In this presentation I introduce the "SFDPH Population Health Division Controlling Infectious Diseases Model." This model integrates concepts from understanding transmission mechanisms, transmission dynamics, and transmission containment. The Model is most useful when facing novel microbial threats and we need simple framework for public health action.

1. Preparing for Microbial Threats to Health:
What Every Professional Should Know
Tom´as J. Arag´on, MD, DrPH
Health Officer, City & County of San Francisco
Director, Population Health Division (PHD), SFDPH
June 9, 2014
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 1 / 33

2. Acknowledgments
Robert S. Nakao, Executive Publisher, Advantage Business Media
SFDPH Population Health Division leadership and staff
Association of Bay Area Health Officials (ABAHO)
California Conference of Local Health Officers (CCLHO)
Center for Infectious Disease & Emergency Readiness*
Cal PREPARE Systems Research Center*
California Department of Public Health (CDPH)
National Association of County & City Health Officials (NACCHO)
Centers for Disease Control and Prevention (CDC)
* UC Berkeley School of Public Health
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 2 / 33

3. Contagion—The movie! vs. Contagion—Your reality!
Glass RJ, et al. Targeted social distancing
design for pandemic influenza. Emerg Infect
Dis. 2006 Nov;12(11):1671-81. PubMed:
17283616.
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 3 / 33

4. Middle East Respiratory Syndrome (MERS), June, 2014
Deadly Virus’s Spread Raises Alarms in Mideast: Saudis
Defend Approach to MERS Outbreak, Even as Cases
Increase. Wall Street Journal Online, April 13, 2014 Saudi Ministry of Health, June 7, 2014
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 4 / 33

5. Overview
1 Challenge of complexity
2 Controlling microbial threats
Transmission mechanisms
Transmission dynamics
Transmission containment
3 Integrated model for controlling microbial threats
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 5 / 33

6. Well established cause of outbreaks!
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 6 / 33

7. Well established response to outbreaks!
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 7 / 33

8. Challenge of complexity
SFDPH PHD Controlling Infectious Diseases (CID) Model
Addressing complexity with a simple framework for action (Tom´as J. Arag´on, 2014)
The PHD CID Model
The PHD CID model is an
integrated model for
preventing and controlling
infectious diseases. Also
consider the following: (1)
Is there asymptomatic
infectiousness? (latent
period is shorter than
incubation period), (2)
What is the generation
time?, (3) What are the
ethical considerations?,
and (4) Do you have the
political and logistical
support to be successful?
A) Microbial Agent in
B) Reservoir or
C) Source
E) Mode of
Transmission
G) Susceptible
Host
D) Portal
of Exit
F) Portal
of Entry
Reservoir / Source
1 Air
2 Water
3 Food
4 People
5 Animals & vectors
6 Vehicles (e.g., injection)
7 Soil & debris
Modes of transmission
1 Contact - direct
2 Contact - indirect
3 Droplets
4 Airborne
5 Vehicle-borne
6 Vector-borne
7 Vertical (mom-child)
The 7 Habits of Uninfected People
1 Safe consumption
2 Personal hygiene
3 Covering your cough
4 Getting vaccinated
5 Using “protection”
6 Reducing special risks
7 Basic infection control
Transmission Containment Strategies
1 Reduce contact rate
2 Reduce fraction of population that is infectious
3 Reduce biological infectiousness
4 Reduce biological susceptibility
5 Interrupt transmission (physical, chemical)
6 Reduce fraction of population that is susceptible
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 8 / 33

9. Challenge of complexity
Complexity and why it matters
What is a complex system?
1 A population of diverse agents, all of which are
2 connected, with behaviors and actions that are
3 interdependent, and that exhibit
4 adaptation and learning.
Why do we care?
Often unpredictable
Can produce large events
Can withstand substantial trauma
Can evolve along divergent pathways
Can produce “tipping points” (e.g., epidemics)
Can produce emergent phenomena (e.g., self-organization)
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 9 / 33

10. Challenge of complexity
Spread of novel influenza A (H1N1) via global air travel
Destination cities and corresponding volumes of international passengers arriving from
M´exico between March 1 and April 30, 2008. A total of 2.35 million passengers flew
from M´exico to 1018 cities in 164 countries. Source: Khan et al. (2009), PMID
19564630
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 10 / 33

