CHAPTER SUMMARIES

BIO3 (Microbiology and Parasitology)

I. Introduction

● Microbiology is the study of small, living microorganisms or microbes that cannot

be seen with the naked eye. These organisms may be cellular (prokaryotes,
eukaryotes, and the like) or acellular such as viruses.
● Microbiology is divided into several fields that deal with the study of bacteria
(bacteriology), viruses (virology), fungi (mycology), protozoa and parasitic worms
(parasitology), algae (phycology), and the immune system (immunology).
● Microorganisms may be beneficial or harmful. Some microorganisms are used in
different industries such as in food and beverage. Some microorganisms are
sources of antibiotics while some are used in the field of biotechnology and genetic
engineering Microorganisms are also important in maintaining a balanced
ecosystem.
● While some microorganisms are essential and have beneficial uses, there are also
numerous microorganisms that produce disease in humans, some of which are
potentially fatal.

Highlights

● Some microorganisms have the potential to be used as biological warfare agents.

● Microorganisms are so miniscule that for them to be visualized, they need to be
● Stained and studied using the microscope. Several types pes of microscopes have
been
● Developed for this purpose-from the compound microscope to the more
sophisticated electron microscopes
● The use of various staining procedures has made visualization of microorganisms
easier. These stains may be classified into simple, differential, and special stains.
● Simple stains make use of a single water or alcohol-based dye that is used to
demonstrate the shape and basic structures of the organism.
● Differential stains are used to distinguish one group of bacteria from another group.
These include the Gram stain and the acid-fast stain.
 ● Special stains are mainly used to demonstrate specific bacterial structures such
as the spores (Dorner or Schaeffer-Fulton), flagella (Fischer & Conn), capsule
(Hiss stain), or the metachromatic granules (LAMB stain).
● Specific culture media are the most ideal in identifying specific organisms. Several
classes of culture media have been developed and these culture media can be
classified into three primary levels: physical state (liquid, semi-solid, solid),
chemical composition (synthetic and non-synthetic), and functional type (general
purpose, enrichment, selective, differential, transport, and anaerobic).

II. Prokaryotic and Eukaryotic Cells

● Living cells can be classified as either prokaryotic or eukaryotic.

● Prokaryotic cells, as exemplified by bacteria, are usually unicellular, do not
possess a true nucleus and membrane-bound organelles, and multiply by means
of binary fission.
● Eukaryotic cells vary from unicellular (e.g., protozoa) to multicellular (e.g., fungi).
They possess a true nucleus surrounded by a nuclear membrane as well as
membrane-bound organelles
● Viruses are not classified as cells since they only possess an outer covering called
capsid and a nucleic acid (either DNA or RNA). As such, they are dependent on
the host cell machinery for their replication and are thus considered as obligate
intracellular parasites.
● Medically important organisms are those which produce significant disease in
humans. These may take the form of viruses, bacteria, fungi, protozoa, and algae
● Viruses are acellular, obligate intracellular parasites possessing only DNA or RNA
and may be classified based on:

(1) type of nucleic acid they possess

(2) shape of the capsid (icosahedral, helical, polyhedral, or complex);
(3) number of capsomeres,
(4) size of the capsid;
(5) presence or absence of an envelope;
(6) type of host they infect (humans, plants, or animals);
(7) type of disease they produce,
(8) target cell or tropism (eg, T helper cells for HIV), and
(9) immunologic or antigenic properties.
 ● Bacteria are prokaryotic organisms that possess both DNA and RNA. Most
possess a cell wall composed predominantly of peptidoglycan.
● Fungi are eukaryotic organisms with a cell wall composed mainly of chitin and cell
membrane that contains ergosterol.
● Protozoa are mostly unicellular parasites that are eukaryotic. Most divide by binary
fission similar to bacteria
● Algae are eukaryotic, aquatic, plant-like organisms. Similar to plants, they are
photosynthetic but unlike plants, they do not have true roots, stems, or leaves.

