Medical microbiology , the large subset of microbiology that
is applied to medicine, is a
branch of medical science concerned with the prevention, diagnosis and
treatment of infectious diseases. In addition, this field of science
studies various clinical applications of microbes for the improvement of
health. There are four kinds of microorganisms that
cause infectious disease: bacteria, fungi, parasites and viruses, and one
type of infectious protein called prion.
A medical microbiologist studies
the characteristics of pathogens, their modes of transmission, mechanisms of
infection and growth. 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.
Epidemiology,
the study of the patterns, causes, and effects of health and disease conditions
in populations, is an important part of medical microbiology, although the clinical
aspect of the field 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. In this respect the entire field, as an applied
science, can be conceptually subdivided into academic and clinical
subspecialties, although in reality there is a fluid continuum
between public health microbiology and clinical microbiology,
just as the state of the art in clinical laboratories depends on continual
improvements in academic medicine and research laboratories.
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).
The site at which a microbe
enters the body is referred to as the portal of entry. These include
the respiratory tract, gastrointestinal
tract, genitourinary tract, skin, and mucous
membranes. The portal of entry for a specific microbe is normally
dependent on how it travels from its natural habitat to the host.
There are various ways in
which disease can be transmitted between individuals. These include:
·
Indirect contact - Touching a contaminated
surface
·
Vector transmission - An organism
that does not cause disease itself but transmits infection by conveying
pathogens from one host to another
·
Fomite transmission - An inanimate object or substance
capable of carrying infectious germs or parasites
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. Replication between viruses is greatly varied and depends on
the type of genes involved in them. Most DNA viruses assemble in the nucleus
while most RNA viruses develop solely in cytoplasm.
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 measlesemploy 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. 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.
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
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.
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.
Polymerase chain reaction
Polymerase chain reaction (PCR)
assays are the most commonly used molecular technique to detect and study
microbes. 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
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.
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.
Antibiotic resistance tests:
bacteria in the culture on the left are sensitive to the antibiotics contained
in the white, paper discs. Bacteria in the culture on the right are resistant
to most of the antibiotics.
In addition to drugs being
specific to a certain kind of organism (bacteria, fungi, etc.), some drugs are
specific to a certain genus or species of
organism, and will not work on other organisms. Because of this specificity,
medical microbiologists must consider the effectiveness of certain
antimicrobial drugs when making recommendations. Additionally, 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. Antimicrobial resistance is an
increasingly problematic issue that leads to millions of deaths every year.
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. 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 bacterial cells can protect the
inner bacteria cells from antimicrobial drugs.
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 penicillin as
well as the development of new antibiotics from the bacterial genus Streptomyces among
many others. Not only are microorganisms a source of antibiotics but some
may also act as probiotics to provide health benefits to the
host, such as providing better gastrointestinal health or inhibiting pathogens.
