Microbiology 1.03 Basic Concepts 1
Microbiology 1.03 Basic Concepts 1
LEARNING
OBJECTIVES
At
the
end
of
the
lecture,
the
student
should
be
able
to:
1. Enumerate
and
discuss
the
different
criteria
used
for
classification
2. Discuss
the
different
methods
used
in
the
laboratory
for
identification
of
bacteria
a. cell
wall
(gram
stain)
Figure
1.
Taxonomic
Ranks
(Organization
of
Bacteria)
b. bacterial
morphology
c. metabolic
characteristics
LEGEND:
Italicized:
quoted
from
lecturer
II.
THE
BACTERIAL
CELL
WALL
References:Clinical
Microbiology
(Gladwin
and
Trattler);
Jawetz
I.
INTRODUCTION
Classification
• Bacteria
are
categorized
into
taxonomic
groups
or
ranks
• Experimental
and
observational
techniques
are
required
to
classify
bacteria
according
to
several
characteristics
o biochemical:
e.g
oxidase
(-‐),
catalase
(+)
coagulase
(-‐)
o physiological:
e.g
facultative
anaerobe,
ferments
lactose
o morphologi:
e.g
gram
(-‐)
rod,
motile
o genetic:
e.g
DNA
sequencing
Nomenclature
• This
refers
to
the
naming
of
an
organism
by
international
rules
(established
by
a
recognized
group
of
medical
professionals)
according
to
its
characteristics
• A
taxonomist
uses
DNA
sequencing
to
determine
the
genetic
relatedness
of
organisms.
Identification
• The
practical
use
of
a
classification
scheme
to:
1. Isolate
and
distinguish
desirable
organisms
from
undesirable
ones
2. Verify
the
authenticity
or
special
properties
of
a
culture
in
a
clinical
setting
3. Isolate
and
identify
the
causative
agent
of
a
disease
Figure
2.The
Bacterial
Cell
Wall
Trans
Group:
REYES,
RICIO,
RIRAO,
RIVERA,
RODIL
Edited
By:
Page 1 of 9
• All
bacteria
have
a
bacterial
cell
wall
-‐-‐peptidoglycan
Additional
Notes:
layer.
• In
figure
2,
it
differs
between
gram
negative
and
gram
positive
organisms.
Usually,
the
peptidoglycan
layer
• They
do
not
block
antibiotics
as
efficiently
as
G-‐
bacteria.
Their
protects
the
cytoplasm
and
the
nucleus
of
the
organism
cell
walls
also
allow
for
the
primary
stain
(in
gram
stain)
to
from
the
environment.
remain.
• In
gram
positive
cell
wall,
the
peptidoglycan
layer
is
very
• Most
G+
cell
walls
contain
considerable
amounts
of
teichoic
thick
-‐-‐20%
of
the
dry
weight
of
the
bacteria.
and
teichouronic
acids.
They
may
also
contain
polysaccharide
• In
gram
negative
cell
wall,
the
peptidoglycan
layer
thin-‐-‐-‐
molecules
about
10%
of
the
dry
weight
of
the
bacteria.
• Teichoic
and
Teichouronic
acids
• Both
are
basically
composed
of
disaccharides
and
amino
o All
wall,
membrane,
or
capsular
polymers
that
contain
acids.
Petidoglycan
layer
unit
=
disaccharide
with
amino
glycerophosphate
or
ribitol
phosphate
residues.
acid
side
chains.
o Responsible
for
the
negative
charge
of
the
G+
cell
surface
as
a
whole.
NOTES:
o There
are
two
types:
1. Wall
teichoic
acid
(WTA)
which
is
covalently
linked
to
• Both
gram
(+)
and
(-‐)
have
more
than
1
layer
peptidoglycan
protecting
the
cytoplasm
and
nucleus
2. Membrane
teichoic
acid
which
is
covalently
linked
to
the
• Just
outside
the
cytoplasmic
membrane
is
membrane
glycolipid.
