed a serologic assay that has been extremely useful for confirming diagnosis, especially during suspected outbreaks. Many State Public Health Labs have included this assay as part of their testing regimen for pertussis. Commercially, there are several different serologic tests used in United States with unproven or unknown clinical accuracy. Generally, serologic tests are more useful for diagnosis in later phases of the disease. For the CDC single point serology, the optimal timing for specimen collection is 2 to 8 weeks following cough onset, when the antibody titers are at their highest; however, serology may be performed on specimens collected up to 12 weeks following cough onset. For most adults and adolescents, who often do not seek medical care until several weeks into their illness, serology is often used to determine whether antibody against pertussis toxin or another component of Bordetella pertussis is present at high levels in the blood of the patient.
Shown below is an image depicting the optimal timing for the different tests used for the diagnosis of pertussis.