Highlights

There are three basic shapes of bacteria: (a) spherical or cocci; (b) rod-shaped or
bacilli, and (c) curved or spiral.

A typical prokaryotic cell is composed of three major components: an outer envelope

with its projecting structures, the cell membrane, and the internal structures. The
envelope Is composed of the following:

○ the outermost covering is the glycocalyx, also known as the capsule. It is

adherent to the cell wall and slime layer when it is loosely attached to the
cell wall.
○ The cell wall or the murein sacculus provides rigid support and shape to
the bacteria. Its main component is peptidoglycan, which is multilayered
in gram-positive bacteria and monolayered in gram-negative bacteria.
● Gram-positive cell wall contains teichoic acids which may function for the
attachment of the bacterium to the host cell, as well as polysaccharide molecules.
● Gram-negative cell walls contain lipopolysaccharide made of a lipid A molecule
and polysaccharides. The lipid A component is responsible for the endotoxic
activity of gram-negative bacteria. The lipopolysaccharide is an integral part of
the outer membrane of gram-negative bacteria. Gram-negative bacteria also have
a periplasmic space where important enzymes are found.
● Acid-fast organisms possess a cell wall that is also made up of an inner layer of
peptidoglycan and an outer layer rich in waxes composed of mycolic acid and
other lipids. This is responsible for the hydrophobic nature of its cell wall and the
main reason why acid-fast organisms cannot be stained using the reagents for
Gram-staining.
● Structures projecting from the bacterial capsule include pili or fimbriae of gram-
negative organisms, flagella, and axial filaments of spirochetes.
● There are two types of pili:
○ common pill which functions for attachment and sex pili which participates
in gene exchange among bacteria in a process called conjugation.
 ● Flagella may be of four patterns:
○ (1) lophotrichous (a tuft of flagella on one end of the bacterium),
○ (2) amphitrichous (a single flagellum on each end of the bacterium),
○ (3) peritrichous (flagella surrounding the bacterium), and
○ (4) monotrichous (only one flagellum at one end of the bacterium).
● Axial filaments are similar in structure to flagella and help propel the spirochetes
forward.

III. Bacterial Morphology

Highlights

● Bacterial cytoplasmic membrane is the functional analogue of the

mitochondria. It is selectively permeable and is the site of ATP production of
aerobic bacteria.
● Bacteria do not have a true nucleus. Its genetic material is packaged in a
structure called nucleoid. Bacterial ribosome is smaller than a typical eukaryotic
ribosome.
● Bacteria possess structures that enable them to withstand adverse
environmental conditions. These structures are the endospores which are
mainly composed of dipicolinic acid.
● Other structures found in bacterial cells are the mesosomes, which play a
role in cell division, and inclusion bodies or granules in some bacteria which
serve as storage for food.

IV. Bacterial Growth Requirement

Highlights

● Bacteria require optimum nutrition and physical conditions for their growth.
 • Nutritional requirements of bacteria include adequate supply of carbon,
nitrogen, sulfur phosphorus, inorganic ions, and growth factors.

● Bacteria are classified into two groups based on their carbon source: autotrophs/
lithotrophs and heterotrophs/organotrophs.

● Autotrophs utilize inorganic compounds for their carbon source while organic
compounds such as glucose serve as the carbon source of heterotrophs.

• Bacteria derive energy by two means: from sunlight or from oxidation of

inorganic substances.

● Physical requirements of bacteria include moisture, oxygen, temperature, pH, and

osmotic conditions.

● Bacterial cells are made up mostly of water, which serves as the medium from
which bacteria derive their nutrients.
● Organisms that require oxygen for optimal growth are called aerobes while those
that cannot survive in the presence of oxygen are called anaerobes.

• Facultative organisms are those which can grow in the presence or absence of
oxygen.

