Chapter 1:

Introduction to Medical Microbiology

Medical microbiology is the study of parasites, fungi, bacteria, and viruses that are the
agents of infectious disease in humans. Modern medicine relies on the control of
microorganisms to maintain human health and quality of life. The divisions of medical
microbiology include bacteriology, the study of bacteria that inhabit and/or colonize the human
body and cause disease; mycology, the study of fungi as causative agents of human disease;
parasitology, the formal study of the human parasitic organisms (protozoans, helminths,
nematodes, trematodes and arthropods); and virology, the study of viruses that cause
infectious syndromes in humans. Sizes for the pathogens considered include the smallest,
viruses (50-100nm), bacteria that range from 0.1 µm (Chlamydiae) to 10µm (Bacillus rods),
fungi ranging from ~8µm (yeasts) up to 10mm in size (filamentous fungi) and metazoan
parasites that are visible to the naked eye.

Medical microbiology as a discipline requires a working knowledge of human anatomy and

histology, and a comprehension of the pathologies associated with the infectious disease
process. The human immune response to pathogens is key to the consideration of infectious
disease. Understanding the relationship between pathogens and antimicrobial pharmacology is
essential as well. Microbiology places information about pathogenic organisms and their
specific characteristics within the context of host disease. Developing connections between
microbiology and immunology will make learning more effective in both disciplines.

Special patient populations are important to consider and should be appreciated for the
distinctive infectious disease presentations they reflect. Age-related immuno-compromised
status makes the elderly and the very young, especially newborn infants, particularly at-risk for
respiratory infections. Health-related immunosuppression can predispose organ transplant
recipients, and patients with immunodeficiency disorders, cancer, and diabetes to difficult
infections. And, unique exposures due to occupation or travel can be a problem for some
patient populations. An immunocompromised person is lacking in some aspect of innate or
adaptive immunity due to either a primary or secondary immune deficiency. Whatever the
route, the net result is that the immunocompromised individual becomes susceptible to infection
with a range of opportunistic pathogens from the commensal microflora and conventional
infectious agents that cause a more severe form of disease than in a 'normal' host. This
depends on how the patient's condition affects each limb of the immune system, which in turn
controls the most likely pathogens. Immunity to infection and sensitivity to normal commensal
microbes as pathogens varies throughout life and not just in 'disease' states.
Host-Parasite Relationships
A parasite is an organism that makes its living at the expense of another organism, so in a
broad sense, all human pathogens fall under the blanket term “parasite”. A parasite derives its
nutrients and ecosystem from the host and is able to grow and reproduce in this environment.
Medical microbiology presents concepts relating host-parasite relationships and the human
immune system’s response to infectious disease. Microbial ecology and system imbalance are
keys to the understanding of many common diseases. The development of an infection and its
eradication frequently involves issues that are defined as much by the host as by the microbial
parasite, a balance between host immunity and the virulence of the infectious agent.

NORMAL FLORA
The normal microbial flora of the human body is located mainly in the superficial layers and
gastrointestinal tract. Gastrointestinal pathogens have some resistance to gastric acid and bile
and agents of skin infections are resistant to drying. Lower respiratory and upper urogenital
tracts are sterile normally, but they are susceptible to microbial “invasion” from adjacent sites.
Contamination occurs when microbes come into contact with host surfaces.

Colonization. The skin of a newborn infant is populated initially by the organisms carried in
the urogenital tract of the mother and acquired by the baby at birth. The mother’s skin and
breath are additional sources of normal bacteria that become the infant’s commensal
population, especially the mucosal normal flora.

The Oral Cavity. Many of the “normal” flora can be disease-causing organisms under the
right conditions. Viridans streptococci are largely responsible for dental caries and pitting of
tooth enamel by Streptococcus mutans acidic metabolic by-products is well documented.

Beneficial Effects. Vitamin synthesis and bile pigment degradation are two beneficial
effects provided by bacteria to the host (Bacteroides species make vitamin K and degrade
intestinal bile). Resident microflora inhibit the of growth of potential pathogens, as well as
providing mechanical advantages such as suppression of competitor’s adherence, antigen
priming of the immune system, maintenance of low redox potential, and bacteriocin secretion
(inhibits the growth of bacterial competitors).
 NUMBER OF MICROORGANISMS
IN COLLECTED SAMPLES
Nasal Washings 106 microbes/ml fluid
Saliva 108 microbes/ml
Tooth Surfaces 108 microbes/ml
Gingival crevices 1011-1012 microbes/ml
PROKARYOTIC cells outnumber EUKARYOTIC
cells in the human body, by a factor of 10 to 1!

