Microbiology and Parasitology
Chapter 1: Scope of Microbiology
A. Microbiology
➢ from the Greek word mīkros - small; bios - life; and /logos - study
➢ the scientific study of microscopic organisms (microorganisms)
➢ includes many sub-disciplines like virology, mycology, parasitology and
bacteriology
❖ Microorganisms – organisms that are too small to see with the
naked eye
➢ Called as microbe
➢ Found in surroundings: air, water, soil, other object and in
the bodies of other organisms.
B. Classification of Microorganisms
➢ Microorganisms are classified according to the following
characteristics: form, size, habitats, nutrition, methods of
reproduction
1. Virus
➢ Smallest microorganisms.
➢ Visible under electron microscope.
➢ Different types of viruses have different shapes.
➢ Size: 0.0006 µm – 0.4 µm / (6 – 400 nm)
➢ a tiny bundle of genetic material carried in a protein coat shell called
the viral coat.
➢ Some viruses have an additional layer around the viral coat called an
envelope.
➢ Exist only to reproduce.
➢ Considered non-living things: DO NOT feed, respire, grow and respond
to stimuli.
➢ found on or in just about every material and environment on Earth
from soil to water to air; anywhere there are cells to infect.
➢ Parasitic and can reproduce only in the host cell.
2. Bacteria
➢ Tiny unicelullar organisms; Size: 0.2 µm – 10.0 µm.
➢ Named and classified by their shapes.
➢ Exist in four major shapes: bacillus (rod shape), coccus (spherical
shape), spirilla (spiral shape), and vibrio (curved shape).
➢ Most have a peptidoglycan cell wall
➢ They reproduce by binary fission, forming spores, or conjugation
➢ They may possess flagella for motility.
➢ Can be grouped based on their response to gaseous oxygen into the
following groups: aerobic (living in the presence of oxygen), anaerobic
(living without oxygen), and facultative anaerobes (can live in both
environments).
➢ Can be classified as heterotrophic/parasitic, saprophytic or autotrophic.
❖ Autotrophs make their own food by using the energy of sunlight or
chemical reactions, in which case they are called chemoautotrophs.
❖ Heterotrophs obtain their energy by consuming other organisms.
❖ Saprophytes use decaying life forms as a source of energy
3. Protozoan
➢ unicellular aerobic eukaryotes
➢ Size: 5 µm – 250 µm.
➢ Shape: various type – round, spherical, spindle-shaped.
➢ Live in bodies of other living things, the sea, fresh water and damp soil.
➢ Most are parasitic and feed on other living things, some are autotrophic
containing chlorophyll and carry out photosynthesis.
➢ traditionally divided based on their mode of locomotion: flagellates
use their whip-like structure (flagella) to propel forward, ciliates have
tiny hair (cilia) that beat to produce movement, amoeboids have false
feet (pseudopodia) used for feeding and locomotion, and sporozoans
are non-motile.
➢ Most reproduce asexually by binary fission; some reproduce sexually
through conjugation (paramecium).
4. Algae
➢ also called cyanobacteria or blue-green algae, are unicellular or
multicellular eukaryotes
➢ Live in water, damp soil, and rocks and produce oxygen and
carbohydrates used by other organisms.
➢ Size: 1 µm – 10 000 µm.
➢ Have various shapes, sizes and colors.
➢ Asexual: by binary fission, fragmentation and spore formation; Sexual:
by conjugation
5. Fungi
➢ Type: unicellular (yeast) / multicellular (mucor).
➢ Range: 10 µm – 100 µm.
➢ Have various shapes, sizes and colours.
➢ Found in outside / inside of living things; decaying organic matter.
➢ Have no chlorophyll; feed on other organisms as parasites/saprophytes
➢ Reproduce via asexual: produce spores, budding and sexual:
conjugation
6. Multicellular Animal Parasites
➢ A group of eukaryotic organisms consisting of the flatworms and
roundworms, which are collectively referred to as the helminths.
➢ Although they are not microorganisms by definition, since they are
large enough to be easily seen with the naked eye, they live a part of
their life cycle in microscopic form.
➢ Since the parasitic helminths are of clinical importance, they are often
discussed along with the other groups of microbes.
C. Microbes Have Changed History
➢ Although not always recognized at the time, microbes have dramatically
altered human history.
