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Microbiology:

Gram stain
 Allows determination of round vs. rod shape
 Gram positive= blue (crystal violet); gram negative=red (safranin)
 Cell wall= peptidoglycan layer repeating disaccharide unit w/4aa extending from
each unit that cross links to others via transpeptidase (inhibited by penicillin)
1. gram + cell wall  extensive cross links of aa side chains & very thick
a) Cell envelope has complex cross linked peptidoglycan, teichoic
acid (acts as antigenic determinant- impo for serologic ID),
polysaccharides, and other proteins.
b) Cytoplasmic membrane touches inner surface of cell wall. Does
not contain cholesterol or other sterols (unlike animal cells)
c) Vulnerable to lysozyme and penicillin attack
2. gram – cell wall  very thin with simple cross links
a) cell envelope has 3 layers (cytoplasmic membrane, pepidoglycan
layer, unique outer cell membrane) & periplasmic space.
b) Periplasmic space btw cytoplasmic membrane and a thin
peptidoglycan layer
c) Peptidoglycan layer does not contain teichoic acid but rather
murein lipoprotein (binds unique outer cell membrane)
d) Outer cell membrane is a lipid bilayer containing
lipopolysaccharide (LPS)
e) LPS composed of covalently linked:
.2.e.1. O-specific side chain or O-antigenouter carbohydrate chains
of 1-50 oligosaccharides (very, thus antigenic determinants)
.2.e.2. Water soluble core polysaccharide
.2.e.3. Lipid A (endotoxin)- disaccharide w/multiple FA tails reaching
into membrane. When lysed fever, diarrhea, & possible fatal
endotoxic shock (or septic shock)
f) Outer membrane contains porins – allow nutrients passage.
g) Resistant to lysozyme and penicillin attack.
Bacterial morphology:
 Cocci- spherical; bacilli-rods (short bacilli- coccobacilli); spiral, pleomorphic- lack
distinct shape.
Disease causing bacteria:
 Gram positive (only 6- 2 cocci and 4 bacilli)
1. Streptococcus – forms strips of cocci.
2. Staphylococcus- forms clusters of cocci
3. Bacillus – forms spores
4. Clostridium – forms spores
5. Corynebacterium
6. Listeria
 Gram negative
1. Nisseria – diplococcus
2. Spirochetes – spiral shaped, ex. Treponema pallidum  syphilis
3. Rest are gram negative rods or polymorphic.
 Exceptions:
1. Mycobacteria – weakly gram positive but stain better w/acid-fast stain. Cause TB
and leprosy
2. Spirochetes – too small thus need to be visualized w/darkfield microscope. They
have an additional phospholipid rich outer membrane for ↑ protection. Also has
periplasmic flagella.
3. Mycoplasma- no cell wall only simple cell membrane so neither gram +/-.
Cytoplasmic structures:
 DNA – usu. Circular dsDNA & plasmids (often contain Ab resistance genes)
 Ribosomes – 70S (animals=80S)  50S + 30S. Erythromycin (50S) & tetracycline
(30S) both block protein synthesis.
Metabolic characteristics
 Oxygen:
1. Oxygen radicals removed via: catalase (breaks down hydrogen peroxide to water
&O2), peroxidase (breaks down H2O2), superoxide dismutase (breaks down
superoxide radicals to H2O2)
2. Obligate aerobes (have all above enzymes), facultative anaerobes (aerobic have
catalase & superoxide dismutase, but can grow w/out O2), microaerophilic
bacteria (use fermentation & no e- transport chain, can tolerate low O2 b/c have
superoxide dismutase), obligate anaerobes (no above enzymes).
 Carbon & E source:
1. autotrophs –use inorganic sources (sulfide and ammonium)
2. heterotrophs – use organic carbon sources
3. chemoheterotrophs – use chemical & organic compounds all medically impo
Cell structures, virulence factors and toxins
 Flagella – fixed to the bacterium via a basal body which spans through entire cell
wall  allows chemotaxis.
1. either 1 polar flagella (ex. vibrio cholera) or many peritrichous flagella (ex.
E.coli & Proteus); Shigella has no flagella.
2. periplasmic flagella (ex. Spirochetes) runs sideways w/in unique outer membrane
sheath. Its rotation spins the spirochetes around.
 Pili (or fimbriae) - straight filaments arising from cell wall (shorter than flagella).
Serve for adherence (adhesins) – many times req for disease (ex. E. Coli, Neisseria
gonorrrhea...)
 Capsules – protective walls composed of simple sugars (Exception is bacillus
anthracis – capsule made of aa) capsules enable increased virulence b/c cant be
phagocytosed.
1. Capsulated bacteria are identified via India ink stain (used to ID Cryptococcus
seen as halo) and Quellung reaction (Ab bind capsule allowing capsule swelling
with water). The process of Ab binding to capsule is called opsonization.
 Endospores – formed by only gram + & only by Bacillus and the anaerobic
Clostridium. They are resistant to heat, cold, drying and chemnical agents.