DISEASE PROGRESSION
The period of total infection is from point of first contact until point of complete elimination
of the pathogen. Overt disease is associated with the onset of symptoms. In a recurrent
infection, the disease reappears over time with a characteristic rise and fall of agent shedding
and symptomatic disease. The seropositive phase occurs where the patient has been
exposed to a pathogen and has mounted an antibody response that is reflected in detectable
levels of specific serum immunoglobulin. Incubation is defined as the period from the point of
first contact until the point of appearance of symptoms of infection (when “disease is present”).
Latent infections remain dormant, and then re-emerge after stress or a lapse in immune
function. During the period of communicability the infectious agent is being continuously
shed by the patient. To complete the cycle of infection, infectious agents are excreted, and the
route of excretion dictates the mechanism of spread. Fecal-oral spread involves excretion
within stool samples and may be aided by diarrhea. Pathogens are often aerosolized in
respiratory secretions by sneezing and coughing. STD agents are transmitted by sexual contact
with vaginal, cervical or urethral fluids. Zoonotic infections are diverse and cause diseases
where humans are either a part of the normal infectious cycle or accidental hosts by contact
with vectors or reservoir animals. Some of these agents are excreted in feces and urine, but
also through parasitemia (widespread presence of the parasite). Examples include bloodstream
parasitemia, to ensure uptake by blood-sucking insects (e.g. Anopheles mosquitos and malaria)
and rabies virus budding from salivary gland cells to aid viral spread through animal bites.

Pathogen Virulence Mechanisms. Host-parasite interactions can be described as

pathogenic vs nonpathogenic (pathogenicity=ability to cause disease or multiply within a
host), or invasive as opposed to a successful commensal avirulent status quo (the human as
an ecological niche). Virulence is a concept of “degree of pathogenicity”. Some viruses and
other pathogenic microbes characteristically cause disease and these may express highly
specific adhesins or toxins. Virulent organisms cause a specific host injury that is removed
when the gene encoding a specific toxin or trait is deleted. The genes controlling the synthesis
of these factors are grouped together under the control of a single promoter in pathogenicity
islands. Examples of virulence factors include the neurotoxin secreted by Clostridium tetani
(tetanospasmin) and the capsule of Streptococcus pneumoniae that subverts phagocytosis by
preventing ingestion. Toxin production is a common virulence factor and bacterial exotoxins
can inhibit host cell protein synthesis, stimulate watery secretions, and cause violent symptoms
of disease in the host. Attachment and adherence via specific epithelial and mucosal receptors
(integrins) is another form of virulence because adhesion protects pathogens from the flushing
of mucosal surfaces. Vibrio cholera binds to sites on the villi of the jejunum or ileum. Virulence
is mediated by strength of attachment phenomena. Specifically pathogenic strains of
Escherichia coli have capsular antigens (K1) that make the bacteria neurotrophic; most strains
of E. coli are harmless commensal organisms that occupy space in the human gastrointestinal
system.

Inhibition of host immune mediators. Inhibiting host immune cell products to blunt the
anti-microbial response is a strategy of many pathogens. Some organisms produce leukocidins
that kill neutrophils and macrophages. Others have intracellular growth patterns that allow them
to avoid detection by the host’s immune system (these will be discussed with the pathogen
groups). Streptococcus pyogenes and Pseudomonas aeruginosa degrade human C5a using a
peptidase enzyme. IgA protease is an immunoglobulin-destroying enzyme produced by
Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae. Complement
compoenent C3b binding is inhibited by HSV envelope glycoprotein and vaccinia virus
accelerates the decay of complement C3 convertase. Staphylococcus aureus produces
catalase and this enzyme breaks down hydrogen peroxide in neutrophil phagolysosomes to limit
bactericidal activity. Each of these mechanisms is a unique process for pathogen survival.