Microbes working with us:
✓ Food preservation and preparation for instance
✓ Beer, wine, bread, cheese, sauerkraut, yogurt
Microbes working against us:
✓ Many microbial diseases have altered the outcome of historical
events.
D. Branches of Microbiology
1. Pure Microbiology
➢ study of microorganisms for the sole purpose of understanding them
better, and not to a specific end
a. Taxonomic Arrangement:
➢ Bacteriology – study of bacteria
➢ Mycology – study of fungi
➢ Phycology – study of microscopic algae
➢ Virology – study of viruses
➢ Protozoology – study of protozoans
➢ Immunology – study of the immune system
b. Integrative arrangement
➢ Microbial cytology
➢ Microbial physiology
➢ Microbial genetics
➢ Microbial ecology
➢ Microbial taxonomy
➢ Cellular Microbiology
➢ Molecular Microbiology
2. Applied Microbiology
➢ study of microorganisms for the sake of using them, or controlling
them in a way that aids humanity.
a. Medical Microbiology
➢ involve the diagnosis, treatment and prevention of the spread of
infection in hospitals and the community.
➢ study of clinically significant microorganisms.
b. Industrial Microbiology
➢ microorganisms are used in industrial processes in the
production of high-value products
c. Pharmaceutical Microbiology
➢ associated field of industrial microbiology that is responsible for
preparation of medications.
E. Significance of Microbiology
1. Medical Microbiology
➢ To understand the types of microbial diseases
➢ To aid in the diagnosis and treatment of diseases caused by microbes
F. Practical Applications of Microbiology
1. Environment
b. Recycling of Elements
d. Microorganisms convert elements into forms available for plant
and animal use.
c. Bioremediation
➢ Microorganisms are used to clean up chemical spills, toxic waste
sites, oil spills etc.
➢ Microbial enzymes and other metabolites are used as cleaning
agents without using harmful chemical
2. Food
➢ Microbes are used in food production
3. Industry
➢ Use of microbes in production of value-added products.
4. Medicine
a. Drugs and Vaccine
➢ Microorganisms produce metabolites used as drugs for other
infections and other types of diseases
➢ Killed and attenuated disease-causing microbes are used as
vaccines to trigger immune response from the body
G. History of Microbiology
1. Discovery Era
a. Aristotle (384-322) and others believed that living organisms could
develop from non-living materials.
b. In 13th century, Roger Bacon described that the disease caused by a
minute “seed” or “germ”.
c. Antony Van Leeuwenhoek (1632 – 1723)
➢ Descriptions of Protozoa, basic types of bacteria, yeasts and
algae.
➢ Father of Bacteriology and protozoology.
➢ In 1676, he observed and described microorganisms such as
bacteria and protozoa as “Animalcules”.
d. The term microbe is used by Sedillot in 1878.
2. Transition Era
a. Francesco Redi (1626 - 1697)
➢ He showed that maggots would not arise from decaying meat,
when it is covered.
b. John Needham (1713 – 1781)
➢ Supporter of the spontaneous generation theory.
➢ He proposed that tiny organism(animalcules) arose
spontaneously on the mutton gravy.
➢ He covered the flasks with cork as done by Redi, Still the
microbes appeared on mutton broth.
c. Lazzaro Spallanzai (1729 – 1799)
➢ He demonstrated that air carried germs to the culture medium.
➢ He showed that boiled broth would not give rise to microscopic
forms of life.
3. Golden Era
a. Louis Pasteur
➢ He is the father of Medical Microbiology.
➢ He invented the processes of pasteurization, fermentation and
the development of effective vaccines (rabies and anthrax).
➢ Pasteur demonstrated diseases of silkworm was due to a
protozoan parasite.
Other contributions of Loius pasteur:
➢ He coined the term “microbiology”, aerobic, anaerobic.
➢ He disproved the theory of spontaneous germination.
➢ He demonstrated that anthrax was caused by bacteria and also
developed live attenuated vaccine for the disease.
b. John Tyndall (1820 - 1893)
➢ discovered highly resistant bacterial structure, later known as
endospore.
➢ Concluded that prolonged boiling or intermittent heating was
necessary to kill the spores, to make the infusion completely
sterilized, a process known as Tyndallisation.
c. Lord Joseph Lister (1827-1912)
➢ He is the father of antiseptic surgery.
