Microbe-host interactions
Nov 15, 2006
Ch. 21
Science 307:1915-20, 2005.
Antimicrobial drug resistance
•
•
Acquired ability to resist effects of a
chemotherapeutic to which it is normally
susceptible
Common mechanisms
1. Lack structure drug targets
2. May be impermeable to drug
3. Organism may be able to modify drug to an inactive
form
4. Organism may modify the target itself
5. Organism may develop a new pathway
6. Organism may be able to pump out the drug
R factors
• Most drug resistant bacteria isolated from
patients contain drug resistance genes on
plasmids
• Many of these plasmids encode enzymes
that inactivate drugs
• Multi-drug resistance plasmids predate
medical use of antibiotics
• Widespread emergence of multi-drug
resistance
Resistance to all known drugs…
Acinetobacter sp.
• Methicillin-
resistant
Staphylococcus
aureus (MRSA)
• Vancomycinresistant
Enterococcus (VRE)
Enterococcus faecalis
Streptococcus pneumoniae
Gram-negative
Gram-positive
Gram-positive/acid-fast
Mycobacterium tuberculosis
Haemophilus ducreyi
Salmonella typhi
Haemophilus influenzae
Neisseria gonorrhoeae
Pseudomonas aeruginosa
Salmonella sp.
Shigella dysenteriae
Shigella sp.
Other gram-negative rods
Staphylococcus aureus
1950
1960
1970
1980
1990
2000
2010
Figure by MIT OCW.
Healthcare-associated infections
• Healthcare-associated infections (HAIs)
are infections that patients acquire during
the course of receiving treatment for
other conditions
• In hospitals alone, HAIs account for an
estimated 2 million infections, 90,000
deaths, and $4.5 billion in excess health
care costs annually
http://www.cdc.gov/ncidod/dhqp/healthDis.html
Changing patterns for HAIs
• 1950s to 1960s gram positive bacteria
were a major problem (Streptococcus
pyogenes and Staphylococcus aureus)
• 1970s and 1980s gram negative bacteria
became a major problem (E. coli and
Pseudomonas spp.)
• Currently, gram positive bacteria are again
emerging as a major problem (S. aureus and
Enterococcus spp.)
Methicillin-resistant
Staphylococcus aureus N315
Image removed due to copyright restrictions.
Hiramatsu et al. Trends Microbiol 9:486, 2001
Terminology
• Normal microbial “flora” or “microflora”
– Better term is microbiota
– Commensal (at the same table)
• Pathogen
– Infection versus disease
• Virulence
• Opportunistic pathogen
Indigenous microbiota
• Microorganisms that inhabit body sites in which
surfaces and cavities are open to the environment
• Skin, oral cavity, upper respiratory tract,
gastrointestinal (GI) tract, and vagina
• Each habitat can be considered a separate
ecosystem
• For every cell in human body (1013) there are 10
viable indigenous bacteria in the GI tract
• The GI tract (1014) harbors 100-fold more
bacteria than the skin (1012)
Major bacteria present Esophagus Prevotella
Streptococcus
Veillonella
Helicobacter
Major physiological
processess
Stomach
Secretion of acid (HCI)
Digestion of macromolecules
pH 2
Small
intestine
Continued digestion
Absorption of monosaccharides,
amino acids, fatty acids, water
pH 4-5
Large
intestine
Absoption of bile acids,
vitamin B12
pH 7
Duodenum
Enterococci
Lactobacilli
Bacteroides
Bifidobacterium
Clostridium
Enterobacteria
Enterococcus
Escherichia
Eubacterium
Klebsiella
Lactobacillus
Peptococcus
Peptostreptococcus
Proteus
Ruminococcus
Staphylococcus
Streptococcus
Organ
Esophagus
Jejumum
Ileum
Colon
Anus
Figure by MIT OCW.
Defining the GI microbiota
• Autochthonous microbiota
– Present during the evolution of an animal and
therefore present in every member of a species
• Normal microbiota
– Common and perhaps even present in every
individual in a given geographic area/community,
but not in every member of the species
• True pathogens
– Acquired accidentally and therefore not
normally present in all members of a community
of an animal species
Dubos et al. J Exp Med 122:67-76, 1965
Ecological principles
• In a stable GI ecosystem, all available habitats are
occupied by indigenous microbiota
• Transient species derived from food, water, or
even another part of the GI tract or the skin will
not establish (colonize)
• Habitats are physical spaces in the GI tract
normally occupied by a climax community of
indigenous microbiota
• Population levels and species composition are
stable and not easily disrupted
Succession & climax populations
• Lactic acid bacteria and coliforms predominate in
infant human and animal GI tracts
• During weaning the microbiota changes drastically
and obligate anaerobic bacteria become
predominant
• The indigenous GI microbiota of adults consists of
climax communities that are remarkably stable
• Each region of the GI tract has a characteristic
population of microbes, in terms of complexity and
population density
Model systems
• Germ free animals
• Delivered by Cesarean section into sterile plasticfilm isolators
• Maintained free of all bacteria, fungi, protozoa,
viruses, and other detectible life forms
• Introducing microorganisms is called association
or colonization
• Contamination is accidental introduction of
unwanted microorganisms
• Germ free animals can be monoassociated with a
singe species or poly associated with multiple
species
ASF 361
Lactobacillus animalis
Lactobacillus murinus
Lactobacillus mali
Lactobacillus salivarius
ASF 360
Lactobacillus acidophilus
Lactobacillus lactis
ASF 500
Clostridium propionicum
Clostridium neopropionicum
ASF 356
Clostridium piliforme
Ruminococcus gnavus
Eubacterium contortum
Roseburia cecicola
ASF 502
Catonella morbi
Acetitomaculum ruminis
ASF 492
Eubacterium plexicaudatum
Johnsonella ignava
Flexistipes sinusarabic
Deferribacter thermophilus
Geovibrio ferrireducens
Colobus Monkey sp.
