Respiratory Pathogens Panel
Not everyone with symptoms of a respiratory infection (e.g., fever, aches, sore throat and cough) is tested. This panel is primarily performed when you are seriously ill, hospitalized, and/or at an increased risk for a severe infection with complications or multiple infections (co-infections).
A sample is collected from the back of your nose and throat (nasopharyngeal swab). This is done by having you tip your head back, then a swab is gently inserted through a nostril until resistance is met (about 1 to 2 inches), then rotated several times and withdrawn. This may tickle a bit and cause the eyes to tear. Alternatively, a nasal wash or aspirate may be collected. A syringe is used to push a small amount of sterile saline into the nose, then gentle suction is applied (for the aspirate) or the resulting fluid is collected into a cup (for a wash).
A variety of viruses and some bacteria can cause infections of the respiratory tract. These disease-causing microbes are called pathogens. The respiratory pathogens panel tests for the presence of multiple disease-causing microbes in a single respiratory sample.
While a wide variety of viruses and bacteria can cause respiratory infections, the list of common ones is much smaller. A healthcare practitioner may have an idea about the cause based upon the season, your signs and symptoms and medical history, and in some cases recent travel, but will not be able to positively identify the microbe without testing.
The respiratory pathogen panel is a molecular test that detects the genetic material (RNA or DNA) of some of the more common pathogens. It can identify co-infections (more than one microbe causing infection) and identify microbes that might be missed with traditional testing, such as culture. Some panels can also identify subtypes or strains of microbes. Results of a respiratory pathogen panel may be available within a few hours, compared to a few days with some traditional testing.
The number and type of microbes tested depends on the specific panel used. Some panels are limited to testing for a few types of viruses that are the most common causes of respiratory infections, while other panels are more comprehensive and test for a wider variety of respiratory viruses and bacteria in a single sample.
Examples of some of the microbes that might be tested include (these can vary from one panel to another):
- Influenza A and B (flu)
- Respiratory syncytial virus (RSV)
- Parainfluenza virus
- Human metapneumovirus
- Bordetella pertussis (whooping cough) and Bordetella parapertussis
- Chlamydia pneumoniae
- Mycoplasma pneumoniae
Respiratory infections are common and can be very contagious, spreading from person to person through coughing, sneezing, and contact with contaminated surfaces. People may be infectious before their symptoms begin to several days after they become sick.
Some examples of common respiratory infections include:
- Common colds—viral infections that cause sneezing, coughing, sore throat and runny or stuffy nose
- Bronchitis—infections can cause inflammation of the airways leading to the lungs (bronchial tubes) with symptoms such as coughing, wheezing and shortness of breath
- Croup—an infection of the windpipe and airways leading to the lungs that causes hoarseness and a cough that sounds like a seal or dog
- Pneumonia—infection of the lower respiratory tract that can cause coughing, fever, chills, muscle aches and shortness of breath
Viral respiratory infections caused by influenza A or B (the flu) and respiratory syncytial virus (RSV) are largely seasonal in the United States, with the cold and flu season running from late fall through early spring. During each season there are multiple strains of influenza and a variety of other viruses causing very similar "flu-like" symptoms, making it difficult to diagnose the cause of infection based on symptoms and medical history alone. Some viruses and bacteria can cause respiratory infections and complications year-round.
Respiratory infections can cause a spectrum of illness, from mild to severe, and can sometimes be fatal. All ages can be affected, but the highest infection rates and the most severe complications are typically seen in the very young, in people with weakened (compromised) immune systems, and especially in the elderly. People in close contact with one another or in confined spaces, such as hospitals, nursing homes, schools, and the military, are also at increased risk of infection.
The number of people with respiratory infections varies from year to year. For instance, according to the Centers for Disease Control and Prevention (CDC):
- Influenza: the number of cases of influenza illness during the 2017-2018 season was the highest it had been since 2009. The CDC estimates that 48.8 million people became sick with influenza, about 959,000 were hospitalized, and 79,400 died.
- RSV: on average there are 2.1 million outpatient visits and 57,527 hospitalizations in children under the age of 5, and 177,000 hospitalizations and 14,000 deaths in adults older than the age of 65.
- Common cold: millions of cases of the common cold occur each year (typically caused by rhinoviruses, but also by other viruses included in the respiratory pathogen panel).
How is the test used?
Respiratory pathogens panels may be used to help diagnose the cause of your respiratory infection and help guide treatment. They are used primarily for people who are seriously ill, hospitalized, and/or are at an increased risk for a severe infection with complications or multiple infections at the same time (co-infection).
Many individuals with respiratory infections are never tested because:
- Many respiratory infections in otherwise healthy people resolve with no specific treatment and with only supportive care (e.g., getting plenty of rest and drinking plenty of fluids).
- When it is strongly suspected you have the flu (it is flu season and the flu is widespread in your community), your healthcare practitioner may make the diagnosis based on your symptoms and treat you with an antiviral medication.
- The panels can diagnose the flu and rule out other illnesses. This can reduce the chances of people using unnecessary antibiotics (which are not effective for viral infections), while increasing the chances that they will receive anti-viral therapy early in the illness, when it is most effective.
