Principles of Diagnosis with Medical Microbiology


Microbial infections are diseases that can affect your skin, lungs, brain, blood and other parts of your body. You get them from single-celled organisms multiplying or releasing toxins in your body. Common bacterial diseases include UTIs, food poisoning, STIs and some skin, sinus and ear infections. They’re often treated with antibiotics.

Microbes that cause disease are called pathogens. There are different types of microbes, such as bacteria, viruses, fungi and parasites. Each type of microbe has its own characteristics, modes of transmission and methods of diagnosis and treatment.

Bacteria are living things with only a single cell that can reproduce quickly. There are millions of bacteria that live all around us — in soil or water and on surfaces in our homes and workplaces. There are even millions of bacteria that live on your skin and inside of your body. Most bacteria aren’t harmful, and many are even helpful. They can help you digest food and kill off other harmful forms of bacteria that try to invade your body. But even the helpful ones can hurt you if they grow where they’re not supposed to.

Some examples of bacterial infections are:

  • Legionnaires’ disease
  • Meningococcal disease
  • Q fever
  • Strep throat
  • Tuberculosis (TB)
  • Whooping cough (pertussis)

Viruses are not made up of cells, but they have genetic material (DNA or RNA) surrounded by a protein coat. They always need to infect humans or other living things to create more copies of themselves. Viruses can cause mild illnesses like the common cold or more serious diseases like AIDS or COVID-19.

Some examples of viral infections are:

  • Chickenpox
  • Cold
  • Flu
  • German measles
  • COVID-19

Fungi are organisms that feed on organic matter. They can be multicellular (like mushrooms) or unicellular (like yeast). Some fungi live on our skin or inside our body without causing any problems. But some fungi can cause infections, especially in people with weakened immune systems.

Some examples of fungal infections are:

  • Athlete`s foot
  • Ringworm
  • Thrush
  • Valley fever

Parasites are organisms that live on or inside another organism (the host) and benefit from it, often at the expense of the host. Parasites can be animals (like worms) or protozoa (single-celled organisms). Some parasites can cause diseases by damaging the host`s tissues, organs or blood cells.

Some examples of parasitic infections are:

  • Giardiasis
  • Malaria
  • Pinworms
  • Toxoplasmosis

To cause an infection, microbes must enter our bodies. The site at which they enter is known as the portal of entry. Microbes can enter the body through the four sites listed below:

  • Respiratory tract (mouth and nose) e.g. influenza virus which causes the flu.
  • Gastrointestinal tract (mouth oral cavity) e.g. Vibrio cholerae which causes cholera.
  • Urogenital tract (urethra) e.g. Escherichia coli which causes urinary tract infections.
  • Skin e.g. Staphylococcus aureus which causes boils or impetigo.

Once inside the body, microbes may multiply and spread to different tissues or organs, causing damage and inflammation. The body`s immune system tries to fight off the infection by producing antibodies and white blood cells. Sometimes, the immune response can also harm the body`s own cells or cause allergic reactions.

The symptoms and severity of microbial infections depend on many factors, such as:

  • The type and number of microbes involved.
  • The portal of entry and the site of infection.
  • The virulence (ability to cause disease) and resistance (ability to evade treatment) of the microbes.
  • The immune status and general health of the host.
  • The availability and effectiveness of treatment options.

Microbial infections can be diagnosed by various methods, such as:

  • Clinical signs and symptoms.
  • Laboratory tests on blood, urine, stool, sputum or other specimens.
  • Imaging techniques like X-rays, ultrasound or MRI.
  • Molecular techniques like polymerase chain reaction (PCR) or gene sequencing.

Microbial infections can be treated by various methods, such as:

  • Antibiotics for bacterial infections.
  • Antivirals for viral infections.
  • Antifungals for fungal infections.
  • Antiparasitics for parasitic infections.
  • Supportive care like fluids, painkillers or oxygen therapy.

Microbial infections can be prevented by various methods, such as:

  • Vaccination for some diseases like measles, polio or tetanus.
  • Hygiene practices like washing hands, covering coughs or sneezes or disinfecting surfaces.
  • Food safety practices like cooking food thoroughly, washing fruits and vegetables or storing food properly.
  • Water safety practices like boiling water, using filters or purifiers or avoiding contaminated sources.
  • Sexual safety practices like using condoms, getting tested or treated for STIs or avoiding multiple partners.
  • Travel safety practices like getting vaccinated, taking prophylaxis or avoiding contact with sick people or animals.

Microbial infections are a major cause of morbidity and mortality worldwide. They can affect anyone at any age, but some groups are more vulnerable than others, such as:

  • Infants and children.
  • Elderly people.
  • Pregnant women.
  • People with chronic diseases like diabetes, cancer or HIV/AIDS.
  • People with weakened immune systems due to medications, transplants or genetic disorders.

Understanding the principles of diagnosis with medical microbiology can help us prevent, detect and treat microbial infections effectively and improve our health and well-being.

Importance of specimen collection and processing in microbiological tests

Specimen collection and processing are crucial steps in the diagnosis of microbial infections. A specimen is any material obtained from a patient that can be examined for the presence of microorganisms or their products. The quality and quantity of the specimen can affect the accuracy and reliability of the microbiological tests. Therefore, it is important to follow some general principles when collecting and processing specimens for microbiological tests:

  • The specimen should be collected as soon as possible after the onset of symptoms or signs of infection, preferably before the administration of any antimicrobial agents that may interfere with the detection or growth of microorganisms.
  • The specimen should be representative of the site and stage of infection, and should avoid contamination from normal flora or other sources. For example, specimens from respiratory tract infections should be obtained by deep coughing or sputum induction, rather than by saliva or nasal swabs. Specimens from skin or wound infections should be obtained by scraping or aspirating the lesion, rather than by swabbing the surface.
  • The specimen should be collected in an appropriate container that is sterile, leak-proof, and labeled with the patient`s name, identification number, date, time, and site of collection. The container should also contain a suitable transport medium that preserves the viability and integrity of the microorganisms during transit to the laboratory. Some transport media may also contain inhibitors or indicators that prevent the growth or enhance the detection of certain microorganisms.
  • The specimen should be transported to the laboratory as soon as possible after collection, preferably within 2 hours. If transport is delayed, the specimen should be stored at an appropriate temperature that prevents the overgrowth or death of microorganisms. For example, specimens containing bacteria should be refrigerated at 4°C, while specimens containing viruses should be frozen at -70°C.
  • The specimen should be processed in the laboratory according to standard operating procedures that ensure the safety of the personnel and the quality of the results. The processing may include steps such as centrifugation, filtration, staining, inoculation, incubation, identification, and susceptibility testing. The processing should be done in a timely manner to avoid delays in reporting the results to the clinician.

By following these principles, specimen collection and processing can ensure that microbiological tests provide accurate and reliable information for the diagnosis and treatment of microbial infections.