➢ He concluded that wound infections too were due to
microorganisms.
➢ He devised a method to destroy microorganisms in the
operation theatre by spraying a fine mist of carbolic acid
into the air.
d. Robert Koch (1893-1910)
➢ He demonstrated the role of bacteria in causing disease.
➢ He perfected the technique of isolating bacteria in pure culture.
➢ Robert Koch used gelatin to prepare solid media .
➢ He Studied toxins and antitoxins in quantitative terms & laid
foundation of biological standardization.
4. Modern Era
Years
Nobel laureates
Contribution
1901
Von behring
Diphtheria antitoxin
1902
Ronald Ross
Malaria
1905
Robert koch
Tb
1908
Metchnikoff
Phagocytosis
1945
Flemming
Penicillin
1962
Watson,Crick
Structure DNA
1968
Holley,Khorana
Genetic code
1997
Pruisner
Prions
e. Fanne Eilshemius Hesse (1850 - 1934)
2002
Brenner, Hervitz
Genetic regulation of organ
➢ One of Koch's assistant
development & cell death
➢ first proposed the use of agar in culture media:
✓ It was not attacked by most bacteria.
Chapter 2: Microbial Control
✓ Agar is better than gelatin because of its higher melting
pointing (96°c) and solidifying (40 – 45°c)points.
A. Techniques for Controlling Pathogenic Microorganisms
f. Richard Petri (1887)
➢ Methods used to control the growth of microorganisms and their
➢ He developed the Petri dish (plate), a container used for solid
transmission of infectious disease involve: stopping the growth of the
culture media.
microorganism for a period of time, reducing the number of
g. Edward Jenner (1749-1823)
microorganisms to a safe level, or destroying the microorganism
➢ First to prevent small pox.
➢ He discovered the technique of vaccination.
I.
Terms Related to Destruction of Microorganisms
h. Alexander Flemming
1. Sterilization: the destruction of all microorganisms, including
➢ He discovered the penicillin from Penicillium notatum that
endospores, on an object or in a material.
destroy several pathogenic bacteria.
i. Paul Erlich (1920)
Sterilizing agents kill all living things, thus removing the living
➢ He discovered the treatment of syphilis by using arsenic
source of contagion.
2. Disinfection: the destruction of pathogens, but not endospores, on an
object or in a material. The number of pathogens is reduced or growth is
inhibited to a level that does not produce disease.
Disinfecting agents kill some microbes, but inhibit the growth of
others. Most techniques only provide disinfection.
3. Antisepsis: chemical disinfection of the skin, mucosal membranes, or
other living tissue
4. Sanitation: the reduction or removal of pathogens on inanimate objects
by chemical or mechanical cleansing
5. Germicide: a chemical agent that kills microorganisms
Specific germicides include:
a. sporicide - kills spores
b. bactericide - kills bacteria
c. viricide - kills viruses
d. fungicide - kills fungi
II.
Factors to consider for effective use of microbial control:
✓ population size
✓ the type of microorganism
✓ their physiological state (stage of growth or formation of endospores)
✓ susceptibility of the microorganism to the agent
✓ the environment in which they are grow in
✓ concentration of the dose used
✓ the duration of treatment
III.
Methods for microbial control
1. Physical methods either exclude microbes, or reduce their numbers in a
solution, or on the surface of a fomite (any non-living material which
might come into contact with the individual)
a. Filtration is the passing of either a solution or gasses through a device
which traps microbes on one side of a container or space, preventing
them from passing to the other.
b. Desiccation (drying) is the removal of moisture from the body of an
organism. Many bacteria are very sensitive to water loss and can be
killed simply by removal of water.
Lyophilisation or freeze-drying, is used to rapidly remove water
from the body of an organism under very cold temperatures in a
partial vacuum.
o used to preserve living bacterial cultures for storage and
transport.
c. Radiation describes a physical phenomenon which occurs when
matter releases either energy, atomic particles, or both.
✓ can affect the chemical makeup of the cell by altering or
disrupting the structure of biological molecules.
d. Temperature or excess heat energy can cause proteins to become
denatured, meaning that they lose their normal three-dimensional
shape.