11. Challenge of complexity
Mitigating complexity
Be humble
Expect to fail
Expect the unexpected
Expect unintended consequences
Expect big events and tipping points (e.g., epidemics)
Beware of pathway dependence (irreversible evolutionary divergence)
Harnessing complexity
Balance exploration (learning) and exploitation (execution)
Develop/use “simple” frameworks for action (this talk!)
Design for agility, adaptability, and responsiveness
Develop/use “simple rules” that spread
Every failure is a learning opportunity
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 11 / 33

12. Controlling microbial threats
Concepts for controlling infectious diseases
Transmission mechanisms
1 Chain model of infectious diseases
2 Natural history of infection and infectiousness
3 Convergence model of microbial threats
Transmission dynamics
1 Reproductive number
2 Infection rate among susceptibles
3 Generation time
Transmission containment
1 Control points, strategies, and measures
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 12 / 33

13. Controlling microbial threats Transmission mechanisms
Chain model of infectious diseases
Chain model
A) Microbial agent
B) Reservoir / Source
C) Portal of exit
D) Mode of transmission
E) Portal of entry
F) Susceptible host
A) Microbial Agent in
B) Reservoir or
C) Source
E) Mode of
Transmission
G) Susceptible
Host
D) Portal
of Exit
F) Portal
of Entry
Reservoir / Source
1 Air
2 Water
3 Food
4 People
5 Animals & vectors
6 Vehicles (e.g., injection)
7 Soil & debris
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 13 / 33

14. Controlling microbial threats Transmission mechanisms
Chain model—Reservoir / Source
Reservoir / Source
Humans
Animals
Environment
A reservoir can always
be a source, but not
all sources are
reservoirs.
For disaster planning
or response, consider
7 sources (see Figure).
A) Microbial Agent in
B) Reservoir or
C) Source
E) Mode of
Transmission
G) Susceptible
Host
D) Portal
of Exit
F) Portal
of Entry
Reservoir / Source
1 Air
2 Water
3 Food
4 People
5 Animals & vectors
6 Vehicles (e.g., injection)
7 Soil & debris
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 14 / 33

15. Controlling microbial threats Transmission mechanisms
Chain model—Modes of Transmission
Modes of transmission
1 Contact—direct
2 Contact—indirect
3 Droplet
4 Airborne
5 Vehicle-borne (food)
6 Vector-borne (bugs)
7 Vertical (mom-child)
A) Microbial Agent in
B) Reservoir or
C) Source
E) Mode of
Transmission
G) Susceptible
Host
D) Portal
of Exit
F) Portal
of Entry
Reservoir / Source
1 Air
2 Water
3 Food
4 People
5 Animals & vectors
6 Vehicles (e.g., injection)
7 Soil & debris
Modes of transmission
1 Contact - direct
2 Contact - indirect
3 Droplets
4 Airborne
5 Vehicle-borne
6 Vector-borne
7 Vertical (mom-child)
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 15 / 33

16. Controlling microbial threats Transmission mechanisms
Chain model—The 7 Habits of Uninfected People
The 7 Habits of
Uninfected People
1 Safe consumption
2 Personal hygiene
3 Covering your cough
4 Getting vaccinated
5 Using “protection”
6 Reducing special risks
7 Basic infection control
A) Microbial Agent in
B) Reservoir or
C) Source
E) Mode of
Transmission
G) Susceptible
Host
D) Portal
of Exit
F) Portal
of Entry
Reservoir / Source
1 Air
2 Water
3 Food
4 People
5 Animals & vectors
6 Vehicles (e.g., injection)
7 Soil & debris
Modes of transmission
1 Contact - direct
2 Contact - indirect
3 Droplets
4 Airborne
5 Vehicle-borne
6 Vector-borne
7 Vertical (mom-child)
The 7 Habits of Uninfected People
1 Safe consumption
2 Personal hygiene
3 Covering your cough
4 Getting vaccinated
5 Using “protection”
6 Reducing special risks
7 Basic infection control
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 16 / 33

