Evolution and Evolution and Ecology of Ecology of PathogensPathogens

Martin PolzMartin Polz

Civil & Environmental EngineeringCivil & Environmental Engineering

Massachusetts 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 cycling

10burial

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

1

2

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 differencerecom

bin

ati

on

rate

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 pathogenesis

Bacteria 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