The thermal death point (TDP) of each organism, which is the
temperature at which all growth stops, is the effective temperature
for the reduction of microbes
Thermal death time (TDT) is the amount of time it takes to kill all
of the microbes in a sample
Decimal reduction factor (DRF) is the amount of time at a
specific heat necessary to reduce the population of microbes in a
sample tenfold.
Common ways:
❖ Flaming and incineration: completely destroy all life.
❖ Dry heat: forcing hot air onto the surface of an object is used,
though many spore formers are capable of withstanding this.
❖ Moist heat: work well for most microbes, but are incapable of
killing organisms which are thermoduric or are spore formers
✓ Autoclave: device that works on the principle of saturated steam.
Autoclaving: the most effective application of moist heat
2. Chemical methods involve the application of specific chemical agents
which inhibit growth or kill microbes on fomites or the surface of skin.
➢ Chemical agents for the control of microbial growth are either:
Microbiocidal agents are sterilizers, which kill all living cells.
Microbiostatic agents kill some cells and inhibit the growth of
others.
Types of chemical agents for microbial control:
a) Antibiotics: produced by microorganisms to kill or inhibit the
growth of other microbes.
❖ generally selectively toxic, and can be naturally produced,
synthesized, or semisynthetic.
b) Antiseptics: synthetic compounds which kill or inhibit the growth of
microbes on the surface of the skin.
c) Disinfectants: chemical compounds which kill or inhibit microbes
on the surface of fomites.
d) Preservatives: inhibit microbial growth in food, usually by
producing osmotic environments which are unfavorable to microbial
growth.
❖ sugars, salt, nitrates, nitrites, sulfate, and sulphites
Classifications of chemical agents for microbial control
1. High-level germicides sterilize fomites, but are toxic to skin and
mucus membranes.
✓ called agents of cold sterilization, since no heat needs to be
applied to increase their activity.
✓ generally alkylating agents, which kill by adding ethyl or methyl
groups to nucleic acids or proteins.
✓ While the agents are capable of killing vegetative cells, spores,
and inactivating viruses, some take up to several hours to
complete their germicidal activity.
Aldehydes (formaldehyde and gluteraldehyde)
✓ fix tissues by alkylating and forming cross-links between
adjacent proteins.
✓ are commonly used as fixative compounds for electron
microscopy, preservatives of specimens and cadavers, in some
synthetic plastic compounds, and can be used to sterilize
anaesthesia tubing and surgical implements.
β-propiolactone
✓ generally used to sterilize bone used in grafts.
✓ quickly breaks down into nontoxic compounds when it comes
into contact with organic matter, but can burn skin.
Ethylene oxide (carboxide)
✓ kills vegetative cells and spores.
✓ generally used in a chamber similar to an autoclave at 60o C for
1-10 hours, where it is mixed in a 9:1 ratio with carbon dioxide
(90% CO2, 10% ethylene oxide), which reduces its toxicity, but
also its flammability.
✓ can be used to sterilize surgical implements and glassware, but
these fomites must be allowed to degas before use, since residues
can stimulate mutations in bacteria.
Ozone (O3)
✓ a powerful oxidizing agent, which kills cells and spores on the
surface of glassware, surgical implements, and bandages, if
applied properly in a chamber
✓ outgasses quickly, leaving no toxic residues
2. Intermediate-level disinfectants and antiseptics kill and inhibit
on fomites and skin, but can be toxic to the user at medium to high
concentrations. Examples include phenolics and halogens.
Phenol (carbolic acid)
✓ one of the earliest disinfectant compounds to be used in health
care facilities and laboratories.
✓ kills microorganisms by denaturing proteins and destabilizing
cell membranes
✓ is bacteriocidal, fungicidal, and virucidal at high concentrations,
and is effective against many potential pathogens, including
mycobacteria, staphylococci, streptococci, and gram-negative
coliforms, such as E. coli, but is not effective against bacterial
endospores
✓ can be used to disinfect garbage cans, surgical operating
facilities, laboratory equipment, feces, urine, and sputum, but it is
very corrosive at higher concentrations and its fumes can be
lethal.
✓ has such a broad-spectrum of activity, and is used as a standard
by which to judge how well other disinfecting compounds work.
