Evolution and Ecology of Pathogens

1. Evolution and Ecology of Pathogens Martin Polz Civil & Environmental Engineering Massachusetts Institute of Technology

2. Outline • Emergence of pathogens • Global importance of microorganisms • What are pathogens? • Evolution of pathogenesis • Re-emergence of pathogens • Antibiotic resistance • Cholera • Conclusions

3. Candice's Germ Poem Germs, germs everywhere Even 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.

4. Microbial communities drive biogeochemical cycles…

5. Example: The Nitrogen Cycle <3 fixation in lightening 100 human activities ATMOSPHERE 200 denitrification 140 biological fixation 15 biological fixation 140 denitrification 36 river flow groundwater 1200 internal cycling 8000 internal cycling 10 burial SOIL OCEANS

6. Nitrogen Cycle Without Microbes <3 fixation in lightening ? human activities ATMOSPHERE 200 denitrification 140 biological fixation 15 biological fixation 140 denitrification ? river flow groundwater 1200 internal cycling 8000 internal cycling ? burial All processes slow. Would life be possible? SOIL OCEANS

7. Microbes • Bacteria • Fungi • Protists • Viruses

8. Bacteria • Small • Efficient • Biochemically diverse • Fast growth

9. Cells/ ml or g x106 Total cells x1026 Marine 0.5 1,000 Freshwater 1.0 1.5 Sediments 4,600 170 Subsurface sediments (0-3,000 m) 0.34-200 38,000 Animal guts 1-105 0.0004 Bacteria are everywhere (Whitman et al. 1998)

10. Plants Bacteria Soil and Aquatic Subsurface Terrestrial 560 26 22-215 Marine 1.8 2.2 303 Global bacterial biomass (Pg of C) Microbial biomass rivals plant biomass but has higher turnover

11. How many bacterialspecies are there? Wilson 1988 Hammond 1995 Total number species: ~ 1.4 million Bacteria: ~3,500 Total number species: ~ 11 million Bacteria: ~10 million

12. microbial community plating DAPI stained marine water sample The great plate count anomaly < 1% of observable bacteria grow on standard culture media

13. Genetic diversity Total nucleic acids 16S ribosomal RNA genes Sequences Identification and quantification Diversity and evolutionary relationships

15. Molecular approach: • great diversity of microbes • pathogens only a minor component • of microbial diversity • allows understanding of evolution • of pathogenesis

16. Emergence of pathogens

17. What is a pathogen? An evolutionary view. Example: Escherichia coli (E. coli) Normally a harmless gut bacterium but… Eterotoxigenic strains Enteropathogenic strains Enteroinvasive strains Enterohemorrhagic strains Enteroaggregative strains Uropathogenic strains

18. Genome analysis provides answer Comparative analysis: Strains closely related Genome structure similar But…. Insertions of ‘foreign’ DNA = pathogenicity islands

19. Comparison harmless and pathogenic E. coli strains A B C E. coli K12 A B C E. coli O157:H7 Foreign DNA = locus of enterocyte effacement Responsible for pathogenicity: allows attachment and toxin productions A harmless bacterium has become a pathogen by ‘stealing’ DNA from another bacterium!

20. Mechanisms of gene transfer: 2 1 3 Transformation: uptake of DNA from environment Transduction: DNA transfer by viruses Conjugation: plasmid transfer between bacterial cells Can all transfer genes from other bacteria that can become incorporated into genome

21. Fate of transferred genes: RecA system = recombination into genome dependent on sequence similarity recombination rate % sequence difference

22. How often does gene transfer happen? Gene transfer is rare e.g., transduction by viruses insert foreign DNA every 108 virus infections But…. Microbes have very large populations e.g., gene transfer in marine environment ~20 million billion times per second! Genes must be advantageous to recipient….

23. 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

24. Re-emergence of pathogens

25. species 1 species 2 common resource Example 1: Antibiotics Antibiotics - natural warfare

26. Example 1: Antibiotics Antibiotics - natural warfare species 1 species 2 antibiotic common resource

27. Example 1: Antibiotics Antibiotics - natural warfare species 1 species 2 antibiotic common resource

28. Example 1: Antibiotics Antibiotics - natural warfare species 1 common resource

29. Antibiotic resistance Bacteria have evolved resistance genes to antibiotics Located on plasmids

30. Plasmid encoded resistance is easily transferred between species because plasmids are mobile Occurrence usually low unless selection through widespread antibiotic use

31. 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

32. Example 2: Cholera and climate Vibrio cholerae and other vibrios ubiquitous in marine, coastal waters Genetically similar non-pathogenic and pathogenic strains co-exist V.cholera

33. Vibrio species identified as agents of human disease

34. Seasonal cholera in Calcutta (Sharma, 1998)

35. Vibrio infections linked to El Nino Dhaka, Bangladesh Cholera cases Seasonality Removed (Pascual, 2000)

36. Possible reasons for seasonality Attachment to algae and zooplankton? Temperature dependent growth? T Algal growth = vibrio growth? Temperature rise = vibrio growth? Links to global warming and/or pollution

37. Conclusions

38. Re-Emergence is an evolutionary/ecological phenomenon Microbial communities extremely diverse Large numbers of individuals Potential for gene transfer Pathogenesis arises via gene transfer Result: harmless bacterial species becomes pathogen because it gains competitive advantage Ecological factors (resistance, alternate hosts, climate) may trigger increased incidence of pathogenesis

39. Outlook for the future Need to understand environmentalcontext of pathogenesis Need to understand gene transfer rates and diversity of co-occurring genomes

40. Thanks to: Silvia Acinas Dan Distel Dana Hunt Vanja Klepac Luisa Marcelino Chanathip Pharino Ramahi Sarma-Rupavtarm Janelle Thompson NSF, NIH, Seagrant, DOE - Genomes to Life