Usually, doctors need to know which specific microorganism is causing a disease. Many different microorganisms can cause a given disease (for example, pneumonia can be caused by viruses, bacteria, or fungi), and the treatment is different for each organism.There are many ways to identify microorganisms.

Examination under a microscope: Despite the development of rapid identification systems, direct microscopic examination of samples taken from the site of infection is often the most rapid method of identifying microorganisms that cause disease. Chemical stains are usually applied to make the microorganisms easier to see. The size and shape of the microorganisms and their stained color can help distinguish between different types. However, the microorganisms must be of sufficient size and number to be seen with a regular microscope. For example, viruses are too small to be seen with a regular microscope.

Culture: Usually, microorganisms are too few or too small to see, so they may be grown in the laboratory until there are enough to be recognized with chemical tests. The process of growing the organism is called a culture. Many microorganisms, such as the bacteria that cause gonorrhea or strep throat, can be grown this way.

Cultures can also be used to test the sensitivity of microorganisms to various antibiotics. This testing can help a doctor determine which drug to use in treating an infected person. This strategy is particularly important because microorganisms are constantly developing resistance to antibiotics that were previously effective.

Tests that detect antibodies: Some microorganisms, such as the bacteria that cause syphilis and the human immunodeficiency virus (HIV), are very difficult to culture. These infections, and many others, can be identified by finding antibodies to the microorganisms in the infected person's blood or body fluids (for example, cerebrospinal fluid).

Antibody-based tests are used to identify many infections, but they are not always reliable. These tests may not become positive for several days or weeks after people become ill. Also, these tests may indicate infection when none is present because they detect antibodies from a previous infection. Antibodies often stay in the body for many years after an infection has gone away.

Nucleic acid amplification tests: These tests, such as the polymerase chain reaction (PCR), identify pieces of the microorganism's genetic material (DNA), which are only present when the organism is present.

These tests are done only when a doctor already suspects a particular disease. Therefore, a doctor's understanding of all the features of a disease, including symptoms, physical examination results, and risk factors, is essential for diagnosing an infection.

Biological warfare is the use of microbiological agents for hostile purposes. Such use is contrary to international law and has rarely occurred during formal warfare in modern history, despite the extensive preparations and stockpiling of biological agents by most major powers during the 20th century. It is uncertain whether other countries or dissident groups have biologic warfare capability. For a variety of reasons (including uncertain military efficacy and the threat of massive retaliation), experts consider the use of biological agents in formal warfare unlikely. However, biological agents are thought by some people to be an ideal weapon for terrorists. These agents may be delivered clandestinely, and they have delayed effects, allowing the user to remain undetected.

Potential biological agents include anthrax, botulinum toxin, brucellosis, encephalitis viruses, hemorrhagic fever viruses (Ebola and Marburg), plague, tularemia, and smallpox. Each of these is potentially fatal and, except for anthrax and botulinum toxin, can be passed from person to person.

Anthrax spores are relatively easy to prepare and, unlike most other agents, can be spread through the air, creating the potential for distribution by airplane. Theoretically, 1 kilogram of anthrax could kill 10,000 people, although technical difficulties with preparing the spores in a sufficiently fine powder would probably limit actual deaths to a fraction of this number.

Despite these theoretical concerns, the only successful terrorist use of anthrax—multiple pieces of contaminated mail delivered to a variety of locations in the United States in 2001—resulted in only a handful of deaths and a small number of serious infections (22 total cases). More people were contaminated with anthrax spores without developing illness, possibly because of extensive use of the antibiotic ciprofloxacin. However, there was extreme public anxiety related to these incidents.

The number of false threats of anthrax reported was very large. In 1999, the FBI received an average of one false report of anthrax use per day. Even more false reports, both hoaxes and those by alarmed citizens misperceiving harmless material for anthrax, were reported after the 2001 anthrax attack.

The only other successful use of a biological agent by a terror group in the United States occurred in 1984. In this event, 751 people developed diarrhea resulting from the intentional contamination of a salad bar with Salmonella in Oregon. The bacteria were introduced by a religious cult trying to influence the results of a local election. No one died, and the election was not affected.

Defense against bioterrorism involves several factors:

• Intelligence information to disrupt the terrorists before they can use the weapons
• Early detection
• Availability of protective antibiotics
• Immunization of selected populations (such as the military)