❖ The phenol coefficient (P.C.) is a mathematical value used to
compare the effectiveness of a test disinfectant to that of phenol
Halogens
✓ are a family of elements with a high affinity for electrons. This
affinity makes them very reactive with biological molecules, and
they can serve to disrupt enzyme activity, break down lipid
structure, and produce oxidizing agents.
a) Chlorine is used as a disinfectant only, either as a gas or in liquid
form which is effective against many vegetative forms of
microbes as well as some viruses such as HIV and hepatitis.
b) Iodine is lethal to all vegetative forms of microorganisms, can
inactivate viruses, and is fairly effective in higher concentrations
against endospores.
c) Iodophore compounds are composed of iodine dissolved in
mild detergent and alcohol.
❖ do not excite pain receptors as readily and can be used to
clean and disinfect large areas of skin prior to invasive
surgical procedures.
3. Low-level disinfectants, such as alcohols, hydrogen peroxide, heavy
metals, and soaps kill some microbes but inhibit the growth of most.
Hydrogen peroxide
✓ a good low-level disinfectant agent when used in concentrations
of 3% or lower.
✓ Higher concentrations are caustic to human skin
✓ used as an antiseptic for the treatment of minor cuts and scrapes
and as a bleaching agent.
Alcohols (ethanol and isopropanol)
✓ are effective antiseptics and disinfectants when used in
concentrations between 70% and 80%.
✓ kill microbes by denaturing proteins, dehydrating (100%
concentration), and as nonpolar solvents which disrupt the
phospholipid structure of the cell membrane, but are relatively
ineffective against spores and viruses.
Heavy metals (mercury, silver, and copper)
✓ tend to combine with sulfur groups in the proteins of microbes,
causing them to denature.
✓ some of the earliest used agents for the control of
microorganisms.
Detergents and soaps
✓ are composed of lipids and compounds having basic pH, such as
sodium hydroxide.
✓ break up surface tension, act as wetting agents which release
particles attached to the surface of objects, and destabilize the
phosphate portions of the plasma membrane of microorganisms.
✓ Detergents are either anionic or cationic, releasing negatively or
positively- charged ions into solution.
➢ Anionic forms are weakly active against gram-positive
bacteria but tend to repel negatively-charged cells, thus they
are generally used in the production of iodophore compounds.
➢ Cationic forms are attracted to bacterial cells and are
bacteriostatic, while remaining relatively mild to the surface of
skin.
➢ Quartenary ammonium compounds (QUATS) are cationic
detergents which contain one or more long-chain akyl groups.
❖ have broad-spectrum inhibitory activity against bacteria,
fungi, and protozoa, are mildly antiseptic and disinfecting
when used as cleaning agents for laboratory fomites and on
the surface of skin, and remain active after drying, but lose
much of their activity when mixed with soaps.
Dyes
✓ can not only be used to stain microorganisms, but also have
antimicrobial activity.
✓ Crystal violet (used in very low concentrations as gentian violet)
can be used to treat oral infections by bacteria such as
Rochlaemia quintana, the agent of trench mouth, and fungal
infections such as Candida albicans, which causes oral thrush.
B. Surgical and Medical Asepsis
Terms Related to Suppression of Microorganisms
➢ Asepsis: the absence of pathogens from an object or area.
➢ Aseptic techniques: prevent the entry of pathogens into the body.
Two types of asepsis:
Medical Asepsis
✓ the reduction of the number of disease-causing agents and their
spread
Methods of Medical Asepsis
➢ Isolation of the patient
➢ Hand washing
➢ Preventive vaccination
➢ Increasing the awareness among visitors and relatives
➢ Use of gloves, masks, and gowns
➢ Use of chemical agents
Surgical Asepsis
✓ the complete elimination of the disease-causing agents and their
spores from the surface of an object
✓ Involves the following:
➢ The proper maintenance and preparation/disinfection of the
environment
➢ Sterilization surgical equipment
➢ Scrubbing of personnel involved in the procedure
➢ Adequate cleaning of the surgical site
✓ Precautionary steps to prevent the contamination of the sterile
environment:
➢ minimize number of personnel taking part in the procedure
➢ keeping the conversations at a minimum as much as possible
➢ reduce movements inside the operating theatre
➢ use of non-perforating devices
➢ maintaining a fair distance of non-scrubbed staff away from
the scrubbed staff
Table 1. Difference between Surgical and Medical Asepsis
Surgical vs Medical Asepsis
Medical asepsis is the reduction of the
Surgical asepsis is the complete elimination of
number of disease-causing agents and
the disease-causing agents and their spores
their spread.
from the surface of an object.