- Some panels can diagnose infections caused by bacteria that may require treatment with antibiotics.
Respiratory pathogen panels are not used to test all respiratory infections or symptomatic patients. Other types of tests include:
- Individual molecular tests for influenza and respiratory syncytial virus (RSV) and other respiratory viruses and bacteria may be performed at the point of care, such as a healthcare practitioner's office or medical clinic.
- Rapid antigen tests for influenza and RSV may also be at the point of care during cold and flu season, even though they can be less sensitive than newer molecular tests.
Since the respiratory pathogen panels are relatively new and relatively expensive to perform, laboratories and healthcare providers are still in the process of determining how to use them to provide the optimum care for patients. Additional tests may be done if a microbe is not identified by the panel and/or if there is a suspicion of a microbe other than those included in the panel.
When is it ordered?
A respiratory pathogen panel may be ordered when you are seriously ill or at increased risk of complications and have signs and symptoms associated with an upper respiratory infection, especially if they are prolonged and do not resolve without treatment. Signs and symptoms may include:
- Coughing, sneezing
- Stuffy or runny nose
- Sore throat
- Weakness, fatigue
- Muscle aches
- Fever, chills
- Wheezing, difficulty breathing
- Low appetite
- In some cases, diarrhea and vomiting
What does the test result mean?
Results are typically interpreted in conjunction with your signs and symptoms and medical history.
A positive result means that the microbe detected is likely causing your signs and symptoms. If more than one result is positive, you may be infected with more than one microbe (co-infection). The following are some exceptions:
- The panels detect the presence of genetic material of the microbes and do not distinguish between dead and living ones. Sometimes, a positive result reflects the presence of dead microbes that are not the cause of infection.
- Sometimes, a positive test result for multiple microbes may mean that one of the microbes is in your respiratory tract but is not the cause of the current symptoms.
- Rarely, a result may be positive when the microbe is not present (false positive). Also, a result may be positive when a different microbe is present. Although uncommon, this can happen when the microbes are genetically similar.
A negative result means that the microbes tested were not detected and your signs and symptoms may be caused by a virus or bacterium not included in the panel or by another condition. The following are some exceptions:
- Viruses can be shed intermittently. This means that the number of viruses present in your respiratory sample can vary greatly during an infection. A negative result may mean that the microbe causing your infection was not present or not present in high enough numbers to be detected in the sample that was collected.
- It is also important that the sample is collected properly to pick up any microbes that might be present. The nasopharyngeal swab should touch the back of your nose and throat and may bring tears to your eyes when done correctly.
- Rarely, you may have a respiratory infection caused by one of the microbes, but the test does not detect it because the amount of viral or bacterial genetic material present in your sample was too small.
If results are negative and symptoms persist and/or if suspicion of an infection remains high, then other tests may be done to help establish a diagnosis.
Like a flu test or strep test, can this test be performed in my healthcare practitioner's office?
In general, no. It requires specialized equipment and expertise. It may be performed in a local laboratory if it is offered or may need to be sent to a reference laboratory. Individual molecular tests are, however, becoming increasingly available in some healthcare practitioners' offices.
What are some traditional tests for respiratory infections?
Traditional testing has included viral or bacterial cultures or testing for the viruses or bacteria one at a time (and sometimes needing multiple samples) using rapid tests and antigen tests. These tests are useful, but some bacteria can be hard to grow successfully in culture, and viral cultures are not routinely available in most clinical laboratories. Many of these tests are also labor-intensive, and it may take 2-3 days or more for results. The rapid tests and antigen tests are quicker, but they may not be as good at detecting infections as molecular methods. Many laboratories are adopting molecular tests that detect genetic material of microbes as the preferred way to diagnose a respiratory infection.
What other lab tests might be done?
Since there are many causes of respiratory infections, and respiratory pathogen panels test for upper respiratory infections, they may be used in conjunction with other tests, such as a bacterial sputum culture, Gram stain, or sometimes a viral culture to help confirm a diagnosis and guide treatment decisions.
Why would my healthcare provider order additional tests?
Additional testing may be done to confirm a positive result using another method, to perform susceptibility testing when the infection is caused by bacteria, or because the cause of your symptoms has not yet been identified.
Can I test negative and still have a respiratory infection?
Yes. You can have an infection but a negative result if:
- The test does not detect the virus or bacterial strain causing your infection
- There was not enough genetic material in the sample to allow it to be detected
- The microbe is a new strain that the test cannot reliably detect
- Your sample was not properly collected
How can I prevent a respiratory infection?
Not every respiratory infection can be prevented, but you can take precautions, such as avoiding close contact with sick people, washing your hands thoroughly and often with soap and water or using a hand sanitizer with at least 60% alcohol, and cleaning and disinfecting surfaces that are touched often and by many people, such as door knobs, counters, toys, etc.
To help prevent the flu, the Centers for Disease Control and Prevention (CDC) recommends annual influenza vaccination for everyone 6 months and older. For more information from the CDC, see Related Content below.
Is there anything else I should know?
When a healthcare practitioner has a strong suspicion as to the cause of an infection, then a test for a specific microbe may be ordered instead of a panel. Some examples include: