1. Sterilization and Disinfection
3. Gram-positive bacilli Aerobic non-spore forming bacilli
4. Gram positive cocci Genus Staphylococci
8. Sexually transmitted diseases (STD) Genus Neisseria
11. (Part – one )Anaerobic Bacteriology
(Part – Two) Spore-forming gram-positive Bacilli: Bacillus and
12. Spore-forming gram-positive Bacilli: Bacillus and Clostridium
14. Central Nervous System Diagnostic Microbiology
15. Gastrointestinal Tract Diagnostic Microbiology
16. Diagnostic Microbiology /Urinary tract infections (UTIs)
17. Eye Diagnostic Microbiology
18. General structure and classification of viruses
25. Human Immunodeficiency Virus
Section I– Microbiology Introductory By Dr. Mohammed Ayad
They populate the healthy human body by the billions as benign passengers (normal flora) and even as
participants in bodily functions. Those relatively few species of microorganisms that are harmful to
the skin or mucous membranes). The major exceptions are diseases caused by introduction of organisms
directly into the bloodstream or internal organs.
Microbial colonization may result in:
1- elimination of the microorganism without affecting the host
3- Transient or prolonged carrier state.
Infectious disease occurs when the organism causes tissue damage and impairment of body function.
All prokaryotic organisms are classified as bacteria, whereas eukaryotic organisms include fungi,
protozoa, and helminths as well as humans.
medical importance, and the archaebacteria, a collection of evolutionarily distinct organisms.
wall surrounding the cell membrane that determines the shape of the organism.
The cell wall also determines whether the bacterium is classified as gram positive or gram negative.
External to the cell wall may be flagella, pili, capsule.
plasmids (small, specialized genetic elements capable of self-replication) including the information
necessary for establishment of antibiotic resistance.
Atypical bacteria include groups of organisms such as Mycoplasma, Chlamydia, and Rickettsiae that,
separate them from the larger group of typical bacteria.
Fungi are nonphotosynthetic, generally saprophytic, eukaryotic organisms. Some fungi are filamentous
and are commonly called molds, whereas others (that is, the yeasts) are unicellular.
Protozoa are single-celled, nonphotosynthetic, eukaryotic organisms that come in various shapes and
humans. Members of this group infect all major tissues and organs of the body.
Section I– Microbiology Introductory By Dr. Mohammed Ayad
Transmission is generally by ingestion of an infective stage of the parasite or by insect bite.
complex body organization. They are divided into three main groups: tapeworms (Cestodes), flukes
(Trematodes), and roundworms (Nematodes).
absorbing body fluids or tissues. Almost any organ in the body can be parasitized.
molecule(s) of DNA (DNA virus) or RNA (RNA virus), but not both, surrounded by a protein coat.
A virus may also have an envelope derived from the plasma membrane of the host cell from which the
require the host’s cellular structures and enzymatic machinery to complete the process of their own
virions to gradual prolonged release of viral particles.
The human body is continuously inhabited by many different microorganisms (mostly bacteria, but also
These microorganisms are termed “normal flora.” The normal flora is also termed commensals, which
normal flora from food and the environment, including from other humans.
The human microbiome is the total number and diversity of microbes found in and on the human body.
identification of normal flora and bacterial pathogens.
However, the recent application of culture-independent molecular detection methods based on DNA
sequencing indicates that the human body contains a far greater bacterial diversity than previously
nonculturable species. Even using advanced molecular techniques, it is difficult to define the human
microbiome because microbial species present vary from individual to individual as a result of
aware of the dominant types and distribution of resident flora, because such knowledge provides an
understanding of the possible infections that result from injury to a particular body site.
Section I– Microbiology Introductory By Dr. Mohammed Ayad
or communication with the outside world, namely, the skin, eye, and mouth as well as the upper
respiratory, gastrointestinal, and urogenital tracts.
I- Skin can acquire any bacteria that happen to be in the immediate environment, but this transient
flora either dies or is removable by washing. Nevertheless, the skin supports a permanent bacterial
skin layers, hair follicles, and sweat and sebaceous glands.
Skin inhabitants are generally harmless, although S. epidermidis can attach to and colonize plastic
catheters and medical devices that penetrate the skin, sometimes resulting in serious bloodstream
While estimate of the skin microbiome using molecular sequencing techniques: The estimate of the
RNA gene sequence to identify bacterial species present on skin samples directly from their genetic
bacteria did not grow and so were not detected. Staphylococcus epidermidis and Staphylococcus aureus
were thought from culture-based research to be dominant. However DNA analysis research finds that,
The conjunctiva of the eye is colonized primarily by S. epidermidis, followed by S. aureus, aerobic
Corynebacteria (diphtheroids), and Streptococcus pneumoniae. Tears, which contain the antimicrobial
enzyme lysozyme, help, limit the bacterial population of the conjunctiva.
III- Buccal cavity and Nasal passages
The mouth and nose harbor many microorganisms, both aerobic and anaerobic. Among the most common
and surrounding gingival tissue are colonized by their own particular species, such as Streptococcus
valves, leading to potentially fatal infective endocarditis.
Some normal residents of the nasopharynx can also cause disease like S. pneumoniae, found in the
and those whose resistance is impaired ((Pneumonia is frequently preceded by an upper or middle
Section I– Microbiology Introductory By Dr. Mohammed Ayad
respiratory viral infection, which predisposes the individual to S. pneumoniae infection of the
In an adult, the density of microorganisms in the stomach is relatively low (103
contents) due to gastric enzymes and acidic pH.
The density of organisms increases along the alimentary canal, reaching 108
contents in the ileum and 1011 per gram of contents in the large intestine.
bacteria in the intestinal tract. However, this endogenous E. coli is a major cause of urinary tract
The low pH of the adult vagina is maintained by the presence of Lactobacillus species, which are the
primary components of normal flora. If the Lactobacillus population in the vagina is decreased (for
example, by antibiotic therapy), the pH rises, and potential pathogens can overgrow.
and bladder is sterile but can become contaminated in the lower urethra by the same organisms that
inhabit the outer layer of the skin and perineum.
Normal flora can provide some definite benefits to the host:
healthy person, an invading pathogen could compete for nutrients and receptor sites.
Second, some bacteria of the bowel produce antimicrobial substances to which the producers
themselves are not susceptible.
Third, bacterial colonization of a newborn infant acts as a powerful stimulus for the development of
Fourth, bacteria of the gut provide important nutrients, such as vitamin K, and aid in digestion and
absorption of nutrients; although humans can obtain vitamin K from food sources, bacteria can be an
important supplemental source if nutrition is impaired.
Clinical problems caused by normal flora arise in the following ways:
The organisms are displaced from their normal site in the body to an abnormal site. An example is
catheters and heart valves, resulting in bacterial endocarditis.
Section I– Microbiology Introductory By Dr. Mohammed Ayad
Potential pathogens gain a competitive advantage due to diminished populations of harmless
competitors; when normal bowel flora are depleted by antibiotic therapy leading to overgrowth by the
resistant Clostridium difficille , which can cause severe colitis.
Harmless, commonly ingested food substances are converted into carcinogenic derivatives by
bladder carcinogen cyclohexamine.
When individuals are immunocompromised, normal flora can overgrow and become pathogenic
where it results in disease)). Typhoid fever is an example of a disease that can be acquired from a
A pathogenic microorganism is defined as one that is capable of causing disease. Some microorganisms
are unequivocally pathogenic, whereas others (the majority) are generally harmless.
An organism may invade an individual without causing infectious disease when the host’s defense
The occurrence of such asymptomatic infections can be recognized by the presence of antibody against
dormant but may be reactivated with the recurrence of symptoms. Moreover, some pathogens cause
infection of an immunocompromised host).
Bacterial mediated pathogenesis
The mechanism of infectious process may vary among bacteria, the methods by which bacteria cause
kill 50 percent of test animals (LD50, where L = Lethal).
Salmonella is approximately 100,000 organisms.
the strength of the host immune response opposing infection.
Section I– Microbiology Introductory By Dr. Mohammed Ayad
These include phagocytosis; the acidic environments of the stomach and urogenital tract; and various
hydrolytic and proteolytic enzymes found in the saliva, stomach, and small intestine.
Bacteria that have an outer polysaccharide capsule (for example, Streptococcus pneumoniae and
Neisseria meningitidis) have a better chance of surviving these primary host defenses.
hydrophobic cell walls that allow them to adhere to the host cell membrane.
The adherence enhances virulence by preventing the bacteria from being carried away by mucus or
that of Neisseria gonorrhoeae in which strains that lack pili are not pathogenic.
are collagenase and hyaluronidase. These enzymes degrade components of the extracellular matrix,
providing the bacteria with easier access to host cell surfaces.
Many bacterial pathogens express membrane proteins known as "invasins" that interact with host cell
Invasion is followed by inflammation, which can be either pyogenic (involving pus formation) or
granulomatous (having nodular inflammatory lesions), depending on the organism.
The pus of pyogenic inflammations contains mostly neutrophils, whereas granulomatous lesions contain
fibroblasts, lymphocytes, and macrophages.
The pathogenic Neisseria species are exceptions in that they do not produce siderophores but instead
utilize host iron-binding proteins, such as transferrin and lactoferrin, as iron sources.
Virulence factors that inhibit phagocytosis
pneumoniae and N. meningitidis.
Section I– Microbiology Introductory By Dr. Mohammed Ayad
protein A of Staphylococcus and M protein of group A Streptococci.
Some bacteria cause disease by producing toxic substances, of which there are two general types:
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