The Rapid Identification of Microorganisms

The Need

  • diagnosis of infection so that the appropriate treatment (e.g., an antibiotic) can be started.
  • testing of food to ensure that it is not contaminated with infectious organisms like
  • to identify the biological agent such as in a possible terrorist attack so that appropriate measures can be taken quickly.


1. Culturing

  • The oldest and still most common.
  • For bacteria, spread samples on culture media and examine the resulting colonies for morphology and metabolic traits [Example]. For viruses, inoculate cultures of living cells.
  • Disadvantage: it make take several days to learn the results.

2. Polymerase Chain Reaction (PCR)

  • Extract DNA from the sample and perform PCR.
  • Advantage: rapid (often less than an hour)
  • Disadvantage: overly sensitive to presence of contaminants
Link to illustrated discussion of PCR

3. Immunoassays

Use a method that exploits the specificity and sensitivity of the reaction between antigen and antibodies.

Example: Enzyme-Linked Immunosorbent Assay (ELISA)

Takes 15 minutes or longer.

4. Biosensors (CANARY)

In the 11 July 2003 issue of Science, a team of scientists at the Lincoln Laboratory in the U. S. reported a new method of rapid identification that exploits living cells. They call their method CANARY (for Cellular Analysis and Notification of Antigen Risks and Yields)

Their "biosensor" is a clone of B lymphocytes (B cells) that have been genetically engineered to express


  • Prepare the sample.
  • Mix – in separate wells – with B-cell clones each specific for a different suspected agent.
  • Place in a sensitive light detector.
  • If a clone has a BCR for an epitope present in the sample, that clone will emit light within a few seconds.


  • highly sensitive: can detect as few as 50 bacteria or 500 virions
  • highly specific: can detect the agent even in the presence of related contaminating agents.
  • fast: time elapsed from sample preparation to signal from the light detector is often less than 5 minutes.
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17 April 2014