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MICROBIOLOGY
Introduction:
‘Microbiology’ should be an easy word to define: the science
(logy) of small (micro) life (bios), or to put it another way,
the study of living things so small that they cannot be seen
with the naked eye.
Microbiology is the science that deals with the study of
micro-organisms, their activates and their influences on
different aspects of life.
The following list of some of the general areas in which the
expertise of a microbiologist might be used:
1-Medical laboratory Sciences
2- Medicine
3- Environmental science
4- Food and drink production
5- Fundamental research
6- Agriculture
7- Pharmaceutical industry
8- Genetic engineering.
Microbiology comprises many disciplines, that are categorized
on either taxonomic or functional bases:
(1) Taxonomic disciplines of microbiology are:
Bacteriology (Study of bacteria)
Mycology
(Study of fungi)
Virology
(Study of viruses)
Parasitology ( Study of parasite) (now in separated section)
(2) Functional disciplines of microbiology are:
Immunology (host reaction to micro-organisms)
Medical Microbiology (role of organism in infectious
disease)
Genetic engineering
Historical background:
• WE NEED TO KNOW OUR PAST SO WE KNOW THE DIRECTION THAT
WE NEED TO FOLLOW IN THE FUTURE.
•Microorganisms had been on the Earth for some 4000 million years, when
Antoni van Leeuwenhoek started out on his pioneering microscope work in
1673. Leeuwenhoek was an amateur scientist who spent much of his spare
time grinding glass lenses to produce simple microscopes.
•the Italian Francesco Redi (1626–1697) showed that the larvae found on
putrefying meat arose from eggs deposited by flies, and not spontaneously as a
result of the decay process. This can be seen as the beginning of the end for
the spontaneous generation theory,
•Pasteur noticed that when lactic acid was produced in wine instead of alcohol,
rod-shaped bacteria were always present, as well as the expected yeast cells.
This led him to believe that while the yeast produced the alcohol, the bacteria
were responsible for the spoilage (swan-necked flasks).
•The first proof of the involvement of bacteria in disease and the definitive
proof of the germ theory of disease came from the German Robert Koch. In
1876 Koch showed the relationship between the cattle disease anthrax and
a bacillus which we now know as Bacillus anthracis.
•These results led Koch to formalise the criteria necessary to prove a causal
relationship between a specific disease condition and a particular
microorganism. These criteria became known as Koch’s postulates, and are
still in use today.
Koch’s postulates:
(1) The microorganism must be present in every
instance of the disease
and absent from healthy individuals.
(2) The microorganism must be capable of being isolated and grown in pure
culture.
(3) When the microorganism is inoculated into a healthy host, the same
disease condition must result.
(4) The same microorganism must be re-isolated from the experimentally
infected host.
•Table (1) The discovery of some major human pathogens
•Year
Disease
Causative agent
Discoverer
•1876 Anthrax
Bacillus anthracis
Koch
•1879 Gonorrhoea Neisseria gonorrhoeae
Neisser
•1880 Typhoid fever Salmonella typhi
Gaffky
•1880 Malaria
Plasmodium sp
Laveran
•1882 Tuberculosis
Mycobacterium tuberculosis
Koch
•1883 Cholera
Vibrio cholerae
Koch
•1883/4 Diphtheria
Corynebacterium diphtheriae
Klebs & Loeffler
•1885 Tetanus
Clostridium tetani
Nicoaier & Kitasato
•Year
Disease
Causative agent
Discoverer
•1886 Pneumonia (bacterial) Streptococcus pneumoniae
Fraenkel
•1892 Gas gangrene Clostridium perfringens
Welch & Nuttall
•1894 Plague
Yersinia pestis
Kitasato & Yersin
•1896 Botulism
Clostridium botulinum
Van Ermengem
•1898 Dysentery
Shigella dysenteriae
Shiga
•1901 Yellow fever Flavivirus
Reed
•1905 Syphilis Treponema pallidum
Schaudinn & Hoffman
•1906 Whooping cough Bordetella pertussis Bordet & Gengou
•1909 Rocky Mountain spotted fever Rickettsia rickettsii
Ricketts
Leeuwenhoek’s microscope
The lens (a) was held between two brass plates and used to view the
specimen, which was placed on the mounting pin (b). Focusing was
achieved by means of two screws (c) and (d).