Because
of
its
intimate
association
peptidoglycan
layer
or
cell
wall
for
both
gram
(+)
and
with
lipids
in
the
cell
membrane,
they
are
also
called
(-‐)
lipoteichoic
acids
(LTA)
o WTA
and
LTA
help
provide
elasticity,
porosity,
tensile
strength,
and
electrostatic
properties
of
the
bacterial
envelope.
o They
constitute
major
surface
antigens
and
may
also
serve
as
antigenic
determinants
as
in
the
case
of
S.
pneumonia
gram
(+)
–
thick
cell
wall
B. Gram-‐Negative
Cell
Wall
gram
(-‐)
–
thin
cell
wall
A. Gram
Positive
Cell
wall
Figure
3.
Gram
Positive
Cell
Wall
• Usually
the
outer
cell
wall
of
gram
positive
comprises
of
Figure
4.
Gram
Negative
Cell
Wall
cross-‐linkages
of
peptidoglycan,
teichoic
acid
which
is
a
protein,
polysaccharides,
and
other
proteins
as
well.
• It
usually
has
three
layers:
• The
lipoteichoic
acid
(LTA)
is
an
antigenic
determinant
for
serologic
identification.
• cytoplasmic
membrane
(red
circle)
–also
present
in
gram-‐positive
bacteria
• Within
the
cytoplasmic
membrane,
it
is
comprised
of
a
****periplasmic
space***
phospholipid
bilayer.Proteins
within
the
phospholipid
• peptidoglycan
layer
(blue
circle)
bilayer
also
serve
as
a
transport
medium
for
nutrient.
• outer
cell
membrane
(green
circle)
-‐-‐-‐almost
exclusive
to
gram
negative
bacteria
Page 2 of 9
• The
inner
cytoplasmic
membrane
–
contains
phospholipid
CLINICAL
APPLICATION!
bilayer
(same
as
gram
positive)
with
proteins
• Gram-‐positive
o Remember
the
peptidoglycan
layer
is
quite
thick
and
• There
is
periplasmic
space
between
the
cytoplasmic
does
not
block
diffusion
of
low
molecular
weight
membrane
and
an
extremely
thin
peptidoglycan
layer.
This
compounds
space
is
filled
with
a
gel
that
contains
proteins
and
enzymes.
o Therefore,
substances
that
damage
the
cytoplasmic
membrane
could
pass
though
(e.g.
antibiotics,
dyes,
detergent)
• Peptidoglycan
layer
-‐
very
thin
and
usually
contains
many
• Gram-‐negative
Organisms
enzymes.
For
gram-‐negative,
it
does
not
have
the
lipotechoic
acid
(LTA)
but
instead
it
has
the
murein
lipoprotein
which
o Outer
LPS
cell
membrane
blocks
the
passage
to
the
serves
as
a
nutrient
transport
system
and
extends
outward
to
peptidoglycan
layer
and
sensitive
inner
cytoplasmic
the
outer
membrane.
membrane
o Therefore,
antibiotics
and
chemicals
are
unable
to
pass
through
-‐>
peptidoglycan
cell
wall
remains
intact
• The
outer
membrane
is
the
lipopolysaccharide
layer
(LPS)
-‐-‐-‐
phospholipid
bilayer
with
hydrophobic
tails
similar
to
other
membranes.
This
is
comprised
of
three
components:
III.
GRAM
STAINING
1. O-‐specific
side
chains
or
O-‐antigen
-‐-‐
outer
carbohydrate
chains
of
1-‐50
oligosaccharide
units
which
differs
from
one
• Bacteria
are
colorless
and
usually
invisible
on
light
microscopy
organism
to
another
and
are
antigenic
determinants.
• Gram
stains
(colorful
stains)
separates:
(TIP:
O
for
outer)
▪ organisms
into
gram
(+)
and
gram
(-‐)
bacteria
▪ Allows
the
clinician
to
determine
the
morphology
2.
Core
polysaccharide
–
central
part
(shape)
of
the
microorganism
3.
Lipid
A
–
interior
to
core
polyssacharide
• a
disaccharide
with
multiple
fatty
acids
• also
known
as
ENDOTOXIN
and
is
toxic
to
human
IMPORTANT
Endotoxins
-‐almost
exclusively
found
in
gram
negativebacteria
except
for
one
gram
positive
which
is
Listeria,
but
this
lipid
A
is
toxic
to
man.
