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 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: • 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. • Cell culture: Human or animal
cell cultures are infected with the microbe of interest. These cultures are then observed to determine the effect the microbe has on the cells. This technique is used for identifying viruses.
Microscopy Culture techniques will often use a microscopic examination to help in the identification of the microbe. Instruments such as
compound light microscopes can be used to assess critical aspects of the organism. This can be performed immediately after the sample is taken from the patient and is used in conjunction with biochemical staining techniques, allowing for resolution of cellular features.
Electron microscopes and
fluorescence microscopes are also used for observing microbes in greater detail for research. The two main types of electron microscopy are scanning electron microscopy and transmission electron microscopy.
Transmission electron microscopy passes electrons through a thin cross-section of the cell of interest, and it then redirects the electrons onto a fluorescent screen. This method is useful for looking at the inside of cells, and the structures within, especially cell walls and membranes.
Scanning electron microscopy reads the electrons that are reflected off the surface of the cells. A 3-dimensional image is then made which shows the size and exterior structure of the cells. Both techniques help give more detailed information about the structure of microbes. This makes it useful in many medical fields, such as diagnostics and biopsies of many body parts, hygiene, and virology. They provide critical information about the structure of pathogens, which allow physicians to treat them with more knowledge.
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, automated 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 specific way, aiding in its identification.
Serological methods are highly sensitive, specific and often extremely rapid laboratory tests used to identify different types of microorganisms. The tests are based upon the ability of an
antibody to bind specifically to an
antigen. The antigen (usually a protein or carbohydrate made by an infectious agent) is bound by the antibody, allowing this type of test to be used for organisms other than bacteria. This binding then sets off a chain of events that can be easily and definitively observed, depending on the test. More complex serological techniques are known as
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. As compared to other methods, sequencing and analysis is definitive, reliable, accurate, and fast. Today,
quantitative PCR is the primary technique used, as this method provides faster data compared to a standard PCR assay. For instance, traditional PCR techniques require the use of
gel electrophoresis to visualize amplified DNA molecules after the reaction has finished.
quantitative PCR does not require this, as the detection system uses
fluorescence and
probes to detect the DNA molecules as they are being amplified. In addition to this,
quantitative PCR also removes the risk of contamination that can occur during standard PCR procedures (carrying over PCR product into subsequent PCRs). Another advantage of using PCR to detect and study microbes is that the DNA sequences of newly discovered infectious microbes or strains can be compared to those already listed in databases, which in turn helps to increase understanding of which organism is causing the infectious disease and thus what possible methods of treatment could be used. This technique is the current standard for detecting viral infections such as
AIDS and
hepatitis. == Treatments ==