Medical

microbiology

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 microbiologist examining
cultures under a dissecting
microscope.
A medical microbiologist studies the characteristics of pathogens, their modes of
transmission, mechanisms of infection and growth. The academic qualification as a
clinical/Medical Microbiologist in a hospital or medical research centre generally
requires a Bachelors degree while in some countries a Masters in Microbiology along
with Ph.D. in any of the life-sciences (Biochem, Micro, Biotech, Genetics, etc.).[1]
Medical microbiologists often serve as consultants for physicians, providing
identification of pathogens and suggesting treatment options. Using this information,
a treatment can be devised. 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 sub-specialties, 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.

History
 Anton van Leeuwenhoek was
the first to observe
microorganisms using a
microscope.

Statue of Robert Koch, father

of medical bacteriology,[2] at
Robert-Koch-Platz (Robert
Koch square) in Berlin

In 1676, Anton van Leeuwenhoek observed bacteria and other microorganisms, using
a single-lens microscope of his own design.[3]

In 1796, Edward Jenner developed a method using cowpox to successfully immunize

a child against smallpox. The same principles are used for developing vaccines
today.[4]

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.[5]
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.[6]

In the years between 1876 and 1884 Robert Koch provided much insight into
infectious diseases. He was one of the first scientists to focus on the isolation of
bacteria in pure culture. This gave rise to the germ theory, a certain microorganism
being responsible for a certain disease. He developed a series of criteria around this
that have become known as the Koch's postulates.[7]

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
differentiated under a microscope. This technique is widely used today.[8]

In 1910 Paul Ehrlich tested multiple combinations of arsenic based chemicals on

infected rabbits with syphilis. Ehrlich then found that arsphenamine was found
effective against syphilis spirochetes. The arsphenamines was then made available in
1910, known as Salvarsan.[9]

In 1929 Alexander Fleming developed one of the most commonly used antibiotic
substances both at the time and now: penicillin.[10]

In 1939 Gerhard Domagk found Prontosil red protected mice from pathogenic
streptococci and staphylococci without toxicity. Domagk received the Nobel Prize in
physiology, or medicine, for the discovery of the sulfa drug.[9]

DNA sequencing, a method developed by Walter Gilbert and Frederick Sanger in

1977,[11] 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.[12] A few months later, the first eukaryotic genome
was completed. This would prove invaluable for diagnostic techniques.[13]

In 2007, a team at the Danish food company Danisco, were able to identify the
purpose of the CRIPR-Cas systems as adaptive immunity to phages. The system was
then quickly found to be able to help in genome editing through its ability to generate
double strand breaks. A patient with sickle cell disease was the first person to be
treated for a genetic disorder with CRISPR in July 2019.[14]

Commonly treated
infectious diseases
Bacterial

Streptococcal pharyngitis[15]
Chlamydia[16]
Typhoid fever[17]
Tuberculosis[18]
Viral

Rotavirus[19]
Hepatitis C[20]
Human papillomavirus (HPV)[21]
Parasitic

Malaria[18]
Giardia lamblia[22]
 Toxoplasma gondii[23]
Fungal

Candida[24]
Histoplasmosis[25]
Dandruff[26]

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).[27]

The site at which a microbe enters the body is referred to as the portal of entry.[28]
These include the respiratory tract, gastrointestinal tract, genitourinary tract, skin, and
mucous membranes.[29] The portal of entry for a specific microbe is normally
dependent on how it travels from its natural habitat to the host.[28]

There are various ways in which disease can be transmitted between individuals.
These include:[28]

Direct contact - Touching an

infected host, including sexual
contact
Indirect contact - Touching a
contaminated surface
Droplet contact - Coughing or
sneezing
Fecal–oral route - Ingesting
contaminated food or water
sources
Airborne transmission - Pathogen
carrying spores
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
Environmental - Hospital-acquired
infection (Nosocomial infections)
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.[30][31]

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.[32] 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.[33]

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:[34]

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.[35]
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.[36] 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.[37]

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.[34]
Polymerase chain reaction
Polymerase chain reaction (PCR) assays are the most commonly used molecular
technique to detect and study microbes.[38] As compared to other methods,
sequencing and analysis is definitive, reliable, accurate, and fast.[39] 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.[40]
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).[38] 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.[39] 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.[41]

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.[42] 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.[43]

Phage therapy is a technique that was discovered before antibiotics, but fell to the
wayside as antibiotics became predominate. It is now being considered as a potential
solution to increasing antimicrobial resistance. Bacteriophages, viruses that only
infect bacteria, can specifically target the bacteria of interest and inject their genome.
This process makes the bacteria halt its own production to make more phages, and
this continues until the bacteria lyses itself and releases the phages into the
surrounding environment. Phage therapy does not kill microbiota since it is specific,
and it can help those with antibiotic allergies. Some drawbacks are that it is a time-
intensive process since the specific bacterium needs to be identified. It also does not
currently have the body of research supporting its effects and safety that antibiotics
do. Bacteria can also eventually become resistant, through systems like CRISPR/Cas9
system. Many clinical trials have been promising though, showing that it could
potentially help with the antimicrobial resistance problem. It can also be used in
conjunction with antibiotics for a cumulative effect.[44]

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.[45] 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.[46]

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