Pioneers in Microbiology:
• Aristotle (384–322BC) believed that life arose from muck, decaying
food, warm rain, or even dirty shirts.
• Antony van Leeuwenhoek (1632–1723)
used a primitive microscope to observe stagnant water, hay infusions, and
scrapings from the teeth.
• John Tyndall (1820–1893) discovered that some bacteria existed in two
forms: a heat stable form and a heat-sensitive form.
THE GOLDEN AGE OF MICROBIIOLOGY • Mid to late 1800’s
HISTORY CONT.
• Louis Pasteur
– France
– Fermentation—with the final result being pasteurization.
• Heating wine and milk to 145.5 degrees to kill bacteria. Without killing
this bacteria, both the wine and the milk would sour. Louis Pasteur cont.
– Developed immunizations for anthrax in cattle and rabies in humans.
• Robert Koch
– Koch’s Postulates
• An organism must be present in ALL cases of the disease.
• The organism must be isolated in pure culture.
• The organism can be removed from the pure culture and placed in another
human or experimental animal and the same symptoms are developed.
• The organism can be removed from this new person and grown again in
pure culture.
• His postulates prove that certain organism cause certain diseases.
• Ignaz Semmelweis—Vienna and Oliver
Wendell Holmes—America
– Discover the importance of hand washing prior to surgery and then between
patients.
Other Introduction:
The word Microbiology is a Greek one: It is the study of very small
organisms (Microorganisms) that can not be seen by naked eye but by
Microscope.
Micro = very small
bio = life
logy = Science
These microorganisms include four major groups:
•Bacteria: studded under the name of Bacteriology.
•Fungi: studded under the name of Mycology.
•Viruses: studded under the name of Virology.
•Protozoa: studded under the term of Parasitology & Protozoology.
Why do we study Microbiology?
Because almost all diseases are caused by microorganisms.
There is a classification for these major groups of microorganisms which
can be distinguished on the bases of their structure and the complex of
their organization.
A- Prokaryotes: Which included Bacteria and blue green algae.
Characteristics of prokaryotes:
1- Very small in size.
2- Lack of nuclear membrane.
3- Lack of mitochondria.
4- Multiplication is by binary fission.
5- Has a single piece of genetic material known as plasmid.
B- Eukaryotes: Which included Fungi and Protozoa.
Characteristics of eukaryotes:
1- Large size.
2- Lack of plasmid.
3- Posses mitochondria.
4- Multiply by sexual multiplication & others (mitosis).
5- Posses nuclear membrane.
Classification of Micro-organisms:
In any discussion on biological classification, it is impossible to avoid
mentioning Linnaeus, the Swedish botanist who attempted to bring order to
the naming of living things by giving each type a Latin name. (Carl von Linn´e!
It was Linnaeus) who was responsible for introducing the binomial system of
nomenclature, by which each organism was assigned a genus and a
species.
The science of taxonomy involves not just naming organisms, but grouping
them with other organisms that share common properties.
In the 20th century, an increased focus on the cellular and molecular
similarities and dissimilarities between organisms led to proposals for further
refinements to the three-kingdom system. One of the most widely accepted
of these has been the fivekingdom system proposed by Robert Whittaker in
1969. This took into account the fundamental difference in cell structure
between procaryotes and eucaryotes, and so placed procaryotes (bacteria)
in their own kingdom, the Monera, separate from single-celled eucaryotes.
Another feature of Whittaker’s scheme was to assign the Fungi to their own
kingdom, largely on account of their distinctive mode of nutrition.
The agents of human infectious belong to five major groups of micro-
organisms ;bacteria, fungi, viruses protozoa and helminthes.
Based upon cell characteristic, living organism are recognized as having
Euocaryotic or procaryotic cell type.
Bacteria belong to the procaryotic, fungi and protozoa are Euocaryotic cell
type. Viruses are classified by some scientist as kingdom viruses they are
acellular (non- cellular)
Differences between Euocaryotes and procaryotes
Euocaryotes
procaryotes
Size
Larger
Relatively small
Structure of cell
Complex
Primitive
DNA content
Nucleus
Nucleoid
Nuclear membrane
Present
Absent
Mitochondria
Present
Absent
Multiplication
Mitotic
Binary fission
Enzyme system
Complex
Simple
Golgi bodies
Present
Absent
Respiration
Via Mitochondria
Cytoplasmic membrane
The kingdom procaryote is further divided into division
orders
families
genera
species
classes
strain
(subspecies)
Practically, only the name of genus and species are used
the generic (genus) name is always given a capital letter
the specific (species) name is given a small letter
the generic and specific name are italicised, or, if this isn’t possible,
underlined.