Techniques
The techniques used in the process are In surgical asepsis, sterile techniques are
called clean techniques.
used.
Occasions/Applications
This procedure is carried out in the
Sterile techniques are followed in changing
administration of enemas, medications,
dressings of a wound, catheterization, and
tube feedings, etc.
surgeries.
C. Antimicrobial agents in therapy
Antimicrobial: An agent that destroys microbes, inhibits their growth,
or prevents or counteracts their pathogenic action.
Antibiotics are only those substances that are produced by one
microorganism that kill, or prevent the growth, of another
microorganism.
➢ Today, the term antibiotic is used to refer to almost any drug that
attempts to rid your body of a bacterial infection.
Chemotherapy: Any chemical treatment intended to be therapeutic
with respect to a disease state.
Infection: An uncontrolled growth of harmful microorganisms in a host.
Selective toxicity: refers to the ability of the drug to targets sites that
are relative specific to the microorganism responsible for infection.
Superinfection: is an additional infection that happens during or
immediately after an existing infection.
➢ The superinfecting organism is usually one which is resistant to the
drugs being used in the treatment of the original infection.
Spectrum of Antimicrobial Activity
I.
Antibiotic Misuse
VI.
Antibiotic Safety
Generally, all types of drugs have side effects on top of the beneficial
effects.
Administering drugs involves assessing the risks against the benefits
(therapeutic index).
Side effects: result of drug or other therapy in addition to or in
extension of the desired therapeutic effect; usually but not necessarily,
connoting an undesirable effect.
Adverse effects/ adverse drug reactions: undesirable, uncomfortable,
or dangerous effects that a drug may have.
✓ usually unexpected reactions to drugs
✓ Can affect the entire body (systemic), or can be limited to a
specific organ.
Drug toxicity: describes adverse effects of a drug that occur because
the dose or plasma concentration has risen above the therapeutic range,
either unintentionally or intentionally (drug overdose).
Drug abuse is the misuse of recreational or therapeutic drugs that may
lead to addiction or dependence, serious physiological injury (such as
damage to kidneys, liver, heart), psychological harm (abnormal
behavior patterns, hallucinations, memory loss), or death.
Anaphylaxis: sudden, life-threatening, whole-body reaction to a drug or
other allergen and characterized by irregular heartbeat, trouble
breathing, swelling, and unconsciousness
❖ Hypersensitivity Test
VII.
Drug Interactions
Synergism: two or more drugs work together against one target,
producing an effect that is greater than the individual effect of the two
drugs together
Antagonism: one drug reduces or blocks the effect of another
Potentiation means that drug A boosts the effects of drug B, often by
increasing the levels of drug B in the blood.
Additive toxicity: Combinations of drugs may result in greater toxicity
than would be seen with single drugs.
➢ Broad spectrum of microbial activity affect a wide range of microbes
➢ Narrow spectrum of microbial activity are able to target specific
types of microbes.
II.
III.
Action of Antimicrobial Drugs
1. Inhibiting cell wall synthesis
2. Inhibiting protein synthesis
3. Injuring the plasma membrane
4. Inhibiting nucleic acid synthesis
5. Inhibiting synthesis of essential metabolites
1)
2)
3)
4)
IV.
V.
Common Antimicrobial Drugs
Antibacterial Drugs
➢ beta-lactam antibiotic (penicillins, cephalosporins)
✓ inhibit bacterial cell wall biosynthesis
➢ Antibiotics from prokaryotes
➢ Antimycobacterial antibiotics
Antifungal Drugs
Antiviral Drugs
Antiprotozoan and Antihelminthic Drugs
Sensitivity Tests
Resistance to Antimicrobial Drugs
Mechanisms of Resistance
✓ Enzymatic destruction or inactivation of the drug
✓ Prevention of penetration to the target site within the cell wall
✓ Alteration of the drug’s target site
✓ Rapid efflux of the antibiotic
✓ Evolution of microbial resistance to drugs