Molecular mimicry. Another pathogen survival mechanism is to change its surface

composition, utilizing a mask to avoid immune detection. One way to do this is simply to
become coated with human “self-antigens”. This method is used by Treponema pallidum (coats
itself with fibronectin); Neisseria meningitidis (coats itself with circulating host IgA); and vaccinia
virus (incorporates host sialic acid into its capsular polysaccharides). Presenting a changing
target is the strategy for Trypanosomes and influenza virus (gene switching changes surface
proteins).
Koch’s postulates are an important set of criteria that can be used to judge whether a
microbe is the cause of a disease in question. First, the organism must occur in every case of
the disease, and must be responsible for the pathological changes observed. Next, the
organism must cause the same disease in a new host exposed to an isolate, and must in turn
be isolated from the new host.
EPIDEMIOLOGY
Epidemiology is the study of disease patterns and trends, of the occurrence, distribution and
control of disease in populations. It also deals with disease tracking and prevention. Disease
transmission is the movement of the infectious agent from one host to another. The risk of
infection is dependent not just upon an individual patient's susceptibility, but on the level of
disease within the population, the extent of population mixing and “herd immunity”, added to the
specific features of disease spread, such as communicable period, route and ease of
transmission (infectiousness).

Modes of Transmission. Numerous modes of transmission contribute to the spread of

human disease. For an infectious agent to persist within a population a cycle of transmission
must be established leading from a contaminated source to a susceptible host and further
propagating through the population.

Composite
diagram illustrating
the various modes
and routes of
disease
transmission.

Direct infection is the movement of a pathogen from human to human. Examples of

organisms causing direct infection are Salmonella typhi and Shigella species, both of which
infect humans only. Indirect transmission involves human to soil, water or surface
dissemination of pathogens and infection of another human through contact with contaminated
materials. This idea encompasses vehicle-borne transmission, whether through infected
everyday objects or surgical instruments. Vibrio cholera is an example of a pathogen that is
transmitted through contaminated water, especially in brakish coastal waters. Zoonotic
transmission occurs through exposure to a nonhuman animal source of infection. The
arthropod-borne agents like Borrelia and Rickettsia are included here as well as Spirillum,
Brucella and Bacillus anthracis, that are contracted through animal bites or contact with animal
products. Elimination is a potential outcome for a healthy host, whereby the parasite is
eradicated at the end of infection cycle.

Routes of Transmission. The direct route means physical contact between humans or
between a human and an animal to cause disease. Portals of entry include the gastrointestinal
tract, respiratory mucosa, genital mucosa, and direct inoculation through the skin. Mucous
membranes are especially important (STDs are transmitted in this way). The airborne route or
respiratory droplet transmission is very important for viral pathogens and respiratory tract
infections (aerosols). Fomites are inanimate objects contaminated with microorganisms, like
drinking cups, towels and computer keyboards. The waterborne route is an especially important
for enteric disease and it’s an important route for fecal-oral transmission (ingestion). Vector-
borne transmission is critical for some viral (arbovirus) & zoonotic infections (arthropod borne
parasites).

MORBIDITY/MORTALITY
Morbidity is the number of cases (or the incidence) of a specific disease per unit population
(cases per 100,000). Mortality is the number of deaths due to a specific disease per unit
population (deaths per 100,000). The “Centers for Disease Control and Prevention” publishes
the Morbidity and Mortality Weekly Report (MMWR), a monthly journal that documents
important disease trends in the United States. http://www.cdc.gov/mmwr/

EUROPEAN BUBONIC PLAGUE STATISTICS

Year
1348 67% 100%
1361 50% 90%
1371 10% 50%
1382 5% 50%
1663-1668 last European pandemic
1890 San Francisco
1903 Sydney, Australia
 Rates of morbidity and mortality; prevalence and incidence. To illustrate
morbidity/mortality concepts, for the U.S., Chagas disease has a low morbidity and low
mortality, because it is present at very low incidence (the disease is not endemic, ie, not a
typical pathogen for the region). Where Chagas’ disease is present, it results in low mortality
because the disease has a chronic nature, and death is not an acute outcome. In contrast, viral
influenza has a high morbidity and relatively low mortality; many people are infected every year,
but a low percentage of those affected will die from the disease. Ebola virus on the other hand
has a low morbidity and a high mortality in the U.S.; it is hardly found, but is nearly always
lethal. Prevalence is defined as “the number of cases of infection per unit of population at a
single point in time”. Disease incidence refers to “the number of new cases of infection per unit
of population over a specified period of time”. Disease levels vary throughout the year for some
types of infection (for example the rise in respiratory tract infections during the winter months)
with others remaining at a steady state (like urinary tract infection). Some infections have
periodic cycles measured over longer scale, for example a four-year cycle for Mycoplasma
pneumonia.
Patterns of infectious diseases vary throughout the world, depending upon factors such as
environment, weather, economic factors, nutrition, behavior and the local healthcare systems. It
is essential that every clinician is aware of regional disease patterns for effective diagnosis,
treatment and control of infection within their own practice of medicine. For serious
communicable diseases in the US, a part of surveillance is the legal requirement for medical
personnel to inform the local health department of every diagnosis of a notifiable disease.

