Evolution and Evolution and Ecology of Ecology of PathogensPathogens
Martin PolzMartin PolzCivil & Environmental EngineeringCivil & Environmental EngineeringMassachusetts Institute of TechnologyMassachusetts Institute of Technology
OutlineOutline Emergence of pathogensEmergence of pathogens
Global importance of microorganismsGlobal importance of microorganisms What are pathogens?What are pathogens? Evolution of pathogenesisEvolution of pathogenesis
Re-emergence of pathogensRe-emergence of pathogens Antibiotic resistanceAntibiotic resistance CholeraCholera
ConclusionsConclusions
Germs, germs everywhereEven on a little pear,
Germs germs all around,Even on the dirty ground.
Germs, germs make me sick,Especially on a candy stick.Germs, germs are so small,
Even on a bouncy ball.
Candice's Germ Poem
Microbial communities drive biogeochemical cycles…
100human activities
140biological
fixation
200denitrification
SOIL
ATMOSPHERE
OCEANS
15biological
fixation
140denitrification
1200internal cycling 8000
internal cycling10
burial
36river flow
<3fixation inlightening
groundwater
Example: The Nitrogen Cycle
?human activities
140biological
fixation
200denitrification
SOIL
ATMOSPHERE
OCEANS
15biological
fixation
140denitrification
1200internal cycling 8000
internal cycling?
burial
?river flow
<3fixation inlightening
groundwater
Nitrogen Cycle Without Microbes
All processes slow.Would life be possible?
MicrobesMicrobes
•Bacteria•Fungi•Protists•Viruses
BacteriaBacteria
•Small•Efficient•Biochemically diverse•Fast growth
Marine
Freshwater
Sediments
Subsurface sediments(0-3,000 m)
Animal guts
Cells/ ml or gx106
Total cellsx1026
0.5
1.0
4,600
0.34-200
1-105
1,000
1.5
170
38,000
0.0004
(Whitman et al. 1998)
Bacteria are everywhereBacteria are everywhere
Global bacterial biomass (Pg of Global bacterial biomass (Pg of C)C)
Soil and Aquatic
Plants Bacteria
Subsurface
Terrestrial
Marine
560
1.8
26
2.2
22-215
303
Microbial biomass rivals plant biomassbut has higher turnover
How many bacterialHow many bacterialspecies are there?species are there?
Wilson 1988
Total number species: ~ 1.4 millionBacteria: ~3,500
Hammond 1995
Total number species: ~ 11 millionBacteria: ~10 million
The great plate count The great plate count anomalyanomaly
microbial community
plating
DAPI stained marine water sample
< 1% of observable bacteria grow on standard culture media
Genetic diversityGenetic diversity
Total nucleic acids
16S ribosomal RNA genes
Sequences
Diversity andevolutionary relationships
Identificationand quantification
Molecular approach:
• great diversity of microbes
• pathogens only a minor componentof microbial diversity
• allows understanding of evolutionof pathogenesis
Emergence of pathogensEmergence of pathogens
What is a pathogen?
An evolutionary view.
Example: Escherichia coli (E. coli)
Normally a harmless gut bacterium but…Eterotoxigenic strains
Enteropathogenic strainsEnteroinvasive strains
Enterohemorrhagic strainsEnteroaggregative strains
Uropathogenic strains
Genome analysis provides answer
Strains closely relatedGenome structure similar
But….
Insertions of ‘foreign’ DNA= pathogenicity islands
Comparative analysis:
Comparison harmless andpathogenic E. coli strains
A B
A B
C
C
E. coli K12
E. coli O157:H7
Foreign DNA= locus of enterocyte effacement
Responsible for pathogenicity:allows attachment and toxin productions
A harmless bacterium has become a pathogenby ‘stealing’ DNA from another bacterium!
Mechanisms of gene transfer:
1 Transformation: uptake of DNA from environment2 Transduction: DNA transfer by viruses3 Conjugation: plasmid transfer between bacterial cells
12
3
Can all transfer genes from other bacteriathat can become incorporated into genome
Fate of transferred genes:
RecA system = recombination into genomedependent on sequence similarity
% sequence differencereco
mbi
nati
on r
ate
How often does gene transfer happen?
Gene transfer is raree.g., transduction by viruses insert
foreign DNA every 108 virus infections
But….
Microbes have very large populationse.g., gene transfer in marine environment
~20 million billion times per second!
Genes must be advantageous to recipient….
Ecology of pathogenesisBacteria grow fast
High population densities
Great competition for resources
Pathogen = normal bacterium that has gained access to a new resource through new genes
--> Competitive advantage
Re-emergence of Re-emergence of pathogenspathogens
Example 1: Antibiotics
Antibiotics - natural warfare
common resource
species 1 species 2
Example 1: Antibiotics
Antibiotics - natural warfare
common resource
species 1 species 2
antibiotic
Example 1: Antibiotics
Antibiotics - natural warfare
common resource
species 1 species 2
antibiotic
Example 1: Antibiotics
Antibiotics - natural warfare
common resource
species 1
Antibiotic resistance
Bacteria have evolved resistance genes to antibioticsLocated on plasmids
Plasmid encoded resistance is easily transferredbetween species because plasmids are mobile
Occurrence usually low unless selection throughwidespread antibiotic use
Antibiotics overuse creates ‘Superbugs’
50 million tons antibiotics per year‘Superbugs’ resistant to most antibiotics Example: Tuberculosis 2.5 million deaths Mycobacterium tuberculosis increasingly resistant
Example 2: Cholera and climate
Vibrio cholerae and other vibriosubiquitous in marine, coastal waters
Genetically similar non-pathogenic andpathogenic strains co-exist
V.cholera
VibrioVibrio species identified as species identified as agents of human diseaseagents of human disease
Clinical presentations a
SpeciesGI Wound/ear
InfectionSepticemia
V. alginolyticus ++V. carchariae +V. cholerae Non-O1 ++ + + O1 ++ (+)V. cincinnatiensis +V. damsela ++V. fluvialis ++V. furnissii ++V. hollisae ++ (+)V. marinus +V. metschnikovii ? ?V. mimicus ++ +V. parahaemolyticus ++ + (+)V. vulnificus + ++ ++
a GI, gastrointestinal; ++, most common; (+) very rare.
Seasonal cholera in CalcuttaSeasonal cholera in Calcutta
(Sharma, 1998)
VibrioVibrio infections infections linked to El Nino linked to El Nino
Dhaka, Dhaka, Bangladesh Bangladesh
Cholera cases Cholera cases
Seasonality Seasonality RemovedRemoved
(Pascual, 2000)
Attachment to algae and zooplankton?Temperature dependent growth?
Possible reasons for seasonality
Algal growth= vibrio growth?
Temperature rise= vibrio growth?
Links to global warming and/or pollution
ConclusionsConclusions
Re-Emergence is an evolutionary/ecological phenomenon
Microbial communities extremely diverseLarge numbers of individuals
Potential for gene transfer
Pathogenesis arises via gene transfer
Result: harmless bacterial species becomes pathogenbecause it gains competitive advantage
Ecological factors (resistance, alternate hosts, climate)may trigger increased incidence of pathogenesis
Outlook for the future
Need to understand environmentalcontext of pathogenesis
Need to understand gene transferrates and diversity of co-occurring
genomes
Thanks to:
Silvia AcinasDan DistelDana HuntVanja KlepacLuisa MarcelinoChanathip PharinoRamahi Sarma-RupavtarmJanelle Thompson
NSF, NIH, Seagrant, DOE - Genomes to Life