-‐Usually,
as
a
man
gets
infected,
the
bacteria
lyses
itself,
this
lipid
A
is
released
to
the
body
and
this
causes
the
clinical
manifestations
of
sepsis
like
fever,
shock,
chills,
and
so
on.
Figure
5:
Gram
staining
Just
remember
VIAS
–
violet,
iodine,
alcohol,
safranin
Porin
channels
also
serve
as
nutrient
transport
system
for
gram
negative
organisms.
For
any
stain,
you
must
first
smear
the
substance
to
be
stained
(sputum,
pus,
etc.)
onto
a
slide
and
then
heat
it
to
fix
the
bacteria
on
the
slide.
There
are
4
steps
to
the
Gram
stain:
Additional
Notes
1)Pour
on
crystal
violet
stain
(a
blue
dye)
and
wait
60
seconds.
• The
outer
membrane
is
responsible
for
blocking
the
entry
2)Wash
off
with
water
and
flood
with
iodine
solution.
Wait
of
harmful
chemicals
into
the
peptidoglycan
layer
and
60
seconds.
the
cytoplasmic
membrane
(this
is
also
the
reason
why
3)Wash
off
with
water
and
then
"decolorize"
with
95%
the
primary
stain
(crystal
violet
in
gram
stain)
does
not
alcohol.
stick
to
the
bacteria)
4)Finally,
counter-‐stain
with
safranin
(a
red
dye).
Wait
30
seconds
and
wash
off
with
water
Page 3 of 9
Additional
notes:
Other
Bacteria
According
to
cell
wall
Characteristics
• Acid-‐Fast
Bacteria
(AFB)
o Constitutes
the
cell
wall
of
Mycobacteria.
o Contain
large
amounts
of
waxes,
and
mycolic
acids
o Very
hydrophobic
and
is
highly
resistant
to
many
harsh
chemicals,
including
detergents
and
strong
acids.
o They
are
called
acid-‐fast
bacteria
because
unlike
other
bacteria,
dyes
that
are
introduced
to
them
by
brief
heating
or
treatment
with
detergents
cannot
be
removed
by
dilute
hydrochloric
acid.
• Mycoplasmas
o They
lack
cell
wall
and
contain
no
peptidoglycan.
o Because
they
lack
cell
walls,
they
vary
in
shape
Figure
6.
Gram
staining
o These
bacteria
lack
a
target
for
cell
wall-‐
inhibiting
antimicrobial
agents
like
penicillins
For
crystal
violet,
gram
positive
bacteria
-‐-‐
the
peptidoglycan
layer
is
and
cephalosporins.
Because
of
this,
they
are
thick,
so
it
retains
the
color
of
violet.
If
it
is
gram
positive,
it
just
stays
resistant
to
these
drugs
there
regardless
of
what
other
stains
you
pour
in.
it
just
remains
blue.
Whereas
if
it
is
gram
negative,
when
you
wash
and
add
iodine
and
alcohol,
the
color
will
be
removed.
When
you
pour
the
final
stain
IV.
BACTERIAL
GROWTH
CURVE
which
is
safranin,
it
retains
the
red
color.
If
a
fixed
volume
of
liquid
medium
is
inoculated
with
microbial
cells
from
a
culture
that
has
previously
been
grown
to
saturation
and
the
population
is
periodically
determined
and
plotted,
a
growth
curve
containing
a
(1)
lag
phase,
(2)
log
phase,
(3)
stationary
phase,
and
(4)
decline
phase
is
observed.
1) LAG
PHASE:
• Period
during
which
cells
are
depleted
of
metabolites
and
enzymes,
adapt
to
the
new
environment
• Enzymes
and
intermediates
start
to
form
and
accumulate
until
optimum
concentrations
that
permit
growth
to
resume
2) LOG
or
EXPONENTIAL
PHASE:
• Cells
are
in
steady
state
GRAM-‐POSITIVE
=
BLUE!
• New
cell
material
is
being
synthesized
at
a
GRAM-‐NEGATIVE
=
RED!
constant
rate
Table
1.