ASF 457
Rodent sp. 1
Rodent sp. 2
Rodent sp. 3
(Bacteroides) merdae
(Bacteroides) distasonis
ASF 519
(Bacteroides) forsythus
CDC DF-3
Esophagus
7
6
5
1
4
Small intestine
2
(% Difference)
Stomach
8
3
8
20
9
15
11
10
19
16 16
Large intestine
14
Figures by MIT OCW.
12
17
13
18
Cecum
Cp of target gene/g
ASF356 : spatial distribution
1.E+11
1.E+10
1.E+09
1.E+08
1.E+07
1.E+06
1.E+05
1.E+04
1
2
3
E1
S1
S2
I1
I2
I3
I4
I5
I6
Gut region
C1
C2
L1
L2
L3
Cp of target gene/g
ASF361 : spatial distribution
1.E+11
1.E+10
1.E+09
1.E+08
1.E+07
1.E+06
1.E+05
1.E+04
1
2
3
E1
S1
S2
I1
I2
I3
I4
I5
I6
Gut region
C1
C2
L1
L2
L3
Cp of target gene/g
ASF457 : spatial distribution
1.E+11
1.E+10
1.E+09
1.E+08
1.E+07
1.E+06
1.E+05
1.E+04
1
2
3
E1
S1
S2
I1
I2
I3
I4
I5
I6
Gut region
C1
C2
L1
L2
L3
Figure by MIT OCW.
Continued...
Cp of target gene/g
ASF492 : spatial distribution
1.E+11
1.E+10
1.E+09
1.E+08
1.E+07
1.E+06
1.E+05
1.E+04
1
2
3
E1
S1
S2
I1
I2
I3
I4
I5
I6
Gut region
C1
C2
L1
L2
L3
Cp of target gene/g
ASF500 : spatial distribution
1.E+10
1.E+08
1
2
3
1.E+06
1.E+04
1.E+02
E1
S1
S2
I1
I2
I3
I4
I5
I6
Gut region
C1
C2
L1
L2
L3
Cp of target gene/g
ASF519 : spatial distribution
1.E+11
1.E+10
1.E+09
1.E+08
1.E+07
1.E+06
1.E+05
1.E+04
1
2
3
E1
S1
S2
I1
I2
I3
I4
I5
I6
Gut region
C1
C2
L1
L2
L3
Figure by MIT OCW.
Human colonic microbiota
• Highest cell densities recorded for any ecosystem
• Diversity at the division level is among the lowest
• Only 8 of the 55 known bacterial divisions have
been identified in colonic bacteria to date
• 2 division dominate
• Cytophaga-Flavobacterium-Bacteroides (CFB)
• Firmicutes (genera Clostridium and Eubacterium)
• Proteobacteria are common, but not dominant
• Compare to many soil communities, where ≥ 20
bacterial division can be present
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Bäckhed et al. Science 307:1915-19, 2005
CF
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Figure by MIT OCW.
Diversity
• > 200,000 16S rRNA
sequence in GenBank
• 1,822 from human gut
• 1,689 are uncultured
• Look at 495 with
length > 900 bp
• ~ 800 species
• > 7,000 strains
Number of Taxonomic Units
104
Strain
1000
Species
Genus
100
10
1
80
85
90
95
100
16S rRNA Sequence Identity (%)
Bäckhed et al. Science 307:1915-19, 2005
Figure by MIT OCW.
Helicobacter pylori
HP­
HP+
Photographs of Barry J. Marshall and J. Robin Warren removed due to
copyright restrictions.Marshall and Warren won the 2005 Nobel prize
in medicine for their discovery of Helicobacter pylori
and its role in gastritis and peptic ulcer disease.
1% p.a.
Duodenal
Ulcer
Gastric
Lymphoma
Gastric Ulcer
Gastric
Cancer
Figure by MIT OCW.
Incidence diagram of Helicobacter
pylori disease in the world today
Gastritis and peptic ulcer
H. pylori strain 26695 genome (1,667,867 bp)
cag pathogenicity island (37,000 bp)
HP0524
(VirD4)
HP0525
(VirB11)
HP0527
(VirB10)
HP0544
(VirB4)
cagA
HP0528
(VirB9)
The proteins encoded by these genes assemble
to form a complex type IV secretion apparatus
capable of delivering CagA from the bacterium
into host cells
Translocation of CagA into gastric
epithelial cells
Phosphorylation of CagA by host-cell
kinases c-Src and Lyn
Binding to and activation of cellular
phosphatase SHP-2
Growth factor-like response in host cell,
cytoskeletal rearrangements
Figure by MIT OCW.
http://www.cdc.gov/ulcer/
H. pylori and gastritis
Images of Helicobacter pylori removed due to copyright restrictions.
Helicobacter pylori on gastric epithelial
cells (false-color SEM)
Suerbaum & Michetti N Eng J Med 2002