Introduction to Bacteria
Bacteria form a large group of unicellular
parasitic,
saprophytic
and
free-living
microorganism, varying in size from .01 – 10
µm long.
They have simple cell structure (procaryotic),
contain both DNA &RNA and multiply by
binary fission
They are classified by their morphology,
staining reaction, culture characteristic,
biochemical reaction, antigenic structure and
genetic composition using specialized
molecular biology techniques.
Morphology of Microorganisms:
Morphology of Bacteria:1- Cocci: round or spherical in shape; singular known as
Coccus. It's diameter ranges between 0.5 – 1 µm. When
microorganism occurs as single it is known as Micrococcus
monococcus = single cell.
When it occurs in pairs, it is known as Diplococci
e.g. Meningococci which cause meningitis.
When it occurs in chain which can be short or long, it is known
as Streptococci
e.g. Streptococcus pyogenes which
cause throat
inflammation.
When it occurs in clusters it is known as Staphylococcus
e.g. Staphylococcus aureus (golden colour).
These arrangements are determined by the orientation and
degree of attachment of the bacteria at the time of cell
division.
2- Rods:in Latin are known as Bacilli. Rod = Bacillus ; it has a stick like shape
and the end may be round cut or square cut (Value of identification).
When rod is single, it is known as bacillus or may be chain known as
streptobacillus
Sometimes the rods may occur in chains but
branching, some have the shape of Chinese
letters and is known as club shaped e.g.
Corynebacterium diphtheriae which causes
diphtheria.
3-Vibrios: It has a comma or curved shape
،،
It is known as Vibrio and e.g. Vibrio cholerae
which causes cholera.
4- Spirillum and Spirochetes:
have the shape of spiral e.g.Treponema palidum
which causes syphilis.
Molecular Structure of Bacteria
1-
Cell Wall: is a component of bacterial cell which
is outside the cell, it is a rigid organelle and also it
gives the bacteria it's shape and also prevents
expansion of cell membrane (protects the cell against
osmotic pressure). The other name of the cell wall is
known as peptidoglycan which is composed of:
polysaccharides:
the main polysaccharides which are found
in the composition are:
N – acetyl glucose amine.
N – acetyl muramic acid.
and this peptidoglycan is only found in the cell wall
of bacteria. It is a target for antibiotics to act on.
Some antibiotics act on the cell wall e.g. penicillins
and cephalosporins. This is known as selective
toxicity.
1. Protoplast:
is a G+ve bacteria with defective cell wall which is
killed by lysozymes or antibiotic (penicillin).
2. Spheroplast:
Is a G-ve bacteria which lost its cell wall
completely or partially due to the action of lysozymes or antibiotic
(penicillin).
3. L-forms:
It may be a G+ve or G-ve bacteria loss their cell wall due to
mutation. They are able to grow and divide or multiply and this is possible in a
hypertonic or concentrated media or isotonic in order to retain its contents and do
not release them. In this medium shrinking may happened but it does not affect.
But in hypotonic media it will expand and then explode.
2. Cell Membrane:
It is very important structure in the bacterial cell, also called
cytoplasmic
membrane
or
sometimes
protoplasmic
membrane. Chemically cytoplasmic membrane is composed
of bilayers of phospholipids.
Basic functions of cell membrane are :
1\ to control the movement of substances.
2\ to secrete hydrolytic enzymes.
3\ responsible for secretion of transport protein and proteins
involved in cell wall synthesis.
3- Cytoplasm: which contains:
a. Genetic Material: a single piece of DNA
without nuclear membrane.
b. Ribosomes: which are known as protein
making organelle.
c. Mesosomes: Which are attached to the
cell membrane and is thought that it is
associated in cell division (binary fission).
Specialized products outside the cell wall
1- Capsule:
this is a layer of loose slime material which
surrounds some bacterial cells. The capsules are
composed of mainly of polysaccharides or peptides.
