1. Pneumococcal Pneumonia

2. Symptoms & signs of pneumococcal pneumonia Sudden onsets of chills, fever 40°C and malaise Cough, tachypnea, dyspnea and chest pain Bloody sputum Auscultation & percussion – loss of vesicular sound (normal sound heard over the lung field), crackling, loss of resonance, egophony (increased resonance) Day 5-10 of illness, crisis, sudden drop in fever and improvement or fatal infection (development of opsonizing antibodies) Pathology: phases of red and white (or grey) hepatization.

3. Progression of pneumococcal pneumonia “Red Hepatization” Hyperemia and Edema

4. Progression of pneumococcal pneumonia “Grey Hepatization”“Yellow Hepatization”

5. Seasonal incidence of pneumonia caused by S. pneumoniae

6. Envelope Structure of Streptococcus pneumoniae

7. Polysaccharide Capsule The single most important virulence factor –antiphagocytic properties –prevents complement deposition –more than 100 serotypes Capsular “Opsonizing antibodies”  "lysis" after "crisis" of pneumococcal pneumonia.

8. Therapy and prevention of S. pneumoniae infections Penicillin, β-lactams if successful Increasing drug resistance –β -lactam resistant S. pneumonia can be resistant to other antimicrobials, 15-20% overall resistance (CDC Surveillance) PCV13 (Prevnar-13, Pfizer: 13 capsular polysaccharide conjugate vaccine): all children 65, high risk individuals (sickle cell anemia, CSF leak, cochlear implant, asplenia, malignancy etc) as primary immunization series PPSV23 (Pneumovax, Merck: 23 purified capsular polysaccharide vaccine, non-conjugated) together with PCV13: –asplenia, spenic dysfunction (sickle cell anemia) –hematological malignancies, heart-lung-disease, alcoholism) –AIDS and other immunodeficiencies –Renal and other transplants

9. Impact of PREVNAR (PCV7 capsular polysaccharide conjugate vaccine) on pneumococcal disease in the United States

10. Serotype replacement following PCV vaccination Carriage rate and temporal prevalence of PCV (pneumococcal conjugate vaccine) VT (vaccine types) and NVT (non-vaccine types) following introduction of PCV7 (2000) and PCV13 (2006) in the UK PCV7 serotype replacement was near complete 5 years after PCV7 introduction. S. pneumoniae carriage rate remained stable throughout the 5 year period. Serotypes unique to PCV13 significantly decreased by 2011. Clonal expansion of existing genotypes was primarily responsible for replacement. Continued surveillance is needed to monitor replacement until equilibrium is reached.

11. Bacterial Pathogenesis & Immunity

12. Oswald Avery studies Streptococcus pneumoniae at Rockefeller University Pneumococcal capsule is made of carboydrate (polysaccharide) Purified pneumococcal polysaccharide does not elicit antibody responses Polysaccharide conjugate to protein elicits antibody responses that are protective against pneumococcal infection Non-capsulating pneumococci are not virulent and their virulence is restored following transformation with DNA from virulent pneumococci

13. Virulent (Smooth) and Avirulent (Rough) Pneumococci

14. The sugar coated microbe Pneumococcal capsular polysaccharide prevents phagocytosis neutrophil pneumococcus

15. The transforming principle DNA for capsule biosynthesis Pneumococcal capsule synthesis genes

16. Bacterial genomes, multi-locus sequence typing (MLST) and genome sequencing tools to unravel the epidemiology of bacterial diseases

17. Bacterial genome sequencing single nucleotide polymorphisms (SNPs) in 616 US & 3,805 Thai S. pneumoniae isolates and their β-lactam resistance phenotypes

18. Bacterial genome sequencing recombination events in 173 isolates of post-PCV7 vaccine escape mutants detect serotype switches and changes in antibiotic resistance

