Epidemiology & Control of Infectious Diseases

Public Health 253B: Epidemiology & Control of Infectious Diseases is a one semester advanced introduction to the epidemiology and control of infectious diseases. The course is taught from the perspective public health communicable disease control officers: frontline practitioners that detect, investigate, control, and prevent infectious diseases in communities. The lectures are given by public health communicable disease and academic experts that practice, teach, investigate, or conduct research in their specific areas. The course will emphasize (1) core concepts in infectious disease transmission mechanisms, dynamics, and containment; (2) evidence-based approaches to designing and implementing infectious disease control and prevention measures; and (3) epidemiologic methods for investigating infectious diseases.

Course Syllabus is available here (PDF).

Student MMWR Presentation Schedule is available here (PDF).

Archived Webcasts will be posted on UC Berkeley Webcast server.

Copyrighted articles are only available to registered UC Berkeley students. Select hyperlinked PubMed ID (PMID).

(01/25) Concepts for the Control and Prevention of Infectious Diseases (Tomás Aragón)

Required reading

• Aragón TJ & Reingold A. Epidemiologic Concepts for the Prevention and Control of Infectious Diseases (Download PDF Slides) | (Download PDF Chapter)
• Pirofski L, Casadevall A. The meaning of microbial exposure, infection, colonisation, and disease in clinical practice. Lancet Infect Dis. 2002;2:628-635 (PMID: 12383613)
• Musher DM. How contagious are common respiratory tract infections? N Engl J Med. 2003 Mar 27;348(13):1256-66. Review. (PMID: 12660390)
• Musher DM, Musher BL. Contagious acute gastrointestinal infections. N Engl J Med. 2004 Dec 2;351(23):2417-27. Review. (PMID: 15575058)
• Roy CJ, Milton DK. Airborne transmission of communicable infection--the elusive pathway. N Engl J Med. 2004 Apr 22;350(17):1710-2. (PMID: 15102996)
• Svoboda T, Henry B, Shulman L, et al. Public health measures to control the spread of the severe acute respiratory syndrome during the outbreak in Toronto. N Engl J Med. 2004 Jun 3;350(23):2352-61. (PMID: 15175437)
• Weinstein RA. Planning for epidemics--the lessons of SARS. N Engl J Med. 2004 Jun 3;350(23):2332-4. (PMID: 15175434)
• Frieden TR, Das-Douglas M, Kellerman SE, Henning KJ. Applying public health principles to the HIV epidemic. N Engl J Med. 2005 Dec 1;353(22):2397-402. (PMID: 16319391)

Optional reading

• Real LA, Biek R. Infectious disease modeling and the dynamics of transmission. Curr Top Microbiol Immunol. 2007;315:33-49. Review. (PMID: 17848059)
• Brankston, G.; Gitterman, L.; Hirji, Z.; Lemieux, C. & Gardam, M. Transmission of influenza A in human beings. Lancet Infect Dis. 2007:7;257-265 (PMID: 17376383). See also letters.
• Tellier R. Aerosol transmission of influenza A virus: a review of new studies. J R Soc Interface. 2009 Dec 6;6 Suppl 6:S783-90. Epub 2009 Sep 22. (PMID: 19773292)
• Rangel JM, Sparling PH, Crowe C, Griffin PM, Swerdlow DL. Epidemiology of Escherichia coli O157:H7 outbreaks, United States, 1982-2002. Emerg Infect Dis. 2005 Apr;11(4):603-9. (PMID: 15829201)

Homework 1: Due Monday, February 8, 2010

• Homework 1: (Download PDF)
• Homework 1: (Download PDF Answer Key)

(02/01) Epidemiologic approach: Steps to public health action (Tomás Aragón)

Required reading

• Aragon TJ. Epidemiologic approach: Steps to public health action (Download PDF Slides)

(02/01) Designing Epidemiologic Studies to Estimate Vaccine Effects (Tomás Aragón)