Differences
between
gram
positive
and
gram
negative
• Continues
until:
Bacteria
o Nutrients
in
the
medium
become
exhausted
o
Toxic
metabolic
products
accumulate
and
inhibit
growth
(e.g.
oxygen)
3) STATIONARY
PHASE
• Exhaustion
of
nutrients
or
• Accumulation
of
toxic
products
causes
growth
to
cease
completely
• Cell
turn
over
takes
place
4) DECLINE/DEATH
PHASE
Page 4 of 9
THINGS
TO
REMEMBER!!
A.
Gram
positive:
2
gram-‐positive
Cocci
• Streptococcus
• Staphylococcus
4
gram-‐positive
Bacilli
• 2
of
them
produce
spores
o Bacillus
o Clostridium
Figure
7.
The
bacterial
Growth
Curve
• 2
are
non-‐spore
formers
o Corynebacterium
BACTERIAL
MORPHOLOGY
o Listeria
have
endotoxins!!!
Bacteria
have
4
major
shapes
• Cocci:
Spherical
B.
Gram
Negative:
o Diplococci:
in
pairs
o Tetrads:
four,
planar
• Only
1
group
of
gram-‐negative
cocci
(diplococcus)
o Sarcinae:
cubical
bundles
(8
cells)
o Neisseria
o Streptococci:
chains
o Staphylococci:
arranged
like
a
bundle
of
grapes
• Bacilli:
Rods
o Cocobacilli:
short
rods
o Diplobacilli:
in
pairs
o Streptobacilli:
in
chains
o Palisade:
arranged
in
parallel
• Only
1
group
of
spiral-‐shaped
organism
• Spiral:
comma-‐shaped,
S-‐shaped,
or
spiral
o Spirochetes:
Treponemapallidum
(causes
syphilis)
• Pleomorphic:
lacks
a
distinct
shape
• The
rest
are
gram-‐negative
rods
or
pleomorphic
EXCEPTIONS
Figure
8.
Bacterial
Morphology
• Mycobacteria
o Weakly
gram-‐positive
o Stains
better
with
acid-‐fast
stain
• Spirochetes
o Gram
negative
but
are
two
small
even
for
light
microscopy
o Visualized
with
darkfield
microscopy
• Mycoplasma
o No
cell
wall
Page 5 of 9
VII.
BACTERIAL
METABOLIC
CHARACTERISTICS
VI. CYTOPLASMIC
STRUCTURES
Usually,
bacteria
can
be
categorized
according
to
their
metabolic
properties.
This
can
include
how
the
bacteria
would
deal
with
oxygen
and
how
the
organism
uses
carbon
and
energy
sources.
A. CRITERIA
FOR
CLASSIFICATION
:
GROWTH
• Types
of
nutrient
• Size
of
colony
Figure
10.
Type
of
nutrient
-‐
Blood
agar
plate
with
hemolysis
Figure
9.
Cytoplasmic
structures
in
the
bacteria
• The
chromosome
just
contains
the
bacterial
DNA.
Usually,
it
is
double
stranded.
Aside
from
the
bacterial
DNA,
there
is
another
structure
which
is
called
plasmid.
This
plasmid
is
also
double
stranded
DNA
and
usually
this
plasmid
carries
the
antibiotic
resistant
gene.
PLASMIDS:
• Smaller
circular
segments
of
double-‐stranded
DNA
Figure
11.
Size
of
colony
–
large
colonies
• Carry
antibiotic
resistant
genes
B. CRITERIA
FOR
CLASSIFICATION
:
OXYGEN
• Extrachromosomal
DNA
• May
occur
in
multiple
copies
• Code
for
special
functions
(e.g.
virulence
factors,
sex
pili
• Molecular
oxygen
is
very
reactive,
and
when
it
snatches
genes,
other
metabolic
factors,
resistance
genes)
up
electrons,
it
can
form:
o
Hydrogen
peroxide
(H2O2)
RIBOSOMES:
o
Superoxide
radicals
(O2
toxic
when
broken
down
• Composed
of
protein
and
RNA
o
Hydroxyl
radical
(OH-‐)
• Involved
in
the
translation
process
during
bacterial
• Own
macrophages
produces
these
oxygen
radicals
as
a
protein
synthesis
defense
to
bacteria.
