Articles in boldface: it's mandatory to read them before the start of the course.

Principles of Molecular Epidemiology

1. Foxman, B and Riley, LW. Molecular epidemiology: focus on infection. Am J Epidemiol. 2001;153:1135-1141.

2. Arbeit, R.D. Laboratory procedures for the epidemiologic analysis of microorganisms. In. Manual of Clinical Microbiology. 7th Edition. p. 116-137.

3. Levin, B.R. et al. Population biology, evolution, and infectious disease: convergence and synthesis. Science. 1999;283:806-9.

4. Maslow, J.N. et al. Molecular epidemiology: the application of contemporary techniques to typing bacteria. Clin. Infect. Dis. 1993;17:153-162

5. Struelens, M.J. and ESGEM. Consensus guidelines for appropriate use and evaluation of microbial epidemiologic typing systems. Clin. Microbiol. and Infection. 1996;2:2-11.

6. Tenover, F.C. et al. How to select and interpret molecular strain tying methods for epidemiological studies of bacterial infections: a review for healthcare epidemiologists. Infect. Control Hosp. Epidemiol. 1997;18:426-439.

7. Tibayrenc, M. Genetic epidemiology of parasitic protozoa and other infectious agents: the need for an integrated approach. Int. J. Parasit. 1998;28:85-104.

8. Yan et al. Evidence for genetic hitchhiking eftect associated with insecticide resistance in Aedes aegypti. Genetics 1998; 148: 793-800.

9. Jarne and Theron. Genetic structure in natural populations of flukes ad snails: a practical approach and review. Parasistology 2000; 123: 827-840.

10. Goering and Tenover. Epidemiological Interpretation of Chromosomal Macro-Restriction FragmentPatterns Analyzed by Pulsed-Field Gel Electrophoresis. J. CLIN. MICROBIOL, 1997, 35: 2432-2433.

11. van Belkum et al. Role of Genomic Typing in Taxonomy, Evolutionary Genetics and Microbial Epidemiology. CLIN. MICROBIOL REV 2001, 14: 547-560.

Overview of Basic Concepts of Epidemiology

12. Grimes and Schulz. An overview of clinical research: the lay of the land. Lancet 2002; 359: 57-61.

13. Grimes and Schulz. Descriptive studies: what they can and cannot do. Lancet 2002; 359: 145-149.

14. Grimes and Schulz. Bias and causal associations in observational research. Lancet 2002; 359: 248-252.

15. Grimes and Schulz. Cohort sutdies: marching towards outcomes. Lancet 2002; 359: 341-345.

16. Schulz and Grimes. Case control studies: research in reverse. Lancet 2002; 359: 431-434

17. Grimes and Schulz. Uses and abuses of screening test. Lancet 2002; 359: 881-884.

18. Reingold. Outbreak investigations: a perspective. Emerging Infectious Diseases 1998; 4: 23-27.

Practice of Molecular Epidemiology

19. Sreevatsan, S. et al. Restricted structural gene polymorphism in the M. tuberculosis complex indicates evolutionary recent global dissemination. Proc Natl Acad Sci, USA. 1997;94:9869-74.

20. Tenover, FC et al. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis criteria for bacterial strain typing. J Clin Microbiol. 1995;33:2233-39.

21. Tenover, F.C. et al. Comparison of traditional and molecular methods of typing isolates of Staphylococcus aureus. J. Clin. Microbiol. 1994;32:407-415.

22. Arbeit, R.D. et al. Genetic diversity among strains of M. avium causing monoclonal and polyclonal bacteremia in patients with the acquired immunodeficiency syndrome (AIDS). J. Infect. Dis. 1993, 167:1384-90.

23. van Embden et al. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized Methodology. J Clin Microbiol. 1993;31: 406-9.

24. van Soolingen, DJ. et al. IS1245 restriction fragment length polymorphism typing of Mycobacterium avium isolates: proposal for standardization. J. Clin. Microbiol. 1998; 36:3051-54.