Required reading

• Aragón TJ. Measuring vaccine effects on infectious diseases (Download PDF Slides)
• Chen RT, Orenstein WA. Epidemiologic methods in immunization programs. Epidemiol Rev. 1996;18(2):99-117. Review. (PMID: 9021306)
• Halloran ME, Struchiner CJ. Study designs for dependent happenings. Epidemiology. 1991 Sep;2(5):331-8. (PMID: 1742381)
• Halloran ME, Struchiner CJ, Longini IM Jr. Study designs for evaluating different efficacy and effectiveness aspects of vaccines. Am J Epidemiol. 1997 Nov 15;146(10):789-803. Review. (PMID: 9384199)
• Halloran ME. Overview of vaccine field studies: types of effects and designs. J Biopharm Stat. 2006;16(4):415-27. (PMID: 16892904)
• Préziosi MP, Halloran ME. Effects of pertussis vaccination on transmission: vaccine efficacy for infectiousness. Vaccine. 2003 May 16;21(17-18):1853-61. (PMID: 12706669)

(02/01) Direct and Indirect Vaccination Effects: Article Example (Wayne Enanoria)

• Enanoria W. Direct and Indirect Vaccination Effects (Download PDF Slides)
• Haber M. Estimation of the direct and indirect effects of vaccination. Stat Med. 1999 Aug 30;18(16):2101-9. (PMID: 10441766)
• Sur D, Ochiai RL, Bhattacharya SK, Ganguly NK, Ali M, Manna B, Dutta S, Donner A, Kanungo S, Park JK, Puri MK, Kim DR, Dutta D, Bhaduri B, Acosta CJ, Clemens JD. A cluster-randomized effectiveness trial of Vi typhoid vaccine in India. N Engl J Med. 2009 Jul 23;361(4):335-44. (PMID: 19625715)
• Kim-Farley R, Bart S, Stetler H, Orenstein W, Bart K, Sullivan K, Halpin T, Sirotkin B. Clinical mumps vaccine efficacy. Am J Epidemiol. 1985 Apr;121(4):593-7. (PMID: 4014148)

(02/08) Public Health Surveillance: Detection and Monitoring (Michael Samuel)

Required reading

• Samuel M. Public Health Surveillance (Download PDF Slides)
• Nsubuga P, et al. Public Health Surveillance: A Tool for Targeting and Monitoring Intervention. Chapter 53 in Disease Control Priorities in Developing Countries (2nd Edition) Published: April 2006 ISBN: 0-8213-6179-1 (Download PDF Chapter)
• CDC. Framework for evaluating public health surveillance systems for early detection of outbreaks: Recommendations from the CDC Working Group. MMWR Recomm Rep. 2004 May 7;53(RR-5):1-11. (PMID: 15129191)
• Centers for Disease Control and Prevention (CDC). Automated detection and reporting of notifiable diseases using electronic medical records versus passive surveillance--massachusetts, June 2006-July 2007. MMWR Morb Mortal Wkly Rep. 2008 Apr 11;57(14):373-6. (PMID: 18401332)
• Centers for Disease Control and Prevention (CDC). Multistate outbreak of Salmonella infections associated with peanut butter and peanut butter-containing products--United States, 2008-2009. MMWR Morb Mortal Wkly Rep. 2009 Feb 6;58(4):85-90. (PMID: 19194370)