Epidemiological data can be presented as age-related incidence (see diphtheria, below);

geographical representation (syphilis); social group affiliation and distribution over time (AIDS).
Diphtheria is the first component of the DPT vaccine (Diphtheria, Pertussis, Tetanus). For
people 55 and older, there is an increase in morbidity because the DPT vaccine was
unavailable 50 years ago, and data represented by age group shows that almost everyone had
the disease at one time. For the example of morbidity and geographical variance, syphilis is
especially high in the rural, southern part of the US, while its incidence is lower nationally. This
is in part due to historical problems with healthcare access in rural areas with high minority
populations (socioeconomic factors).

Finally, AIDS is a unique example of epidemiology in many respects. Initially thought to be

a disease of specific population segments (Haitians, hemophiliacs, heroin addicts,
homosexuals), it is now recognized to have more complexity (social group demographic). It is
also a group of diseases that reflect primary underlying immunodeficiency, and this is a
recurring theme throughout the study of infectious disease. And finally, the appearance of AIDS
is changing over time, with increases in the incidence among the female and pediatric
populations in the US, as well as in the MSM population (the CDC definition of “men who have
sex with men” encompasses the highest-risk homosexual and bisexual male population).

The changing US
mortality rates for
HIV infection over
time in the young
adult population,
compared with
other leading
causes of death in
this population.

DISEASE DEFINITIONS
A cluster of cases in a specific area or a single household is termed an outbreak, and is
usually related to a local exposure source. An increase in case incidence over a larger region,
perhaps an entire state or country, is described as an epidemic. This is less likely to be caused
by a single source, and a concerted effort might be required to control the spread. An increase
in incidence over a much larger area, several countries or a hemisphere, is described as a
pandemic. Effective control of outbreaks requires prompt diagnosis, descriptive epidemiology
[source(s) of infection, mode/route of transmission, identification of additional people at risk] and
the rapid use of an effective way to abort the infection cycle.

CDC EMERGING INFECTIONS PRIORITY ISSUES, 1999-2004

• Antimicrobial resistance
• Opportunistic infections
• Food and water safety
• Vectors and animal health
• Blood safety
• Infections that cause chronic diseases
• Vaccine development (malaria; rotavirus; influenza virus)
• Maternal and child health
• Health of travelers and refugees
PATHOGEN – DISEASE PAIRS
Staphylococcus aureus – staphylococcal toxic shock syndrome
Streptococcus pyogenes – Strep sore throat
Streptococcus pneumoniae – otitis media and pneumococcal pneumonia
Neiserria gonorrhoeae – sexually transmitted infection
Neiserria meningitidis - meningitis
Legionella pneumophila – Legionairre’s disease
Bordetella pertussis – respiratory disease
Corynebacterium diphtheria - Diphtheria
Clostridium perfringens – Gas gangrene
Clostridium tetani - Tetanus
Salmonella typhimurium - Salmonellosis
Shigella dysenteriae – Bacillary dysentery
Vibrio cholerae - Cholera
Yersinia pestis – Bubonic plague
Treponema pallidum - Syphilis
Propionibacterium acnes - Acne

REFERENCES:
Centers for Disease Control and Prevention, http://www.cdc.gov/,
information accessed 11-10-2004.
Merck Manual of Diagnosis and Therapy, “The Biology of Infectious Diseases”. (1999) 17th
Edition, Merck Res. Labs, Whitehouse Station, NJ, pp 1088-1097.
Murray, PR, Rosenthal, KS, Kobayashi, GS, and Pfaller, MA (2002) Medical Microbiology, 4th
Edition, Mosby, Inc., St. Louis, MO pg 1-24; 78-81; 175-184.