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Medical microbiology

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Title: Medical microbiology  
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Collection: Clinical Pathology, Medical Specialties, Microbiology, Pathology
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Medical microbiology

A microbiologist examining cultures under a dissecting microsope.

Medical microbiology is a branch of bacteria, fungi, parasites and viruses and one type of infectious protein called a prion.

A medical microbiologist studies the characteristics of pathogens, their modes of transmission, mechanisms of infection and growth.[1] Using this information a treatment can be devised. Medical microbiologists often serve as consultants for physicians, providing identification of pathogens and suggesting treatment options. Other tasks may include the identification of potential health risks to the community or monitoring the evolution of potentially virulent or resistant strains of microbes, educating the community and assisting in the design of health practices. They may also assist in preventing or controlling epidemics and outbreaks of disease. Not all medical microbiologists study microbial pathology; some study common, non-pathogenic species to determine whether their properties can be used to develop antibiotics or other treatment methods.

Whilst epidemiology is the study of the patterns, causes, and effects of health and disease conditions in populations, medical microbiology primarily focuses on the presence and growth of microbial infections in individuals, their effects on the human body and the methods of treating those infections.


  • History 1
  • Commonly-treated infectious diseases 2
    • Bacterial 2.1
    • Viral 2.2
    • Parasitic 2.3
    • Fungal 2.4
  • Causes and transmission of infectious diseases 3
  • Diagnostic tests 4
    • Microbial culture 4.1
    • Microscopy 4.2
    • Biochemical tests 4.3
    • Polymerase chain reaction 4.4
  • Treatments 5
  • See also 6
  • Notes and references 7


Anton van Leeuwenhoek, is considered to be the one of the first to observe microorganisms using a microscope.

In 1676, microscope of his own design.[2]

In 1796, using an ancient Chinese technique for smallpox vaccination, Edward Jenner developed a method using cowpox to successfully immunize a child against smallpox. The same principles are used for developing vaccines today.

Following on from this, in 1857 Louis Pasteur also designed vaccines against several diseases such as anthrax, fowl cholera and rabies as well as pasteurization for food preservation.[3]

In 1867 Joseph Lister is considered to be the father of antiseptic surgery. By sterilizing the instruments with diluted carbolic acid and using it to clean wounds, post-operative infections were reduced making surgery safer for patients.

In the years between 1876-1884 Koch's postulates.[4]

A major milestone in medical microbiology is the Gram stain. In 1884 Hans Christian Gram developed the method of staining bacteria, to make them more visible and differentiable under a microscope. This technique is widely used today.

In 1929 Alexander Fleming developed the most commonly used antibiotic substance both at the time and now: penicillin.

DNA sequencing, a method developed by Walter Gilbert and Frederick Sanger in 1977,[5] caused a rapid change the development of vaccines, medical treatments and diagnostic methods. Some of these include synthetic insulin which was produced in 1979 using recombinant DNA and the first genetically engineered vaccine was created in 1986 for Hepatitis B.

In 1995 a team at The Institute for Genomic Research sequenced the first bacterial genome; Haemophilus influenzae.[6] A few months later, the first eukaryotic genome was completed. This would prove invaluable for diagnostic techniques.[7]

Commonly-treated infectious diseases





Causes and transmission of infectious diseases

Infections may be caused by bacteria, viruses, fungi, and parasites. The pathogen that causes the disease may be exogenous (acquired from an external source; environmental, animal or other people, e.g. Influenza) or endogenous (from normal flora e.g. candidiasis).[19]

The site at which a microbe enters the body is referred to as the portal of entry.[20] These include the respiratory tract, gastrointestinal tract, genitourinary tract, skin, and mucous membranes.[21] The portal of entry for a specific microbe is normally dependent on how it travels from its natural habitat to the host.[20]

There are various ways in which disease can be transmitted between individuals. These include:[20]

Like other pathogens, viruses use these methods of transmission to enter the body, but viruses differ in that they must also enter into the host's actual cells. Once the virus has gained access to the host's cells, the virus' genetic material (RNA or DNA) must be introduced to the cell. Most viruses achieve this through the use of enzymes to break up the viral genome so that only nucleic acids are present for expression, whilst other viruses such as poxviruses, utilize two stages for expression: enzymatic breakdown followed by the release of viral DNA which is mediated by the gene products created during the initial infection.[22]

The mechanisms for infection, proliferation, and persistence of a virus in cells of the host are crucial for its survival. For example, some diseases such as measles employ a strategy whereby it must spread to a series of hosts. In these forms of viral infection, the illness is often treated by the body’s own immune response, and therefore the virus is required to disperse to new hosts before it is destroyed by immunological resistance or host death.[23] In contrast, some infectious agents such as the Feline leukemia virus, are able to withstand immune responses and are capable of achieving long term residence within an individual host, whilst also retaining the ability to spread into successive hosts.[24]

Diagnostic tests

Identification of an infectious agent for a minor illness can be as simple as clinical presentation; such as gastrointestinal disease and skin infections. In order to make an educated estimate as to which microbe could be causing the disease, epidemiological factors need to be considered; such as the patient's likelihood of exposure to the suspected organism and the presence and prevalence of a microbial strain in a community.