Optional reading

• CDC. Updated guidelines for evaluating public health surveillance systems: Recommendations from the Guidelines Working Group. MMWR Recomm Rep. 2001 Jul 27;50(RR-13):1-35. (PMID: 18634202)
• Dato V, Wagner MM, Fapohunda A. How outbreaks of infectious disease are detected: a review of surveillance systems and outbreaks. Public Health Rep. 2004 Sep-Oct;119(5):464-71. (PMID: 15313109)
• Perry HN, McDonnell SM, Alemu W, Nsubuga P, Chungong S, Otten MW Jr, Lusamba-dikassa PS, Thacker SB. Planning an integrated disease surveillance and response system: A matrix of skills and activities. BMC Med. 2007 Aug 15;5:24. (PMID: 17697387)
• CDC. Case definitions for infectious conditions under public health surveillance. Centers for Disease Control and Prevention. MMWR Recomm Rep. 1997 May 2;46(RR-10):1-55. (PMID: 9148133)
• CDC. Framework for program evaluation in public health. MMWR Recomm Rep. 1999 Sep 17;48(RR-11):1-40. (PMID: 10499397)

Homework 2: Due Monday, March 1, 2010

• Homework 2: (Download PDF)
• Homework 2: (Download PDF Answer Key)

(02/22) Mathematical Modeling of Infectious Diseases: Concepts and Applications (Travis Porco)

Optional reading

• Garnett GP. Sex Transm Infect. 2002 Feb;78(1):7-12. An introduction to mathematical models in sexually transmitted disease epidemiology. (PMID: 11872850)
• Garnett GP. Role of herd immunity in determining the effect of vaccines against sexually transmitted disease. J Infect Dis. 2005 Feb 1;191 Suppl 1:S97-106. (PMID: 15627236)
• Aral SO. Determinants of STD epidemics: implications for phase appropriate intervention strategies. Sex Transm Infect. 2002 Apr;78 Suppl 1:i3-13. (PMID: 12083444)

Homework 3: Due Monday, March 8, 2010

• Homework 3: (Download PDF)
• Homework 3: (Download PDF Answer Key)

(03/01) Epidemiology and Control of Tuberculosis (Jennifer Flood)

Required reading

• Maartens G, Wilkinson RJ. Tuberculosis. Lancet. 2007 Dec 15;370(9604):2030-43. Review. (PMID: 17719083)
• Banerjee R, Allen J, Westenhouse J, Oh P, Elms W, Desmond E, Nitta A, Royce S, Flood J. Extensively drug-resistant tuberculosis in california, 1993-2006. Clin Infect Dis. 2008 Aug 15;47(4):450-7. (PMID: 18616396)

Optional reading

• Taylor Z, Nolan CM, Blumberg HM; American Thoracic Society; Centers for Disease Control and Prevention; Infectious Diseases Society of America. Controlling tuberculosis in the United States. Recommendations from the American Thoracic Society, CDC, and the Infectious Diseases Society of America. MMWR Recomm Rep. 2005 Nov 4;54(RR-12):1-81. (PMID: 16267499) Erratum in: MMWR Morb Mortal Wkly Rep. 2005 Nov 18;54(45):1161.

(03/01) Prevention and Control of Pandemic Influenza (Bela Matyas)

Required reading

• Sullivan SJ, Jacobson RM, Dowdle WR, Poland GA. 2009 H1N1 influenza. Mayo Clin Proc. 2010 Jan;85(1):64-76. Epub 2009 Dec 10. Review. (PMID: 20007905).
• Louie JK, Acosta M, Winter K, Jean C, Gavali S, Schechter R, Vugia D, Harriman K, Matyas B, Glaser CA, Samuel MC, Rosenberg J, Talarico J, Hatch D; California Pandemic (H1N1) Working Group. Factors associated with death or hospitalization due to pandemic 2009 influenza A(H1N1) infection in California. JAMA. 2009 Nov 4;302(17):1896-902. (PMID: 19887665).