17. Controlling microbial threats Transmission mechanisms
Good infection control starts with common sense:
Cover the source!
Source: American Society of Microbiology
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 17 / 33

18. Controlling microbial threats Transmission mechanisms
Disease scare at San Jose airport: 5 on flight from Asia
examined—none found with SARS I
San Francisco Chronicle, Wednesday, April 2, 2003
In a false alarm heard ’round the world, the Santa Clara County health
system jumped into high alert Tuesday morning when an American Airlines
flight from Tokyo radioed that it might have five cases of the mysterious
flulike illness known as SARS on board.
[Joan] Krizman said she had no hard feelings about being treated as a
potential health threat. The couple had just completed an exhausting,
monthlong journey that included stops in Vietnam, Thailand and Hong
Kong—three Southeast Asian hot spots for SARS.
“There were four fire trucks and eight police cars and four or five
ambulances,” she recalled. “I couldn’t believe it. I thought, ‘Wow! What’s
going on here?’ Little did I know that we were to be the ‘victims.’ ”
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 18 / 33

19. Controlling microbial threats Transmission mechanisms
Disease scare at San Jose airport: 5 on flight from Asia
examined—none found with SARS II
The couple were asked twice to go to Valley Medical Center, and twice
they politely declined. “And then,” Krizman said, “they soon opened up
the ambulance doors and said, sorry, we’re taking you to the hospital.”
At the hospital, according to Krizman, “we were the only ones there not
wearing masks.” When word got out just who they were, she said, “People
started running like crazy, like we were the bubonic plague. They put us in
a room full of people with plastic boots and face shields and masks.”
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 19 / 33

20. Controlling microbial threats Transmission mechanisms
Nurse wearing N-95 respirator outside of intensive care unit
Associated Press: In a ward at Sunnybrook and Womens Hospital in
Toronto, a nurse waits outside the door of a patient diagnosed with the
illness [SARS].
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 20 / 33

21. Controlling microbial threats Transmission mechanisms
Public-devised infection control, SARS outbreak, 2003
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 21 / 33

22. Controlling microbial threats Transmission mechanisms
Infection control practices, SARS outbreak, 2003
Reuters: An Indian woman diagnosed with SARS sits on her bed at the
Doctor Naidu Infectious Diseases Hospital in the western city of Pune.
Doctors reported India’s first case of the disease in a marine engineer from
the western coastal state of Goa on Friday, April 18, 2003.
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 22 / 33

23. Controlling microbial threats Transmission mechanisms
WHO: Infection control gaps helped fuel UAE MERS surge
CIDRAP News, June 6, 2014
“Infection control breaches led to a
list of factors that contributed to the
April surge of MERS-CoV cases in
the United Arab Emirates (UAE),
the World Health Organization
(WHO) said today after a team of
WHO and partner experts spent 5
days assessing the situation there.”
Source: http://www.cidrap.umn.edu
WHO finds hospital breaches worsened MERS
outbreak in UAE. Source: ArabianBusiness.com,
June 7, 2014
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 23 / 33

24. Controlling microbial threats Transmission mechanisms
Natural history of infection and infectiousness (A vs. B)
Susceptible Latent period Infectious period
Incubation period Symptomatic period
Time of
infection
Non-infectious
Non-diseased
No symptoms,
Infectious
Susceptible Latent period Infectious period
Incubation period Symptomatic period
Time of
infection
Non-infectious
Symptomatic,
Not infectious
Non-diseased
A
B
When the latent period is shorter than the incubation period (B), an infected person becomes
infectious before symptom onset.
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 24 / 33

25. Controlling microbial threats Transmission mechanisms
Convergence model for human-microbe interaction
Institute of Medicine. Microbial threats to health: Emergence, Detection, and Response.
National Academy Press, 2003
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 25 / 33

26. Controlling microbial threats Transmission dynamics
Epidemic curve in action, SARS outbreak, 2003
Number of probable cases of severe acute respiratory syndrome, by date of fever onset
and reported source of infection, Singapore, Feb 25-Apr 30, 2003. Source: CDC MMWR
(2003) PMID: 12807088
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 26 / 33

