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Diagnosing Nontuberculous Mycobacterial Infections

Nontuberculous mycobacteria are a type of bacteria found in water and soil. These bacteria are typically harmless. However, when they enter the body, they can cause skin lesions, soft tissue infections, and serious lung problems. 

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NYU Langone doctors offer a team approach to diagnosis and care, which may include a pulmonologist, or lung specialist, an infectious disease specialist, chest radiologist, and a cardiopulmonary therapist.

There are more than 25 different species of mycobacteria that cause nontuberculous mycobacterial infections. One of the most common is Mycobacterium avium, which can cause symptoms similar to tuberculosis, such as cough, fever, fatigue, and weight loss. Another is Mycobacterium abscessus, which can lead to lung damage and infections of the skin and soft tissue, which includes cartilage, tendons, and the layers of fat and muscle underneath the skin. 

The disease tuberculosis is caused by a different strain from the same broad family of bacteria. However, while tuberculosis spreads from person to person, nontuberculous mycobacterial infections of any kind are not contagious.

You may develop a nontuberculous mycobacterial infection if you drink contaminated water. Bacteria can also enter the body through a break in the skin, such as a puncture wound that gets contaminated with water or soil. Inhaling the bacteria also puts you at risk for infection. 

Not everyone who is exposed to mycobacteria develops an infection. Why infection occurs in some people but not others isn’t known, but scientists believe that those who become ill may sometimes have an underlying lung condition, such as bronchiectasis; or another immune system problem that leaves them vulnerable to infection. 

People with gastroesophageal reflux disease, or GERD, who accidentally inhale water that is contaminated with nontuberculous mycobacteria may develop a nontuberculous mycobacteria-related lung infection. People with damaged lung tissue or airways from conditions such as emphysema or cystic fibrosis, or a previous tuberculosis infection, are also at increased risk. 

Signs and Symptoms

Diagnosing nontuberculous mycobacterial infections can be difficult because symptoms resemble those associated with other lung conditions, such as chronic bronchitis. Symptoms may include a cough that produces sputum or blood, fever, fatigue, weight loss, and night sweats.

Skin symptoms may include visible ulcerations, open sores, red rashes, or boils. If soft tissue is infected, it may have lesions or ulcerations that ooze pus. 

Soft tissue infections are usually limited to the skin and are visible to the eye. However, in immunosuppressed people, such as people with HIV and AIDS or people who have recently had an organ transplant, internal tissue such as the spleen or intestinal wall may be involved and may require radiographic imaging to determine the extent of the infection.

Diagnostic Tests

NYU Langone doctors first take a medical history and perform a physical exam. Your doctor may want to know if you are an avid gardener, or if you frequent hot tubs or steam rooms where these organisms can be more common. Your family history of lung disease is also important. 

Several tests are commonly used to diagnose nontuberculous mycobacterial infections.

CT Scan

A CT scan uses X-rays and a computer to create three-dimensional, cross-sectional images of the body. A CT scan of the lungs can help a doctor identify a current infection, a previous infection that may have caused tissue damage, or other conditions that may have put you at risk for a nontuberculous mycobacterial infection. A CT scan can identify areas of dilated airways, thickened airways, and pulmonary nodules, all of which may be signs of early or advanced lung disease.

Sputum Culture

Our doctors test a person’s sputum—the mucus that is coughed up from the lungs—for the presence of mycobacteria. A microbiologist places the sputum in a special dish and observes it to see if any mycobacteria grow. Several sputum cultures, or tests, are often necessary. One positive test does not always mean the infection is present, so doctors use multiple cultures to confirm a diagnosis.


Bronchoscopy is a test that allows a doctor to look inside the airways of the lungs and take samples of mucus or lung tissue to test them for signs of a mycobacterial infection. During the test, the doctor inserts a thin, flexible tube called a bronchoscope into the nose or mouth, then passes it down the throat into the airways. The bronchoscope has a light and small camera that allow your doctor to see the airways and take pictures. This procedure is often used with mild sedation to help you relax, but it may also be performed using general anesthesia.

Bronchoscopy enables a doctor to identify an infection and rule out other lung problems, such as a tumor or excess mucus in the airways. During the procedure, a doctor can take samples of mucus or lung tissue to test them for signs of a mycobacterial infection.

Respiratory Exam

During this exam, a doctor reviews your medical history and asks if you’ve had any respiratory symptoms or illnesses. The doctor observes your breathing and listens with a stethoscope for any unusual sounds, such as wheezing or crackling. He or she may also feel or tap your chest to see if some areas of the lungs are functioning better than others.


Spirometry measures how much and how quickly a person can blow air out of the lungs by breathing into a device called a spirometer. Doctors may also measure your lung volumes and how well you are using oxygen. Doctors may use spirometry to check for signs of lung damage from a nontuberculous mycobacterial infection, and may repeat them to see how well you are responding to treatment. 

Exercise Testing

Doctors monitor how far you can walk in six minutes, usually on a treadmill, and what level of oxygen you have at rest and while you are walking. This test is used to measure overall lung function. If lung function appears compromised, your doctor may give you supplemental oxygen.

Tissue Biopsy

If a person has a skin or soft tissue infection, a doctor may drain the pus or take a sample of the skin and send it to a lab to identify the type of mycobacteria that is causing the infection.

Our Research and Education in Nontuberculous Mycobacterial Infections

Learn more about our research and professional education opportunities.