1. Have multi-layered protective coat consisting of: cell membrane, thick
peptidoglycan, another cell membrane, wall of keratin-like protein, and an outer
later called the exosporium.
 Biofilms- an extracellular polysacch that forms a mechanical scaffold around
bacteria.
 Facultative intracellular organisms- these bacteria inhibit the fusion of the
phagasome w/the lysozyme and thus once phagocytosed are safe from Ab
1. Listeria monocytogenes, salmonella typhi, yersinia, francisella tularensis,
brucella, legionella, mycobacterium.
Toxins:
 Exotoxins:
1. Proteins released by both gram + & - .
2. Released by all major gram + except listeria monocytogenes (endotoxin)
3. Gram – such as E.coli and vibrio cholera.
4. Neurotoxins – exotoxins that act on nerves or motor end plate to cause paralysis
(tetanus, botulinum)
5. Enterotoxins- exotoxins that act on GI & cause osmotic diarrhea by inhibiting
NaCl resorption, activate NaCl secretion, or kill intestinal epithilial cells.
a) Results in Infectious diarrhea (E.coli, Campylobacter jejuni, and
shigella dysnenteriae) & food poisoning (bacillus cereus and
staphylococcus pyogenes)
6. Pyrogenic exotoxins- stimulate cytokines release can cause rash, fever and toxic
sock syndrome (staphylococcus aureus and streptococcus pyogenes)
7. Tissue invasive exotoxins- inc enzymes that can destroy DNA, collagen, fibrin,
RBCs and WBCs.
 Endotoxins
1. Lipid A on gram – released when the bacteria is lysed.
a) Present on only gram – (exception is listeria monocytogenes)
 Septic shock or endotoxic shock
1. Sepsis- bacteremia (bacteria in the blood) that causes a systemic immune
response to the infection.
2. Septic shock- sepsis that results in dangerous drop in blood pressure and organ
dysfunction (hypotension and death). Chain of events:
a) Fromn a Localized infection or bacteremia the bacteria releases
exo or endooxinsthat circulate in the blood stream and stimulate
immune cells such as macrophages and neutrophilis to release host
proteins calles endogenous mediators
b) The most famous endogenous mediator is Tumor Necrosis Factor
(TNF) which is also called cachectin b/c released from tumors,
producing a wasting (weight loss) syndrome, called cachexia.
c) In sepsis, TNF triggers release of cytokine interleukin 1 from
macrophages and endothelial cells, which in turn cause release of other
cytokines and prostaglandins. These mediators act on blood vessels and
organs and produce vasodilation, hypotension and organ dysfunction.
d) Mortality rate: up to 40% of patients will die, this increases with
additional organ failure (15-20% for each organ)
e) Treatment
.2.e.1. Localize infection and kill the bacteria- most common site is
the lungs (pneumonia) followed by the abdomen and urinary tract.
.2.e.2. Dopamine and NE used maintain B.P.
Bacterial Genetics:
 Bacteria are haploid (1 circular dsDNA)
 4 ways to exchange genetic materia:
1. Transformation
a) Naked DNA fragments uptaked by competent bacteria (able to
bind, usually recepient is similar to the donor bacteria) and
incorporated into genome.
b) Can be used in mapping b/c the frequency of transformation
leading to 2 traits to be transferred is relative to their distance.
2. Transduction
a) When a bacteriophage which carries a piece of bacterial genome
transfers it to another.
b) Bacteriophages contain a capsid, attach to the bacterial cell surface
via adsorption followed by penetration. The phage’s injected DNA
takes over the host bacteria’s RNA polymerase, copies its genome and
forms capsids which are released when the bacteria lyses.
c) Virulent phages- infection, reproduction, lysis of bacteria
d) Temperate phages- its DNA gets incorporated into the bacteria’s
genome as a prophage
e) Virulent phages are involved in generalized transduction:
.2.e.1. Sometimes during reproduction of the virus, some pieces of the
bacterial DNA remain intact and are accidentally incorporated
into the phage’s capsid and thus transferred to the next bacteria.
f) Temperate phages are involved Specialized transduction:
.2.f.1. When the prophage is activated it is spliced out of the bacterial
chromosome and can take with it a piece of the bacterial
chromosome leading to its incorporation in capsids.
3. Conjugation
a) Direct DNA transfer via cell-to-cell contact.
b) Requires presence of F-plasmid (F+ bacteria) donor and an F-
recepient via the sex pilus.
c) Rarely, the F plasmid gets incorporated into the bacterial
chromosome, and the bacterial cell is called Hfr cell.
.3.c.1. Under normal conjugation, the entire bacterial genome can be
transferred to the recepient
.3.c.2. The integrated F plasmid can be excised at a different site
from that of integration causing the F plasmid to now contain
chromosomal genes (now called F’ plasmid)
4. Transposons
a) Mobile genetic elements. They can insert themselves into a donor
chromnosome w/out having DNA homology and can carry genes for
Ab resistance and virulence factors.
b) Transposon gene that confers a particular drug resistance can move
to the plasmids of different bacterial genera, resulting in the rapid
spread of resistant strains.

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