Infectious diseases are caused by micro-organisms, such as bacteria, viruses, fungi, and parasites. Doctors suspect an infection based on the person’s symptoms, physical examination results, and risk factors. First, doctors confirm that the person has an infection rather than another type of illness. For example, a person with a cough and difficulty breathing may have pneumonia (a lung infection). However, the person may instead have asthma or heart failure, which are not caused by infection. In such a person, a chest x-ray can help doctors distinguish pneumonia from the other possible disorders.

Once doctors confirm that the person has an infection, they usually need to know which specific microorganism is causing the infection. Many different microorganisms can cause a given infection. For example, pneumonia can be caused by viruses, bacteria, or, rarely, fungi. The treatment is different for each microorganism.

Many different types of laboratory tests can identify micro-organisms. Laboratory tests use a sample of blood, urine, sputum, or other fluid or tissue from the body. This sample may be


  • Stained and examined under a microscope
  • Cultured (placed in conditions that encourage the growth of microorganisms)
  • Tested for antibodies (molecules produced by the person’s immune system in response to the microorganism)’
  • Tested for a microorganism’s antigens (molecules from the microorganism that can trigger an immune response in the body)
  • Tested for genetic material (such as DNA or RNA) from the microorganism

No single test can identify every microorganism, and tests that work well for one microorganism often do not work well for another. Doctors must choose the test based on which microorganisms they think are most likely to cause a disorder.

Sometimes several different tests are done, typically in a specific order, based on the results of the previous test. Each test further narrows the possibilities. If the right test is not done, doctors may not identify the cause of infection.

When a microorganism is identified, doctors can then do tests to determine which drugs are most effective against it (susceptibility tests), and effective treatment can be started sooner.