Infectious diseases are caused by tiny microorganisms such as bacteria, viruses, fungi, and parasites. To help identify the organism responsible for infection, doctors usually obtain samples of body fluid or tissue for laboratory analysis. Depending on the suspected infection, any fluid in the body&$151;including blood, urine, sputum, cerebrospinal fluid, and genital secretions—may be examined, as well as stool or tissue biopsies. Microscopic examination and cultures are two of the primary methods used to help diagnose infectious diseases; the other, antigen/antibody testing.

Microscopic examination can provide a preliminary, tentative identification of certain infectious agents by revealing their size, shape, and cellular structure. The Gram stain test—in which a sample is smeared on a microscopic slide and stained with a special dye—is used to classify all bacteria as either gram positive (blue staining) or gram negative (red staining). The presence of specific inflammatory cells may also provide clues about the type of infection. The acid-fast smear involves spreading a sample on a slide, dyeing it, and treating it with an acid-alcohol solution to identify acid-fast bacteria (which will not be decolorized by the acid-alcohol). This test is often used to examine sputum and support a diagnosis of tuberculosis, or TB (since cultures for TB may take up to 2 months to grow). In addition, microscopic exams are necessary to identify parasites and their eggs.

Cultures generally take longer to perform than microscopic exams—from a day to several weeks—but are necessary to identify the organism with certainty and provide a definitive diagnosis. This technique involves placing a specimen in an environment, or medium, that is designed to promote the growth of specific organisms. (The medium is typically a jelly-like substance that contain nutrients to encourage the organisms to reproduce.) Cultures can be used to screen for a wide variety of bacteria, or can be focused to look for specific agents. In some cases, various antimicrobial drugs (such as antibiotics) are then added to a culture to determine which treatment is most effective for killing the offending organism; this is known as drug sensitivity testing.

Purpose of the Cultures and Microscopic Exams for Infectious Disease

  • To identify the microorganism capable of causing diseases and infections, in some cases, to help determine the best course of treatment
  • The acid-fast bacilli test may be done to monitor treatment for tuberculosis

Who Performs Cultures and Microscopic Exams for Infectious Disease

  • Varies according to what type of tissue or fluid sample is required.

Special Concerns

  • Several rapid diagnostic tests have recently been developed to detect the influenza virus, or “the flu,” within 30 minutes (viral culture for the flu usually takes days). These tests are increasingly being used to identify the flu early, and thus reduce unnecessary use of antibiotics (which are only effective for bacterial infections) and help to determine if antiviral treatment should be prescribed.
  • Many sexually transmitted diseases, such as Chlamydia and gonorrhea, are now diagnosed by DNA probe—a test that is positive if DNA from the particular bacterium is present—which requires only a urine sample.
  • Recent antimicrobial therapy, for example, with antibiotic drugs, can interfere with the accuracy of this test.

Before the Cultures and Microscopic Exams for Infectious Disease

  • Preparation varies according to what type of tissue or fluid sample is required. Your doctor will provide specific instructions.

What You Experience during Cultures and Microscopic Exams for Infectious Disease

  • A sample of body fluid, tissue, cells, or stool is obtained and sent to a laboratory for analysis. A variety of procedures may be used, depending on what type of sample is needed. These techniques vary from noninvasive—such as collecting fluid with a swab (as with a throat culture)—to more invasive means involving significant risks, such as tissue biopsy, bronchoscopy, bone marrow aspiration, or lumbar puncture.

Risks and Complications

  • Possible risks vary according to what type of tissue or fluid sample is required.

After the Cultures and Microscopic Exams for Infectious Disease

  • Post-test care varies according to what type of tissue or fluid sample is required.

Results of Cultures and Microscopic Exams for Infectious Disease

  • The sample is sent to a microbiology or bacteriology laboratory for microscopic examination and/or culturing.
  • In many cases, your doctor will issue a preliminary diagnosis and prescribe a treatment based on your history, symptoms, physical exam, and the results of any initial microscopic studies. Once the final results of a culture and/or drug sensitivity test are in, treatment may be refined accordingly.


The Johns Hopkins Consumer Guide to Medical Tests

Simeon Margolis, M.D., Ph.D., Medical Editor

Updated by Remedy Health Media

Publication Review By: the Editorial Staff at

Published: 05 Jan 2012

Last Modified: 05 Jan 2012