They resist phagocytosis and so their presence on a
bacterium is associated with virulence. They are
identified by negative staining due to their low affinity
for simple staining.
* e.g. of capsulated bacteria:
Klebsiella pneumoniae
(polysaccharide)
Bacillus anthraces (poly – D – glutamic acid)
* The capsule is used for rapid and
accurate diagnosis where agglutination
reaction
happens
between
the
antibodies and the antigen (capsular
antigen).
2- Flagella:
These are filaments that originate from the cytoplasm.
They function as organs of motility. They are therefore seen
only in organisms that are motile. They are made of protein
(Flagellin). They have characteristic patterns of arrangement
on the bacterial cell:
A) Monotrichate: one flagellum at one pole.
b)Amphitrichate: one flagellum at each pole
c) Lophotrichate: tuff flagella at one or both poles.
d) Peritrichate: flagella completely surrounding the
bacterial cell.
stained preparations, but become visible only in silver
impregnated preparation or in electron microscopy.
The functions of flagella are:
1. motility (mainly)
2. attachment to site of infection e.g. stomach.
3. Diversity of antigens, this is used for diagnosis and
this is mainly in Salmonella typhi (the causative agent
of typhoid fever).
4. Invasion.
5. Colonization (form colony).
3- Pili:
Extended from cytoplasmic membrane, they
are shorter and finer filaments than the flagella.
These are the pili. They are made of protein
(pilin).
Pili are divided into two groups:
a. Sex pili, referred to as sex pili because of their
role during conjugation when genes are
transferred from one cell(donor) to another cell
(recipient).
b. Common pili, or Fimbriae: these are thought
to be the organs of adhesion that help bacteria to
attach to the host cells (Virulent Factor).
4- Spores:These are dense structure produced by some
bacteria, e.g. the Bacilli and Clostridia groups, that enable
them to survive adverse environmental conditions.
They
develop within and at the expense of the
vegetative cell. The spore comprises the
chromosomal material surrounded by several
walls layers.
Chemically, endospore has a large amount of Ca++ and less
number of enzymes. Dpiclonic acid is also presents in spore.
Spores
are
resistant
to
heat,
stains,
desiccation,
chemicals and disinfectants.
Each spore germinates to produce a vegetative cell during
favorable conditions.
The location and shape of the spore in the cell may be of
diagnostic assistance, e.g. the spores of
Clostridium
tetani are terminal, and the diameter is greater than that of
the parent cell, so that they are characteristically of drum
stick appearance.
The positions of the spores are described as:
Terminal
, Sub terminal , or Central
The shapes of spores are described as:
Ovoid (Oval) , Spherical
, Cylindrical
.
Classification of bacteria:
1- phenotypic classification: The microscopic and
macroscopic morphologies of bacteria were the first
characteristic used to identify bacteria. The phenotypic
classification include:
* Microscopic morphology (cocci, bacilli, curved, spiral,
spirochetes and Vibrio), also the ability to retain the gram stain
into gram positive and gram negative.
* Macroscopic morphology (appearance of colonies of
bacteria on culture media (colonies size, shape, pigment
production and reaction on media.
* Biotyping (using biochemical test or reaction)
*Serotyping (by detection bacterial antigens using
serological test.
* phage typing (susceptibility to viruses that infect bacteria)
2- Analytic classification: using chromatographic pattern
include:
* Cell wall fatty acid analysis
* Whole cell lipid analysis
* Whole cell protein analysis
* Multilocus enzyme electrophoresis
3- Genotypic classification: the most precise method for
classifying bacteria is by analysis by their genetic material
that include:
* Guanine plus cytosine ratio
* DNA hybridization
* Nucleic acid sequence analysis
* plasmid analysis
* chromosomal DNA fragments
* Ribotyping
•Others useful classification:
* According to their oxygen requirement into:
1- Aerobic
2- Anaerobic
3- Facultative
anaerobic
4- Microaerophilic.
* According to temperature into:
1- Thermophilic 2- Mesophilic 3- Psychrophilic
* According to their growth factors into:
1- Fastidious organism (required special growth
factor)
2- non fastidious (simple)
Cell wall of gram positive bacteria
Bacterial terminal spores (Clostridium tetani)
Bacterial flagellum