• Bacterial
ribosome:
70S
particle
that
has
2subunits:
large
• SOME
BACTERIA
ARE
SMART
THOUGH:
(50S)
and
small
(30S)
o Possess
enzymes
to
break
down
these
oxygen
• Bacterial
ribosomes
are
important
because
some
products:
antibiotics
act
on
the
ribosomes
since
it
disrupts
the
ribosome
production,
it
also
disrupts
the
protein
synthesis
▪ Catalase
-‐
breaks
down
hydrogen
peroxide
of
the
bacteria,
therefore,
killing
the
bacteria.
▪ Peroxidase
▪ Superoxide
dismutase
-‐
breaks
down
superoxide
radical
Page 6 of 9
• BACTERIA
OXYGEN
SPECTRUM
1. Obligate
Aerobes
• Use
glycolysis,
Krebs
TCA
cycle,
&
electron
transport
chain
with
oxygen
• Possesses
all
above
enzymes
2. Facultative
Anaerobes
• Use
oxygen
in
electron
transport
chain
&
have
catalase
and
superoxide
dismutase
• Can
grow
in
the
absence
of
oxygen
by
using
fermentation
for
energy
3. Microaerophilic
(aerotolerant
anaerobes)
• Use
fermentation,
have
no
electron
transport
system
• Can
tolerate
low
amounts
of
oxygen
(because
they
possess
superoxide
dismutase)
4. Obligate
Anaerobes
• Hate
oxygen,
NO
enzymes
to
utilize
oxygen
Figure
13.
They
keep
the
bacteria
moving
around
and
they
are
affixed
to
a
basal
body.
This
basal
body
spans
through
the
entire
cell
wall,
C. CRITERIA
FOR
CLASSIFICATION
:
CARBON
AND
ENERGY
SOURCE
binding
the
outer
and
inner
cell
membrane
of
most
organisms.
The
basal
body
acts
as
a
hook
to
the
flagella.
• All
medically
important
bacteria
are
chemotrophs
-‐
use
chemical
&
organic
compounds
(glucose)
for
energy
• Basal
Body
of
flagellum
• Fermentation
(glycolysis)
-‐
Fermentation
is
usually
used
o Spins
around
and
spins
the
flagellum
by
many
bacteria
for
their
oxygen
metabolism.
Usually,
o Causes
the
flagellum
to
undulate
in
a
coordinated
manner
glucose
is
broken
down
to
pyruvic
acid
and
therefore
to
move
the
bacteria
toward
or
away
from
a
chemical
when
pyruvic
acid
is
broken
down,
you
will
yield
ATP.
concentration
gradient
(chemotaxis)
• Respiration
• Obilgate
Intracellular
organisms
–
not
capable
of
B. PILI
metabolic
pathways
for
ATP
synthesis,
thus
consume
host’s
ATP
VIII.
CELL
STRUCTURES
AS
VIRULENCE
FACTORS
A. FLAGELLA
Figure
14.Bacterial
Pili
• looks
like
spikes
outside
the
bacterial
cell
wall.
They
are
shorter
than
the
flagella
and
do
not
move.
They
usually
serve
as
ADHERENCE
factor.
• Functions:
A. Attachment:
-‐ Neisseria
gonorrhea,
the
pili
are
being
used
to
attach
to
the
mucous
membrane.
-‐ E.
coli
and
Campylobacter
jejuni.
Pili
are
used
to
attach
to
the
GI
lining
which
eventually
leads
to
diarrhea.
-‐ Bordetella
pertussis
where
the
pili
is
being
used
to
attach
to
the
respiratory
system
leading
to
the
whooping
cough.
Figure
12.
Flagella
are
protein
filaments.
Usually,
they
extend
as
long
B. Conjugation/Sexual
Reproduction
hair
or
long
tails
from
the
bacterial
cell
membranes.
-‐
Sex
pili
make
the
exchange
of
genetic
substances
between
two
organisms.
Page 7 of 9
Antibodies
directed
against
bacterial
capsules
helps
the
macrophages
C. ENDOSPORES
and
neutrophils
bind
to
and
phagocytize
the
encapsulated
bacteria
(opsonization).
This
is
the
principle
behind
pneumococcal
vaccines.
• Formed
only
by
2
bacteria:
-‐
both
are
gram-‐positive:
Bacillus
(aerobic)
and
the
IX.
