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Diagnosing Infections After Stem Cell or Organ Transplants

NYU Langone specialists are experts at recognizing the signs of infection after a stem cell or organ transplant. An organ transplant is a procedure that replaces a damaged organ, such as the liver or a kidney, with an organ from a living or deceased donor. Stem cell transplantation is performed to treat some cancers, including leukemia, lymphoma, or multiple myeloma, and is also used to treat some noncancerous conditions, such as sickle cell disease and immune deficiency syndromes. Stem cells can be taken from a person’s own body or from a living donor.

Following either type of transplant, people take long-term medications that suppress the body’s immune system. When someone has received a donor organ, medications prevent the immune system from rejecting it. Someone who has received a stem cell transplant may need such medications to prevent and treat graft versus host disease, which results when the immune cells in the donor’s stem cells attack the recipient’s tissues.

These medications are known as immunosuppressants, because they reduce, or suppress, immune system activity. They can weaken immune function and compromise a person’s ability to fight common infections. Infections are one of the leading causes of hospitalization in people who have had a transplant.

To diagnose an infection after stem cell or organ transplantation, an NYU Langone doctor first takes a medical history and performs a detailed physical examination. During the exam, your doctor looks for signs of infection, such as skin lesions or boils, and listens to the lungs for possible fungal pneumonia. Other tests help a doctor make an accurate diagnosis, which helps determine the most effective treatment.

Blood Test

A doctor may take a blood sample to determine whether you have a high number of white blood cells. If so, it signals that the immune system is fighting an infection.

Certain antibiotic-resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA), can be detected in a blood sample in as little as two hours. The test can determine whether MRSA or a less dangerous bacterium is causing the infection.

A blood test called a blood culture is the primary method for diagnosing infections with bacteria or fungi that may have spread through the bloodstream.

Specialized blood tests are now available at NYU Langone that look for newly recognized indicators of systemic bacterial infection such as sepsis, or fungal disease due to Aspergillus or Candida. They can also detect viruses such as influenza and other respiratory viruses, as well as viruses found in people with immune suppression, like cytomegalovirus.

Tissue Cultures

A doctor may take a sample of pus from a wound or a tissue sample of the infected area and send it to a laboratory for testing. For a wound infection, a swab is usually rubbed across the skin’s surface. For a lung infection, a doctor may take a sample of lung tissue through a procedure called a bronchoscopy, which is used to look inside a person’s airways.

A pathologist places the sample in a Petri dish, a round, shallow container with nutrients that encourage bacteria or fungi to grow over 24 to 48 hours. He or she adds different antibiotics, such as methicillin or vancomycin, or antifungal medications, such as fluconazole or voriconazole, to the dish to see how the bacteria or fungi react. Their reaction tells a doctor which medications the organism is resistant to and which would be effective. This can help a doctor choose the best medication.


If a person has an infection in the respiratory tract—which includes the lungs; the trachea, or windpipe; and the bronchi, the two branches off the windpipe leading into the lungs—a doctor may perform a bronchoscopy.

During the procedure, a doctor inserts a thin, flexible tube called a bronchoscope into your nose or mouth. He or she passes the tube down the throat and into the airways. The bronchoscope has a light and small camera that allow your doctor to see your windpipe and airways and take a tissue sample, if needed. You’re usually given a sedative so that you feel relaxed.

Bronchoscopy helps a doctor to identify the cause of a lung problem. While inspecting the airways, he or she can look for signs of infection, tumor, or excess mucus.

CT Scans

A CT scan uses X-rays and a computer to create three-dimensional, cross-sectional images of the body. A CT scan can help a doctor determine whether the lungs, sinuses, or brain have been infected or damaged.

Sputum Cultures

Doctors test a person’s sputum, the mucus that is coughed up from the lungs, for the presence of bacteria such as MRSA and mycobacteria, among others. The sputum is examined under a microscope and placed in a Petri dish in a laboratory. Several sputum tests are often necessary to confirm a diagnosis because one positive test does not always mean an infection is present.

Our Research and Education in Infections After Stem Cell or Organ Transplants

Learn more about our research and professional education opportunities.