19. Uses of bacterial genome sequencing DNA sequencing is cheap, analysis and long term data storage are expensive Epidemiology: follow the evolution and the spread of a pathogen and analyze changes in carriers and patients Evolution of antibiotic resistance in commensals and pathogens colonizing or infecting humans and their animals Consequences of bacterial vaccines on the carriage rate and disease rates of isolates from a specific pathogen Determine the source of infectious disease outbreaks and identify individuals responsible for transmission and the route of transmission Characterize, inventory and follow microbiota surrounding humans for their impact on health and disease

20. Epidemiology of bacterial disease: S. pneumoniae drivers: disease susceptibility, mortality, immunity, single (variable) virulence trait, transformation & recombination to generate capsule diversity

21. Vaccines against bacterial disease: S. pneumoniae drivers: vaccine serotypes, immunity, transformation & recombination to generate new (capsule) serotypes

22. Epidemiology of bacterial disease: C. diphtheriae drivers: disease susceptibility, mortality, immunity, toxin=virulence, toxoid=immunity, monomorphic clone

23. Transposons

24. Bacterial conjugation- Josh Lederberg

25. Lysogenic or Lytic Bacteriophage Infections - Lwoff Lysogenic Lytic

26. Bacteriophage transduction - Norton Zinder

27. Assembly of bacteriophage lambda and related phages

28. Rules of thumb for bacterial pathogens If you want to invade a host - stick to it If you don’t want to get killed - bring your weapons and fight If you want to invade another host - get out if you can If you want to get all of it done - bring your proteins out

29. Bacterial Pathogen Rule # 1 If you want to invade a host - stick to it

30. Where does bacterial adherence and infection occur?

31. Listeria attachment to epithelial cells leads to invasion and dissemination

32. Bacterial Pathogen Rule # 2 If you don’t want to get killed - bring your weapons and fight

33. S. aureus adenosine and deoxyadenosine synthesis

34. Vibrio cholera pathogenesis – secretion of cholera toxin, an AB type toxin

35. Bacterial Pathogen Rule # 3 The goal is to invade another host – bacteria must get out Physical contact Diarrhea, oral uptake Runny nose, respiratory droplets Purulent exsudate Insect (vector) borne transmission (mosquitoes, fleas, lice, ticks, mites) Sexual intercourse IVDA, needle sharing

36. Bacterial Pathogen Rule # 4 If you want to get all of it done - bring your proteins out

37. Secretion Pathways of Bacterial Pathogens Protein Translocation by the Sec Pathway

38. Secretion pathways of Gram-negative bacteria Autotransporter: secretion into the periplasm, insertion into outer membrane, self-catalyzed cleavage and transport into the extracellular medium

39. Secretion pathways of Gram-negative bacteria Type I secretion: ATP fueled, single transport step from the cytoplasm across the entire envelope into the extracellular medium

40. Secretion pathways of Gram-negative bacteria Type II secretion: secretion into the periplasm, then secretin- mediated transport across the outer membrane into the extracellular medium

41. Secretion pathways of Gram-negative bacteria Type III secretion: transport from the bacterial cytoplasm through a needle complex directly into host cells

42. Yersinia pestis injects type III effector Yops into immune cells

43. Secretion pathways of Gram-negative bacteria Type IV secretion: transport from the bacterial cytoplasm through a secretion machine into the cytoplasm of host cells Agrobacterial type IV secretion of T-DNA

44. Iron (Fe) limitation during bacterial infection LTF=lactoferrin, NGAL=lipocalin, TF=transferrin, HP=haptoglobin, HPX=haemopexin

45. Iron acquisition during bacterial infection Similarities and differences between Gram-negative and Gram- positive bacteria

46. Host molecules counteracting siderophores Lipocalins (siderocalins) sequester siderophores

47. Glucosylation of siderophores (enterobactin) prevents sequestration by lipocalin

48. The human microbiome Interindividual variation among fecal samples from 648 individuals

49. The human microbiome Intraindividual variation among fecal samples from 2 individuals

50. The human microbiome Intraindividual variation among vaginal samples from 2 individuals

51. The human microbiome Factors influencing the human microbiome

52. The human microbiome Hypotheses on how to perturb the interactions between microbiota, host and pathogen