27. Controlling microbial threats Transmission dynamics
Reproductive number in action, SARS outbreak, 2003
Probable cases of severe acute respiratory syndrome, by reported source of infection,
Singapore, Feb 25-Apr 30, 2003. Source: CDC MMWR (2003) PMID: 12807088
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 27 / 33

28. Controlling microbial threats Transmission dynamics
In Contagion, Dr. Erin Mears (Kate Winslet) explains R0
Contagion is a 2011 public health thriller
directed by Steven Soderbergh.
The reproductive number (R) is the number of
infectious cases produced by an infectious case
during its infectious period. R0 is the initial R
when an index case is introduced into a
completely susceptible population with no
control measures. Source (figure): PMID:
19620267
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 28 / 33

29. Controlling microbial threats Transmission dynamics
Dynamics: Reproductive number and infection rate
Basic reproductive number
R0 = d × c × p
Transmission probability (p)
Biologic infectiousness
Biologic susceptibility
Interruptors (e.g., PPE)
Effective reproductive number
R(t) = R0 × x(t)
Infection rate among susceptibles
I(t) = c × p × P(t)
Source (figure): PMID: 19620267
d = duration of infectiousness
c = contact rate
p = transmission probability
x = fraction of population that is susceptible
P = fraction of population that is infectious
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 29 / 33

30. Controlling microbial threats Transmission dynamics
Reproductive number vs. Infection rate in susceptibles
Control strategies are derived from control points
Parameter control points
d = duration of infectiousness
c = contact rate
p = transmission probability
x = fraction of population
that is susceptible
P = fraction of population
that is infectious
Design control strategies
All communicable disease
control strategies are designed
to affect the five control
points.
A) Microbial Agent in
B) Reservoir or
C) Source
E) Mode of
Transmission
G) Susceptible
Host
D) Portal
of Exit
F) Portal
of Entry
Transmission
probability (p)
Contact
rate (c)
Fraction of population
that is infectious (P)
Fraction of population
that is susceptible (x)
Duration of
infectiousness (d)
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 30 / 33

31. Controlling microbial threats Transmission containment
Transmission containment
Control strategies
1 Reduce contact rate (c)
2 Reduce fraction of population that is infectious (P)
3 Reduce biological infectiousness (affects p)
4 Reduce biological susceptibility (affects p)
5 Interrupt transmission (physical, chemical) (affects p)
6 Reduce fraction of population that is susceptible (x)
Control measures . . .
are interventions designed to address control strategies. Always consider
mutliple perspectives: host, agent, infectious sources, and environment
(physical, social, economic, political, etc.)
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 31 / 33

32. Integrated model for controlling microbial threats
SFDPH PHD Controlling Infectious Diseases (CID) Model
Transmission mechanisms, dynamics, and containment (Tom´as J. Arag´on, 2014)
The PHD CID Model
The PHD CID model is an
integrated model for
preventing and controlling
infectious diseases. Also
consider the following: (1)
Is there asymptomatic
infectiousness? (latent
period is shorter than
incubation period), (2)
What is the generation
time?, (3) What are the
ethical considerations?,
and (4) Do you have the
political and logistical
support to be successful?
A) Microbial Agent in
B) Reservoir or
C) Source
E) Mode of
Transmission
G) Susceptible
Host
D) Portal
of Exit
F) Portal
of Entry
Reservoir / Source
1 Air
2 Water
3 Food
4 People
5 Animals & vectors
6 Vehicles (e.g., injection)
7 Soil & debris
Modes of transmission
1 Contact - direct
2 Contact - indirect
3 Droplets
4 Airborne
5 Vehicle-borne
6 Vector-borne
7 Vertical (mom-child)
The 7 Habits of Uninfected People
1 Safe consumption
2 Personal hygiene
3 Covering your cough
4 Getting vaccinated
5 Using “protection”
6 Reducing special risks
7 Basic infection control
Transmission Containment Strategies
1 Reduce contact rate
2 Reduce fraction of population that is infectious
3 Reduce biological infectiousness
4 Reduce biological susceptibility
5 Interrupt transmission (physical, chemical)
6 Reduce fraction of population that is susceptible
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 32 / 33

33. Integrated model for controlling microbial threats
Thank you! Any questions?
Tom´as J. Arag´on, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health June 9, 2014 33 / 33