(03/08) Conducting an Outbreak Investigation (Tomás Aragón)

Required reading

• Aragon TJ. I Left My Heart (and more) in San Francisco. (Download PDF Student Version) | (Download PDF Instructor Version)
• Aragon TJ, Enanoria WT, Reingold A. Conducting an outbreak investigation in 7 steps (or less) --- A Quick Reference Guide (Download PDF)
• Reingold AL. Outbreak investigations---A perspective. Emerg Infect Dis 1998;4(1):21-7. (PMID: 9452395)
• CDC. Nosocomial group A streptococcal infections associated with asymptomatic health-care workers--Maryland and California, 1997. MMWR Morb Mortal Wkly Rep, 1999, 48, 163-166 (PMID: 11699845)
• CDC. Shigella sonnei outbreak among men who have sex with men--San Francisco, California, 2000-2001. MMWR Morb Mortal Wkly Rep, 2001, 50, 922-926. (PMID: 10079063)

Optional reading

• NCCPHP. Overview of Outbreak Investigations. FOCUS on Field Epidemiology. (Download PDF Newsletter | Discussion)
• NCCPHP. Anatomy and Physiology of an Outbreak FOCUS on Field Epidemiology. (Download PDF Newsletter | Discussion)
• NCCPHP. Embarking on an Outbreak FOCUS on Field Epidemiology. (Download PDF Newsletter | Discussion)

Homework 4: Due Monday, March 29, 2010

• Homework 4: (Download PDF)
• Homework 4: (Download PDF Anwser Key)
• Winthrop KL, Abrams M, Yakrus M, Schwartz I, Ely J, Gillies D, Vugia DJ. An outbreak of mycobacterial furunculosis associated with footbaths at a nail salon. N Engl J Med. 2002 May 2;346(18):1366-71. (PMID: 11986410)

(03/15) Epidemiology & Control of Sexually Transmitted Infections (Gail Bolan)

Required reading

• Bolan G. Emerging Issues in STD Prevention and Control (Download PDF Slides)
• Low N, Broutet N, Adu-Sarkodie Y, Barton P, Hossain M, Hawkes S. Global control of sexually transmitted infections. Lancet. 2006 Dec 2;368(9551):2001-16. Review. (PMID: 17141708)
• Ward H. Prevention strategies for sexually transmitted infections: importance of sexual network structure and epidemic phase. Sex Transm Infect. 2007 Aug;83 Suppl 1:i43-49. Epub 2007 Mar 27. Review. (PMID: 17389716)
• Donovan B. Sexually transmissible infections other than HIV. Lancet. 2004 Feb 14;363(9408):545-56. Review. (PMID: 14975619)
• Hogben M, Leichliter JS. Social determinants and sexually transmitted disease disparities. Sex Transm Dis. 2008 Dec;35(12 Suppl):S13-8. Review. (PMID: 18936725).

Optional reading

• CDC. Sexually transmitted diseases treatment guidelines, 2006. MMWR Recomm Rep. 2006 Aug 4;55(RR-11):1-94. (PMID: 16888612) Erratum in: MMWR Recomm Rep. 2006 Sep 15;55(36):997. (View HTML)
• Please note update: CDC. Update to CDC's sexually transmitted diseases treatment guidelines, 2006: Fluoroquinolones no longer recommended for treatment of gonococcal infections. MMWR Morb Mortal Wkly Rep. 2007 Apr 13;56(14):332-6. (PMID: 17431378)

(03/29) Epidemiology and Control of Selected Vector-borne Infectious Diseases: Plague, Hantavirus, West Nile Virus, and Lyme Disease (Curtis Fritz & Anne Kjemtrup)

Required reading

• Fritz C. Plague (The Black Death) and Hantavirus Disease (Download PDF Slides)
• Kjemtrup A. West Nile Viruse and Lyme Disease (Download PDF Slides)
• Prentice MB, Rahalison L. Plague. Lancet. 2007 Apr 7;369(9568):1196-207. (PMID: 17416264)
• CDC 2006. Human plague--four states, 2006. MMWR Morb Mortal Wkly Rep. 2006 Sep 1;55(34):940-3. (PMID: 16943764)
• Klein SL, Calisher CH. Emergence and persistence of hantaviruses. Curr Top Microbiol Immunol. 2007;315:217-52. (PMID: 17848067)
• Reisen W, Brault AC. West Nile virus in North America: Perspectives on epidemiology and intervention. Pest Manag Sci. 2007 Jul;63(7):641-6. (PMID: 17373672)
• Gubler DJ. The continuing spread of West Nile virus in the western hemisphere. Clin Infect Dis. 2007 Oct 15;45(8):1039-46. Epub 2007 Sep 14. (PMID: 17879923)
• Vázquez M, Muehlenbein C, Cartter M, Hayes EB, Ertel S, Shapiro ED. Effectiveness of personal protective measures to prevent Lyme disease. Emerg Infect Dis. 2008 Feb;14(2):210-6. (PMID: 18258112)