25. Riley, LW et al. Evaluation of isolated cases of salmonellosis by plasmid profile analysis: introduction and transmission of a bacterial clone by precooked roast beef. J Infect Dis. 1983;148:12-17.

26. Riley, LW et al. The significance of hospitals as reservoirs for endemic multiresistant Salmonella typhimurium causing infection in urban Brazilian children. J Infect Dis. 1984;150:236-41.

27. Friedman CR et al. Transmission of multidrug-resistant tuberculosis in a large urban setting. Am J Respir Crit Care Med. 1995;152:355-59.

28. Small P et al. The epidemiology of tuberculosis in San Francisco: a population-based study using conventional and molecular methods. N Engl J Med. 1994;330:1703-09.

29. Tornieporth, N.G. et al. Differentiation of pathogenic E. coli in Brazilian children by polymerase chain reaction. J. Clin. Microbiol. 1995;33:1371-74.

30. Kimura R. et al. Restriction-site-specific PCR as a rapid test to detect enterohemorrhagic Escherichia coli O157:H7 strains in environmental samples.Appl Environ Microbiol. 2000;66:2513-19.

31. Zhang. L., B. et al. Molecular epidemiologic approaches to urinary tract infection gene discovery in uropathogenic Escherichia coli. Infect. Immun. 2000;68:2009-2015.

32. Bender JB, et al. Surveillance for Escherichia coli O157:H7 infections in Minnesota by molecular subtyping. N Engl J Med. 1997;337:388-94.

33. Enright, M.C., and Spratt BB. Mulitilocus sequence typing. Trends in Microbiol. 1999;7;482-487.

34. Friedman CR et al. Widespread dissemination of a drug-susceptible strain of M. tuberculosis. J Infect Dis. 1997;176:478-84.

35. Ehrt S. et al. A novel antioxidant gene from M. tuberculosis. J Exp Med. 1997;186:1885-96.

36. Ko AI. et al. Clonally related penicillin-nonsusceptible Streptococcus pneumonia serotype 14 from cases of meningitis in Salvador, Brazil. Clin Infect Dis. 2000;30:78-86.

37. Suffys PN et al. Usefulness of IS6110-restriction fragment length polymorphism typing of Brazilian strains of Mycobacterium tuberculosis and comparison with an international fingerprint database. Res Microbiol. 2000;151;343-351.

38. Ferrazoli L et al. Transmission of tuberculosis in an endemic urban setting in Brazil. Int J Tuberc Lung Dis. 2000;4:18-25.


40. Ribeiro et al. Prevention of Haemophilus influenzae Type b (Hib) Meningitis and Emergence of Serotype Replacement with Type a Strains after Introduction of Hib Immunization in Brazil. J. Infect. Dis 2003:187 :109.

41. McGee et al. Nomenclature of Major Antimicrobial-Resistant Clones of Streptococcus pneumoniae Defined by the Pneumococcal Molecular Epidemiology Network. J. CLIN. MICROBIOL 2001, 39: 2565-2571.

42. Maiden et al. Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. PNAS 1998, 95: 3140-3145.

43. Norris DE.Genetic markers for study of the anopheline vectors of human malaria.Int J Parasitol. 2002 Dec 4;32(13):1607-15.

44. Pinto J et al.Genetic structure of Anopheles gambiae (Diptera: Culicidae) in Sao Tome and Principe (West Africa): implications for malaria control. Mol Ecol. 2002 Oct;11(10):2183-7.

45. Curtis J et al. Schistosome genetic diversity: the implications of population structure as detected with microsatellite markers. Parasitology. 2002;125 Suppl:S51-9.

46. Ayres CF et al. Genetic Diversity in Brazilian populations of Aedes albopictus. Mem Inst Oswaldo Cruz. 2002 Sep;97(6):871-5.