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.
Stained and examined under a microscope
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
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.
Samples for Testing
A sample is taken from an area of the person's body likely to contain the microorganism suspected of causing the infection. Samples may include
Blood
Sputum
Urine
Stool
Tissue
Cerebrospinal fluid
Mucus from the nose, throat, or genital area
Some samples sent for testing, such as sputum, stool, and mucus from the nose or throat, normally contain many types of bacteria that do not cause disease. Doctors need to distinguish between these bacteria and those that could cause the person's illness.
Staining and Examination Using a Microscope
Doctors sometimes can identify a microorganism simply by looking at it under a microscope.
For bacteria, doctors often first use Gram stain (a violet-colored stain). Bacteria are classified as follows:
Gram-positive (they look blue because they retain the violet Gram stain)
Gram-negative (they look red because they do not retain the stain)
Doctors can sometimes decide what antibiotics to use based on whether bacteria are gram-positive or gram-negative. Gram-positive and gram-negative bacteria tend to be susceptible to different groups of antibiotics.
Culture of Microorganisms
Testing a Microorganism's Susceptibility and Sensitivity to Antimicrobial Drugs
resistance to drugs that were previously effective. Thus, susceptibility testing is done to determine how effective various antimicrobial drugs are against the specific microorganism infecting the person. This testing helps doctors determine which drug to use for a particular person's infection (see Selecting an Antibiotic).
Cultures are often used for susceptibility testing. Once a microorganism has been grown in a culture, doctors add different antimicrobial drugs to see which ones kill the microorganism. They also test how sensitive the microorganism is to a drug—that is, whether a small or a large amount of a drug is needed to kill the microorganism (sensitivity testing). If a large amount is needed to kill the microorganism in the laboratory, doctors usually do not use that drug.
Sometimes genetic testing can be used to detect genes in the microorganism that cause resistance to certain antimicrobial drugs. For example, methicillin-resistant Staphylococcus aureus (MRSA) bacteria can be identified by testing for the mecA gene.
Because susceptibility testing occurs in the laboratory, the result does not always match what happens in the person's body when a drug is given. Factors related to the person receiving the drug can influence how effective a drug is (see also Overview of Response to Drugs). They include the following:
How well the person's immune system is working
How old the person is
Whether the person has other disorders
How the person's body absorbs and processes the drug
Tests That Detect Antibodies to or Antigens of Microorganisms
Antibodies, produced by the person's immune system in response to the microorganism
A microorganism's antigens (the molecules from the organism that trigger an immune response in the body)
Antibody tests
Antibody tests are usually done on a sample of the infected person’s blood because antibodies circulate in the blood. They also can be done on samples of cerebrospinal fluid or other body fluids.
Antibodies are substances produced by a person's immune system to help defend against infection. They are produced by certain types of white blood cell when these white blood cells encounter a foreign substance or cell. It typically takes several days to produce the antibody.
An antibody recognizes and targets the specific foreign substance (antigen) that triggered its production, so each antibody is unique, made for a specific type (species) of microorganism. If a person has antibodies to a particular microorganism, it means that the person has been exposed to that microorganism and has produced an immune response. However, because many antibodies remain in the bloodstream long after an infection has resolved, finding antibodies to a microorganism does not necessarily mean the person is still infected. The antibodies may remain from a previous infection.
Did You Know...
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Doctors may test for several antibodies, depending on which infections they think are likely. Sometimes doctors just test whether an antibody is present or not. But usually they try to determine how much antibody is present. They determine the amount of antibody by repeatedly diluting the sample in half until it no longer tests positive for the antibody. The more dilutions it takes until the test is negative, the more antibody there was in the infected person's sample.
Because it takes several days to weeks for the immune system to produce enough antibody to be detected, diagnosis of an infection may be delayed. Antibody tests done right after people become ill are often negative. Thus, doctors may take one sample immediately and then take another one several weeks later to see whether antibody levels have increased. If levels of an antibody are low on the first test after people become ill, finding an increase in the antibody levels several weeks later suggests an active, current or recent (rather than a previous) infection.
Antigen tests
To do antigen tests, doctors take a sample from a person and mix it with a test antibody to the suspected microorganism. If there are antigens from that microorganism in the person's sample, they attach to the test antibody. Different methods can be used to detect the antigen-antibody combination. But whatever method is used, the presence of the antigen means that the microorganism is present and probably is the cause of the infection.
Tests That Detect Genetic Material in Microorganisms
Nucleic acid–based tests
If a microorganism is difficult to culture or identify by other methods, doctors can do tests to identify pieces of the microorganism’s genetic material. This genetic material consists of nucleic acids: deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). Some of the DNA and RNA in each organism are unique to that organism. Thus, finding some of that DNA or RNA means that specific microorganism is present.
The polymerase chain reaction (PCR) is an example of this type of test. The PCR technique is used to produce many copies of a gene from a microorganism, making the microorganism much easier to identify.
Each genetic test is specific to only one specific microorganism. That is, a genetic test for hepatitis C virus detects only that virus and not any other. Thus, these tests are done only when a doctor already suspects a particular disease.
Most nucleic acid–based tests are designed to identify the presence of a microorganism (called qualitative testing). However, for certain infections, such as HIV and hepatitis C, tests also can measure how much of the microorganism's genetic material is present (called quantitative testing) and thus determine how severe the infection is. Quantitative tests can also be used to monitor how well treatment is working.
Other Tests Used to Identify Microorganisms
Non-nucleic acid–based identification tests
These tests are so named because they are not based on identifying the microorganism's genetic material, which consists of nucleic acids (DNA and RNA).
For example, tests can be done to identify the following:
The substances that the microorganism can grow in or grows best in when it is cultured
Enzymes produced by the microorganism (which help the microorganism infect cells or spread through tissues faster)
Other substances in the microorganism (such as proteins and fatty acids) that help identify it
