Evolution of Virulence

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Evolution of Virulence

• P. I. Tarr
• Bio5392
• February 9, 2009

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Definitions and Mechanisms

• Evolution intergenerational changes in the
  genome of a species, results in fitness,
  emergence, extinction
• Natural Selection (mutations confer advantages
  or disadvantages to organisms)
• Genetic drift random acquisition of mutations

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Definitions

• Virulence Ability of an organism to directly
  injure a host, or to precipitate a auto-injurious
  process in the host
• Pathogen An organism that can injure a host
• Evolution of virulence acquisition of phenotype
  that lead to host injury

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Additional Considerations

• Pathogen is often host specific (host
  susceptibility)
• Injury is often a function of a series of events,
  before the host is actually injured, so enabling
  pre-injury events could also be considered to be
  virulence factors
• Host susceptibility is a variable concept
• Habitat is another determinant what is
  reservoir?

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Evolutionary Weapons

• DNA acquisition

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How to Evolve?

• DNA acquisition (lateral transfer)
• DNA loss
• DNA rearrangements within organisms
• Allelic variation

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DNA Acquisition

• Plasmids (transformation)
• Bacteriophages (transduction)
• Insertion sequences and transposons
• Integrons

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Acquisition Plasmids

• Extra chromosomal, replicate autonomously
• Usually circular
• Frequently encode resistance, bacteriocins,
  proteases
• Promiscuous
• Interact with loci on genome

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Acquisition Bacteriophages

• Integrate in chromosomes (variably stable
  prophages) or lytic phages
• Can encode virulence factors

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Acquisition Transposable Elements (Jumping Genes)

• Insertion sequences
• Small 750-2500 base pairs
• Genes only for mobility (transposase,
  transposase regulators)
• Inverted repeats on ends

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Acquisitions Transposons

• IS elements flanking other genes
• Variable size, TN5, Tn10
• Inverted repeats on ends

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Acquisitions Integrons

• Assembly platforms
• Acquire genes in cassettes, and enable their
  expression
• Superintegrons hundreds of genes, major
  components of chromosomal architecture

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DNA Loss

• Black holes
• Shigella all species seem to have lost LDC
• Replacement attenuates virulence
• Mechanism unknown

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Changing existing genes

• - intragenic mutations
• single nucleotide polymorphisms (substitutions)
  SNPs probably random
• small insertions or deletions (irreversible
  reversible
• Duplications
• Fusions
• Change in locations into operons/clusters/island
  s

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Architecture

• Most pathogens are mosaics backbones
  interspersed with pathogenicity islands
• V. cholerae 2 chromosomes
• Large metabolism, LPS, virulence
• Small drug resistance, DNA metabolism,
  potential virulence loci

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Genomic islands

• Transferred DNA regions (different GC content,
  conservation in distant organisms)
• Stable, integrated at tRNA synthase genes
• Resemble IS elements
• Can encode integrases and transposases

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Fitness is Goal of a Successful Mutation

• Fitness ( f ) capability to increase the number
  of offspring (survive and reproduce)
• f 1 best available phenotype under defined
  conditions

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Fitness effects of mutationsfnewfold -
neutralfnewgtfold - adaptivefnewltfold -
deleterious

• Natural selection fnew gt fold
• Genetic drift fnew fold
• fnew gt fold
• fnew lt fold

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• Diversifying selection
• acts when fnew gt fold only temporary, but
  repeatedly

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Bottlenecks - Restores populations after a
drastic reduction of the size from some
catastrophic event - Can fix adaptive changes and
lead to genetic homogenization.
die
survive
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Founder effect - bottleneck-like process when a
small sample of organisms spatially separates
from the main population
stays (e.g. on a continent)
moves (e.g. to an island)
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Gene hitchhiking - increase in frequency by a
physical linkage to an adaptive change that is
under positive selection
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Why do non-pathogens become pathogens?

• Virulence is a coincidental by-product of
• a commensal, not needed for pathogen
• population expansion
• (ii) Virulence is adaptive for the pathogen

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Virulence is Coincidental

• Injured host is a bystander
• Evolution seeks to increase fitness in
  predominant reservoir
• e.g., E. coli O157H7

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Virulence is adaptive for pathogen

• The symptoms induced by the organism enable its
  propagation
• Example V. cholerae, S. Typhi

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Case Study

• Riley Bloody diarrhea in MI and OR in 1982.
  Rare E. coli serotype isolated from many patients
  (O157H7)
• Karmali children with kidney failure following
  diarrhea, many had E. coli O157H7, and O26 and
  O111 in their stools

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E. coli O157H7

• Makes toxin(s) (Shiga toxin(s))
• Worldwide
• Outbreaks and sporadic cases
• Reservoir is apparently healthy cattle

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Multilocus Sequence Typing

• 35 enzymes in gel mobility patterns
• 34/35 O157H7 enzymes are identical to those of
  E. coli O55H7
• differs only in gnd (6 PGD), adjacent to rfb

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Gene hitchhiking - increase in frequency by a
physical linkage to an adaptive change that is
under positive selection
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What else do we know about O157H7?

• stx1 and stx2
• eae (intimin)
• LEE region
• large plasmid
• close relative in Germany
• TAI
• Fim is useless

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Case Study
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pO157 acquired ? LEE expression
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pO157 acquired ? LEE expression
pO157 ? ? ability to adhere to epithelial cells,
bovine and human gene acquisition promotes
colonization phenotype
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• TAI acquired
• Fe acquisition, promotes adherence
• Type 1 fimbrial adherence lost

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Stx2 acquired Stx increases expression of
nucleolin Stx kills bovine leukemia virus cells
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Genome Sequencing

• Focus on backbone (syntenic, stable, single
  copy)
• Examine SNPs
• Most stochastic mutations
• Synonymous neutral
• Nonsynonymous change protein structure,
  deleterious

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111 SNPs
28/30 North American pathogenic isolates are on
this main radiating branch
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Bottlenecks - Restores populations after a
drastic reduction of the size from some
catastrophic event - Can fix adaptive changes and
lead to genetic homogenization.
die
survive
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'Source - Sink' Model of Habitat Expansion
Introduced as ecological model by HR Pulliam in
1988
'Source' habitat - population is self-sustaining
(rgt0)
'Sink' habitat - population is not
self-sustaining (rlt0), but supported by
immigration from the 'Source'
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Types of Source-Sink dynamics
SOURCE
closed SINK
SOURCE
black-hole SINK
SOURCE
reciprocal SINK
Time
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Other Lessons from EHECConvergent repertoires

• intimin alleles are ? (O157H7) or ? (almost all
  other EHEC) or other (birds)
• stx alleles are also quite variable, and lineage
  and host range specific

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In host evolution

• H gradients 6 orders of magnitude
• Proteolysis
• Saponification
• Defensins
• IgA
• Anaerobiasis

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In host evolution

• H gradients
• Proteolysis
• Saponification Phage induction
• Defensins
• IgA Hitchhiking rfb/gnd
• Anaerobiasis Special fimbriae

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Summary

• Illuminate structure and function
• Demonstrate control strategies
• Define Intra-bacterial networks
• Speculation vs. Sequencing