What is microscopy and culture?

To determine the cause of an infection, it may be necessary to grow fluids and tissue samples in a laboratory. This is done in order to identify and test bacteria and fungal infections. When using microscopy, it is possible to find and identify micro-organisms and analyse samples to diagnose diseases in tissue samples.

What can it show?

The micro-organisms that cause sickness (pathogens) are separated into several different groups, according to their type. The most important are viruses, bacteria and chlamydia (virus-like bacteria). Other groups include eggs and larvae from different parasites and protozoa (which are one-celled parasites such as an amoeba).

The standard way to identify bacteria is through using a culture (bacteria grown in the laboratory). In this process a non-contaminated group, which can be identified, is purified and tested as a comparison.

Fungi can also be grown and purified in the same way as bacteria, but this procedure is not often used.

It is more difficult to analyse viruses and chlamydia, which require more advanced laboratory examinations. Some viruses and other micro-organisms are so difficult to culture that it is necessary to examine the person's blood (serum) for antibodies against the micro-organism.

Worms, larvae, eggs and protozoans are clearly visible under a microscope and can easily be identified by a trained microbiologist without further examination.

Bacteria culture

All the body's exterior surfaces (hair and skin) and interior areas such as the mucous membranes in the nose and throat, intestines, stomach and sexual organs, contain many bacteria. These bacteria are harmless under normal circumstances. Many of them are even part of a healthy functioning body and keep away harmful bacteria.

If a doctor thinks that a patient is infected by a bacterium, they will usually take a sample from the place they think is infected. If, for instance, it is in the intestine, a sample may be taken from the stools. If it is in the bladder or the kidneys, a urine sample will be taken, and so on. This sample - along with the patient's details - will then be sent to cultured at a microbiologist's laboratory.

There are many different ways to grow culture in the laboratory. Samples can be taken from blood or saliva, for example. It is also possible to take samples from the mouth, skin, outer ear canal, throat, wounds and other areas.

How is a culture produced?

When the sample arrives at the laboratory, it is spread out on a special gel in a plastic bowl, which is then covered with a lid. Extracts of live substances such as meat, bread or chocolate may be added to the gel in order to give it more nourishment. If the sample is thought to hold a particular bacterium, the gel can be mixed with specific substances that encourage the growth of this particular bacterium and suppress the growth of others.

The test is then placed in a heating cupboard at approximately 100ºF (about 35ºC) the temperature at which disease-causing bacteria thrive best. Often, several different bacteria will grow, but the one that causes the disease (the pathogen) will be dominant compared to the non-pathogen.

How is microscopy of bacteria performed?

The bacteria are taken and spread on a small glass plate which can be placed under a microscope, and then dried. After that, it is possible to stain the bacteria. Often a special kind of stain called the Gram stain is used, which will determine whether the bacteria are Gram-positive or Gram-negative - see below. It should be noted that the following list does not include all Gram-positive and Gram-negative bacteria, and only the most frequent diseases are described.

Gram-positive bacteria

Staphylococci: these may cause pneumonia, toxic shock syndrome, wound infections and pimples.

Streptococci: these may cause blood poisoning, sore throat, and infection of the inside of the heart.

Anthrax, Bacilli and Clostridium: these may cause tetanus and gangrene.

Gram-negative bacteria

Salmonella, Shigellosis and Campylobacter: these may infect the stomach-intestine canal.

Legionella: this may cause legionnaires' disease.

Meningococcus: this may cause cerebrospinal meningitis.

Gonorrhoea bacteria: this may cause gonorrhoea.

Apart from those mentioned above, many Gram-negative bacteria cause urinary tract infections and blood poisoning in chronically ill people.

There are several other ways of identifying bacteria. All bacteria from the intestines, both the natural ones and those that cause diseases, are Gram-negative and look practically the same under a microscope. They can, however, be identified because they are capable of making different kinds of sugar ferment, and so can be distinguished from one another.

How is fungal and protozoan microscopy performed?

Micro-organisms that are only a little bit bigger than bacteria can be identified by using microscopy. Thrush or oral candidiasis can be identified using a sample from the mouth or the sexual organs.

Protozoa that may cause amoebic dysentery (infection in the intestines), malaria or trichomonas (a sexually transmitted disease that causes a vaginal infection) can be isolated from stools, blood sample and discharge.

Parasites such as roundworm and hookworm can often be identified through eggs or worms in the stools.

Micro-organisms that are smaller than bacteria, such as chlamydia, rickets and viruses can be identified through blood samples that are then analysed for antibodies against the micro-organism.

How is a cell and tissue test performed?

Use of the microscope is very important in the study of tissue structure and cells with unusual appearances. It is, for example, possible to diagnose cancer, as cancer cells very often have an unusual shape and form irregular patterns.

When the pathologist receives a biopsy (tissue sample) it is separated into small pieces that are dipped into formalin or a similar fixing chemical. The fixed tissue is then placed in paraffin before being cut into extremely thin slices, which can be placed under a microscope. The paraffin is then removed, and the tissue is stained to make the microscopic details easier to see. Then it is ready for microscopy. If certain types of cells are expected to be present, the sample can be stained in colours that are particularly helpful in detecting them.

Unfortunately, it can sometimes take up to a week before the result of a tissue test is ready. Sometimes it takes even longer if the sample needs further staining. In an emergency, the result can be ready within half an hour, as the tissue can be frozen before it is cut into slices. This may be necessary if the patient urgently needs an operation for which the results of the test are crucial.