Diagnosis of infectious disease is nearly always initiated by consulting the patient's medical history and conducting a physical examination. More detailed identification techniques involve microbial culture, microscopy, biochemical tests and genotyping. Other less common techniques (such as X-rays, CAT scans, PET scans or NMR) are used to produce images of internal abnormalities resulting from the growth of an infectious agent.

Microbial culture

Four nutrient agar plates growing colonies of common Gram negative bacteria.

Microbiological culture is the primary method used for isolating infectious disease for study in the laboratory. Tissue or fluid samples are tested for the presence of a specific pathogen, which is determined by growth in a selective or differential medium.

The 3 main types of media used for testing are:[25]

  • Solid culture: A solid surface is created using a mixture of nutrients, salts and agar. A single microbe on an agar plate can then grow into colonies (clones where cells are identical to each other) containing thousands of cells. These are primarily used to culture bacteria and fungi.
  • Liquid culture: Cells are grown inside a liquid media. Microbial growth is determined by the time taken for the liquid to form a colloidal suspension. This technique is used for diagnosing parasites and detecting mycobacteria.[26]
  • Cell Culture: Human or animal cell cultures are infected with the microbe of interest. These cultures are then observed to determine the effect this new microbe has on the cell. This technique is used for identifying viruses.


The previously mentioned Electron microscopes and fluorescence microscopes are also used for observing microbes in greater detail.[27]

Biochemical tests

Fast and relatively simple biochemical tests can be used to identify infectious agents. For bacterial identification, the use of metabolic or enzymatic characteristics are common due to their ability to ferment carbohydrates in patterns characteristic of their genus and species. Acids, alcohols and gases are usually detected in these tests when bacteria are grown in selective liquid or solid media, as mentioned above. In order to perform these tests en masse, Vitek machines are used. These machines perform multiple biochemical tests simultaneously, using cards with several wells containing different dehydrated chemicals. The microbe of interest will react with each chemical in a certain way, aiding in its identification.

immunoassays. Using a similar basis as described above, immunoassays can detect or measure antigens from either infectious agents or the proteins generated by an infected host in response to the infection. [28]

Polymerase chain reaction

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  9. ^ Vos T; et al. (December 2012). "Years lived with disability (YLDs) for 1160 sequelae of 289 diseases and injuries 1990-2010: a systematic analysis for the Global Burden of Disease Study 2010". Lancet 380: 2163–96.  
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Notes and references

See also

Medical microbiology is not only about diagnosing and treating disease, it also involves the study of beneficial microbes. Microbes have been shown to be helpful in combating infectious disease and promoting health. Treatments can be developed from microbes, as demonstrated by Alexander Fleming's discovery of probiotics to provide health benefits to the host, such as providing better gastrointestinal health or inhibiting pathogens.[35]

Whilst drug resistance typically involves microbes chemically inactivating an antimicrobial drug or a cell mechanically stopping the uptake of a drug, another form of drug resistance can arise from the formation of biofilms. Some bacteria are able to form biofilms by adhering to surfaces on implanted devices such as catheters and prostheses and creating an extracellular matrix for other cells to adhere to.[32] This provides them with a stable environment from which the bacteria can disperse and infect other parts of the host. Additionally, the extracellular matrix and dense outer layer of cells can protect the inner cells from antimicrobial drugs.[33]

In addition to drugs being specific to a certain kind of organism (bacteria, fungi, etc.), some drugs are specific to a certain strains of an organism may be resistant to a certain drug or class of drug, even when it is typically effective against the species. These strains, termed resistant strains, present a serious public health concern of growing importance to the medical industry as the spread of antibiotic resistance worsens.

Antibiotic resistance tests: The bacteria in the culture on the left are sensitive to the antibiotics contained in the white, paper discs. The bacteria in the culture on the right are resistant to most of the antibiotics.

Medical microbiologists often make treatment recommendations to the patient’s physician based on the strain of microbe and its antibiotic resistances, the site of infection, the potential toxicity of antimicrobial drugs and any drug allergies the patient has.

Once an infection has been diagnosed and identified, suitable treatment options must be assessed by the physician and consulting medical microbiologists. Some infections can be dealt with by the body’s own immune system, but more serious infections are treated with antimicrobial drugs. Bacterial infections are treated with antibacterials (often called antibiotics) whereas fungal and viral infections are treated with antifungals and antivirals respectively. A broad class of drugs known as antiparasitics are used to treat parasitic diseases.


. Hepatitis and AIDS This technique is the current standard for detecting viral infections such as [30]

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