(04/05) Epidemiology and Control of HIV Transmission (Moupali Das)

Required reading

• Das M. HIV Prevention and Control (Download PDF Slides)
• Fox J, Fidler S. Sexual transmission of HIV-1. Antiviral Res. 2010;85(1):276-85. Epub 2009 Oct 27. (PMID: 19874852)
• Frieden TR, Das-Douglas M, Kellerman SE, Henning KJ. Applying public health principles to the HIV epidemic. N Engl J Med. 2005 Dec 1;353(22):2397-402. (PMID: 16319391)

(04/12) Intentional Microbial Threats (Tomás Aragón)

Required viewing

• CDC. The History of Bioterrorism. (View Video Page)
• PBS Nova: The Anthrax Investigation (View Video Page)

Required reading

• Rotz LD, Khan AS, Lillibridge SR, Ostroff SM, Hughes JM. Public health assessment of potential biological terrorism agents. Emerg Infect Dis. 2002 Feb;8(2):225-30. (PMID: 11897082)
• Inglesby TV, O'Toole T, Henderson DA, et al. Anthrax as a biological weapon, 2002: updated recommendations for management. JAMA. 2002;287(17):2236-52. Erratum in: JAMA 2002 Oct 16;288(15):1849. (PMID: 11980524)
• Arnon SS, Schechter R, Inglesby TV, et al. Botulinum toxin as a biological weapon: medical and public health management. JAMA. 2001;285(8):1059-70. Erratum in: JAMA 2001 Apr 25;285(16):2081. (PMID: 11209178)
• Henderson DA, Inglesby TV, Bartlett JG, et al. Smallpox as a biological weapon: medical and public health management. JAMA. 1999 Jun 9;281(22):2127-37. (PMID: 10367824)
• Inglesby TV, Dennis DT, Henderson DA, et al. Plague as a biological weapon: medical and public health management. JAMA. 2000;283(17):2281-90. (PMID: 10807389)
• Borio L, Inglesby T, Peters CJ, et al. Hemorrhagic fever viruses as biological weapons: medical and public health management. JAMA. 2002;287(18):2391-405. (PMID: 11988060)
• Audi J, Belson M, Patel M, Schier J, Osterloh J. Ricin poisoning: a comprehensive review. JAMA. 2005;294(18):2342-51. (PMID: 16278363)

Optional reading

• Shane S. F.B.I., Laying Out Evidence, Closes Anthrax Case. NY Times. February 19, 2010 (View Article Page)
• U.S Department of Justice. The Amerithrax Investigative Summary. February 19, 2010 (Download PDF Report)

(04/19) Biology, Epidemiology, and Control of Malaria (Phil Rosenthal, MD & Grant Dorsey)

Required reading

• Greenwood BM, Bojang K, Whitty CJ, Targett GA. Lancet. Malaria. 2005 Apr 23-29;365(9469):1487-98. (PMID: 15850634)
• Greenwood BM, Fidock DA, Kyle DE, Kappe SH, Alonso PL, Collins FH, Duffy PE. Malaria: progress, perils, and prospects for eradication. J Clin Invest. 2008 Apr;118(4):1266-76. (PMID: 18382739)
• Enayati A, Hemingway J. Malaria management: past, present, and future. Annu Rev Entomol. 2010;55:569-91. (PMID: 19754246)