● Bacteria may be grouped into three based on their temperature requirements:

○ (1) those that require high temperature (thermophiles);

○ (2) those that require temperature c 20°C-40°C (mesophiles); and
○ (3) those that require temperatures of 10°C-20 (psychrophiles).
● Acidophiles are organisms that grow best in pH < 6.0. Neutrophiles grow at pH
of 7.0-7.2 while alkaliphiles are those that grow best at pH of 8.4-9.0.
● Organisms that require salt for growth are called halophiles. Osmophiles are
those that need high osmotic pressure for maximal growth.
● Based on their nutritional and physical requirements, most medically important
bacteria are chemoorganotrophs, facultative, mesophiles, and neutrophiles.
 ● The bacterial growth curve illustrates the phases of growth of a bacterial
population grown in a culture of fixed volume. It is divided into a lag phase, log
phase, stationary phase, and death or decline phase.

V. Normal Flora of the Human Body

Highlights

● Normal or indigenous flora refers to organisms that inhabit the body of a normal
healthy individual
● Resident flora, also known as normal flora, refers to microorganisms that are
regularly found in a given area at a given age.
● Transient flora are those organisms that inhabit the skin and mucous membrane
temporarily for a few hours, days, or weeks. They do not establish themselves
permanently in the body tissues
● Normal flora have important roles in the body which can be beneficial or harmful.

Advantages of normal flora include:

1. Inhibition of growth of pathogenic organisms by priming of the immune system

2. Synthesis of vitamin B12 and vitamin K in the intestines.
3. Synthesis of substances that may inhibit growth of pathogenic organisms (eg.,
enzymes, fatty acids, bacteriocins).

Disadvantages of normal flora include.

1. Production of disease if the individual becomes immunocompromised or if they

change their usual anatomic location.
2. Production of disease since most of them are pathogens or opportunistic
pathogens.

● Most of the normal flora in the skin are found in moist, intertriginous areas.
Diphtheroids and Staphylococcus epidermidis are the predominant flora of the
skin.
● The tongue and buccal mucosa are inhabited mostly by Streptococcus viridans
group, which includes S. mutans, S. milleri, S. salivarius, and S. sanguis. The
gingival crevices and the tonsillar crypts are primarily inhabited by anaerobic flora.
 ● There may be transient carriage in the pharynx of potentially pathogenic
organisms.These include Harmophilus influenzae, Streptococcus pneumoniae,
Neisseria meningitidis, and Mycoplasma.
● In the upper respiratory tract, initial colonization by pathogenic organisms may
be seen. These include Neisseria meningitidis, Corynebacterium diphtheriae, and
Bordetella pertussis.
● Most of the bacteria cultured in the small intestine include streptococci,
lactobacilli, and Bacteroides which are all transient.
● The colon is inhabited predominantly by anaerobes (95%-99%) which includes
Bacteroides fragilis most common in (predominant breastfed infants), Esharterium,
Peptostrepteners, and Charrio vaginal flora varies depending on the age, hormonal
levels, and vaginal pH.
● In female infants, the predominant vaginal flora is Lactobacillus spp.
● From 1 month of age until puberty, microorganisms which may inhabit the vagina
include Staphylococcus epidermidis, Streptococci, diphtheroids, and Enterichia.
● At puberty the predominant flora include Lactobacillus acidophilus,
Corynebacterium Peptostreptococcus, Streptococci, Bacteroides, and
Staphylococci.
● Fungi such as Torulopsis and Candida may also be found (10%-30%).

VI. Medical and Surgical Asepsis

Highlights

● Sepsis is a clinical condition where infectious agents are spread throughout the
body of an individual from a localized site of infection and manifest with symptoms
of vegan damage
● Asepsis is the absence of disease-producing organisms and is divided into
medical asepsis and surgical asepsis.
● Medical asepsis is aimed at reducing the number of disease-producing organisms
to prevent its spread from healthcare workers to the patients and vice versa.
● Surgical asepsis is aimed at total elimination of disease-producing organisms
particularly in areas in the body where surgical procedures will be performed as
well as the location where the surgical procedure will be carried out.
 ● Handwashing is the most basic and universally accepted measure used to
prevent the spread of infection. Routine hand washing for at least 15 seconds with
a 10-second rinse is recommended.
● Personal protective equipment (PPE) are specialized equipment and attire used
in healthcare facilities to protect not only the healthcare workers but also the
patients and visitors against infections. These include masks, gowns, and goggles.
Guidelines have been set in the proper use of these personal protective
equipment.
● Universal precautions are specific measures geared towards handling of patients
with an infection from an unknown pathogen to decrease the risk of transmission.
These precautions apply to all body fluids including blood, skin, and mucous
membranes
● Transmission-based precautions have been developed to further prevent the
spread of infectious agents. These precautions are based on the mode of
transmission of the infectious agents and are classified into:

(1) contact precautions,

(2) droplet precautions, and
(3) airborne precautions

● The operating room is one of the most sterile areas in the hospital. Strict measures
must be followed to ensure sterility not only of the operating room but also of the
instruments and materials to be used in a surgical procedure. All healthcare
personnel entering the operating room must observe strict precautions to maintain
its sterility.
● The best way to prevent the spread of infection is at the community level. Proper
health education on the sources of infection as well as the transmission of disease-
producing microorganisms is essential. Preventive measures such as vaccination
must also be emphasized.

VII. Sterilization and Disinfection

Highlights

Sterilization is the process of removing all microbial forms, including spores

Factors that affect the effectivity of physical methods of sterilization include
 1. Nature of the heat

2. Temperature and time

3. Number of microorganisms

4. Nature of microorganisms

5. Type of material

6. Presence of organic material

Heating is the most common physical method of sterilization. It acts by the

following mechanisms

1. formation of single-strand breaks in bacterial DNA

2. coagulation and denaturation of proteins

3. accumulation of toxic levels of electrolytes

4. alteration of cell membrane structure

● An effective chemical disinfectant must have a broad spectrum of activity, be

fast-acting, inexpensive, easy to apply, odorless, and non-toxic to human tissues.
● Chemical agents used for disinfection and sterilization are classified based on
their massive mechanisms of action.
● Agents that cause damage to the cell membrane include surface active agents,
phenols compounds, and alcohols.
● Acids and alkalis, alcohol and acetone, phenols and cresols all cause
denaturation of proteins.
● Modification of functional protein groups is the mechanism of action of heavy
metals halogens, and alkylating agents,

Antimicrobial Activity

Highlights
● Synthetically produced in laboratories. These agents are designed to either kill the
target bacteria (bactericidal) or inhibit its growth (bacteriostatic).
● An Ideal antimicrobial agent must have a broad spectrum of activity, be stable
when and in either solid or liquid form, remain in target tissues for a specified
amount destroy the target organisms before it has a chance to produce disease,
and not cause damage and harmful effects on the host
● Antimicrobial activity classified in several ways:

1. Based on the spectrum of activity (broad spectrum or narrow-spectrum)

2. Based on their antimicrobial activity (bactericidal or bacteriostatic)

3. Based on their absorbability from the site of administration (systemic or local)

4. Based on their mechanism of action

● Based on the mechanism of action, antibiotics may be classified into

1. Agents that inhibit the synthesis of the bacterial cell wall

2. Agents that alter the function or permeability of the cell membrane

● Agents that inhibit protein synthesis

3. Agents that act on the nucleic acid

4. Agents that interfere with bacterial metabolic pathways

● The indiscriminate use of antibiotics, together with inaccurate diagnosis and poor
patient compliance have contributed to the emergence of drug resistance of
microorganisms. Resistance may be innate or acquired.
● Innate resistance is encoded in the chromosome of the organism.
● Acquired resistance is not normally coded in the chromosome of the organism
but may be the result of chromosomal mutation or genetic exchange between
organisms
● Acquisition of resistance genes through genetic exchange can occur in three
way transformation, transduction, and conjugation.
● There are several mechanisms developed by bacteria that enable them to develop
resistance to selected antimicrobials. These include

(1) drug modification or interaction,

(2) prevention of cellular uptake or efflux,
(3) modification of target sites,
(4) production or bypass of target enzyme, and
(5) target mimicry.