TOXINS
AS
VIRULENCE
FACTORS
anaerobic
Clostridium
• Metabolically
dormant
forms
of
bacteria
that
are
resistant
to
A. EXOTOXINS
heat
(boiling),
cold,
drying
and
chemical
agents
o Activated
when
exposed
to
a
favorable
nutrient
or
• Proteins
released
by
both
gram-‐positive
and
gram–negative
environment
bacteria
• They
have
a
multilayered
protective
coat
consisting
of:
• Causes
a
variety
of
disease
manifestations
o a
cell
membrane
o a
thick
peptidoglycan
mesh
1.
Neurotoxins
-‐
act
on
nerves
and
motor
endplates
causing
paralaysis;
ex.
tetanus
toxin
and
botulinum
toxin
o another
cell
membrane
o a
wall
of
keratin-‐like
protein
2.
Enterotoxins
-‐
acts
on
the
GIT
to
cause
diarrhea
o an
outer
layer
called
the
exosporium
• Inhibits
NaCl
absorption
→
activates
NaCl
secretion
or
kills
• Spores
form
when
there
is
a
shortage
of
needed
nutrients
and
intestinal
epithelial
cells
→
osmotic
pull
of
fluid
into
the
can
lie
dormant
for
years.
Surgical
instruments
are
heated
in
intestine
→
diarrhea
an
autoclave,
which
uses
steam
under
pressure,
to
121°C
for
15
minutes,
in
order
to
ensure
the
destruction
of
Clostridiumand
Bacillusspores.
D. CAPSULE
• Infectious
diarrhea
:
Vibrio
cholera,
Escherichia
coli,
Campylobacter
jejuni,
Shigella
dysenteriae
Figure
15.
Remember
that
the
capsule
is
different
from
the
cell
• Food
poisoning:
Bacillus
cereus
and
Staphylococcus
membrane
and
not
all
organisms
have
capsules.
Usually,
they
serve
aureus
as
a
protective
wall
outside
the
cell
membrane,
and
usually,
they
are
composed
of
simple
sugar
residues
and
they
secrete
these
which
3.
Pyrogenic
exotoxins
eventually
coat
the
outer
wall
of
such
organisms.
One
unique
• Stimulates
release
of
cytokines
that
causes
rash,
fever
and
organism
would
be
Bacillusanthracis
because
their
cell
wall
is
toxic
shock
syndrome
comprised
of
amino
acid
residues.
Eventually,
these
capsules
serve
as
a
virulent
factor
because
the
macrophages
are
unable
to
• Ex.
Staphylococcus
aureus,
Streptococcus
pyogenes
phagocytise
this
encapsulated
organism.
Usually,
as
the
first
defense
of
the
body,
the
macrophage
would
swallow
some
bacterium
but
because
of
the
capsule,
sinusuka
lang
niya
(it
spits
it
out).
One
example
would
be
Streptococcus
pneumoniae.
The
thicker
the
capsule,
the
more
protected
the
organism
is.
Figure
17.
Rashes
caused
by
pyrogenic
exotoxins.
Figure
16.
Streptococcuspneumoniae
with
capsule.
Page 8 of 9
4.
Tissue
invasive
exotoxins
–
allows
bacteria
to
destroy
and
tunnel
through
tissues
Figure
18.
Tissue
invasion
by
bacteria
Miscellaneous
exotoxins
–
can
cause
disease
unique
to
the
individual
bacterium
Toxin
production
–
e.g.
hemolysin
Figure
19.
Gamma
hemolysis
=
there
is
no
hemolysis.
Alpha/green
hemolysis
=
there
is
partial
destruction
of
red
blood
cells.
Beta
hemolysis
=
complete
hemolysis
of
red
blood
cells.
B. ENDOTOXINS
Released
when
the
bacterial
undergoes
lysis
• Only
present
in
gram-‐negative
bacteria
with
one
• Exception:
Listeria
monocytogenes-‐
Gram
positive
• Septic
shock
• Because
endotoxin
often
triggers
the
immune
response
that
results
in
sepsis
and
shock
(eventually
leading
to
circulatory
collapse
and
organ
dysfunction)
Page 9 of 9