Preparing for Microbial Threats to Health:

What Every Professional Should Know

Tomas J. Aragon, MD, DrPH

Health Officer, City & County of San Francisco

Director, Population Health Division (PHD), SFDPH

July 24, 2014

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 1 / 33
 Acknowledgments

Michael Janiga, CFE, Business Continuity Manager, VP

Bank of the West
Muntu Davis, MD, MPH, Health Officer, Alameda County
SFDPH Population Health Division leadership and staff
Association of Bay Area Health Officials (ABAHO)
California Conference of Local Health Officers (CCLHO)
California Department of Public Health (CDPH)

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 2 / 33
 ContagionThe movie! vs. ContagionYour reality!

Glass RJ, et al. Targeted social distancing

design for pandemic influenza. Emerg Infect
Dis. 2006 Nov;12(11):1671-81. PubMed:
17283616.
Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 3 / 33
 Middle East Respiratory Syndrome (MERS), June, 2014

Deadly Viruss 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

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 4 / 33
 Overview

1 Challenge of complexity

2 Controlling microbial threats

Transmission mechanisms
Transmission dynamics
Transmission containment

3 Integrated model for controlling microbial threats

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 5 / 33
 Well established cause of outbreaks!

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 6 / 33
 Well established response to outbreaks!

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 7 / 33
 Challenge of complexity
SFDPH PHD Controlling Infectious Diseases (CID) Model
Addressing complexity with a simple framework for action (Tomas J. Aragon, 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?
Tomas J. Aragon, MD, DrPH (SFDPH)
D) Portal F) Portal
of Exit of Entry
E) Mode of
Transmission
A) Microbial Agent in
G) Susceptible
B) Reservoir or
Host
C) Source
Reservoir / Source Modes of transmission The 7 Habits of Uninfected People
1 Air 1 Contact - direct 1 Safe consumption
2 Water 2 Contact - indirect 2 Personal hygiene
3 Food 3 Droplets 3 Covering your cough
4 People 4 Airborne 4 Getting vaccinated
5 Animals & vectors 5 Vehicle-borne 5 Using protection
6 Vehicles (e.g., injection) 6 Vector-borne 6 Reducing special risks
7 Soil & debris 7 Vertical (mom-child) 7 Basic infection control
Transmission Containment Strategies
1 Reduce contact rate 4 Reduce biological susceptibility
2 Reduce fraction of population that is infectious 5 Interrupt transmission (physical, chemical)
3 Reduce biological infectiousness 6 Reduce fraction of population that is susceptible
Preparing for Microbial Threats to Health July 24, 2014 8 / 33
 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 evolve along divergent pathways
Can produce tipping points (e.g., epidemics)
Can produce emergent phenomena (e.g., herd immunity)

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 9 / 33
 Challenge of complexity

Spread of novel influenza A (H1N1) via global air travel

Destination cities and corresponding volumes of international passengers arriving from

Mexico between March 1 and April 30, 2008. A total of 2.35 million passengers flew
from Mexico to 1018 cities in 164 countries. Source: Khan et al. (2009), PMID
19564630
Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 10 / 33
 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 path dependence and practical drift

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

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 11 / 33
 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

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 12 / 33
 Controlling microbial threats Transmission mechanisms

Chain model of infectious diseases

D) Portal F) Portal
of Exit of Entry
Chain model E) Mode of
A) Microbial agent Transmission

B) Reservoir / Source
A) Microbial Agent in
G) Susceptible
C) Portal of exit B) Reservoir or
Host
C) Source
D) Mode of transmission
E) Portal of entry
F) Susceptible host Reservoir / Source
1 Air
2 Water
3 Food
4 People
5 Animals & vectors
6 Vehicles (e.g., injection)
7 Soil & debris

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 13 / 33
 Controlling microbial threats Transmission mechanisms

Chain modelReservoir / Source

Reservoir / Source D) Portal F) Portal

of Exit of Entry
Humans
E) Mode of
Animals Transmission

Environment
A) Microbial Agent in
G) Susceptible
B) Reservoir or
A reservoir can always C) Source
Host
be a source, but not
all sources are
reservoirs.
Reservoir / Source
1 Air
For disaster planning 2 Water
3 Food
or response, consider 4 People
5 Animals & vectors
7 sources (see Figure). 6 Vehicles (e.g., injection)
7 Soil & debris

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 14 / 33
 Controlling microbial threats Transmission mechanisms

Chain modelModes of Transmission

D) Portal F) Portal
Modes of transmission of Exit of Entry
E) Mode of
1 Contactdirect
Transmission
2 Contactindirect
A) Microbial Agent in
3 Droplet B) Reservoir or
G) Susceptible
Host
C) Source
4 Airborne
5 Vehicle-borne (food)
6 Vector-borne (bugs)
Reservoir / Source Modes of transmission
1 Air 1 Contact - direct
7 Vertical (mom-child) 2 Water 2 Contact - indirect
3 Food 3 Droplets
4 People 4 Airborne
5 Animals & vectors 5 Vehicle-borne
6 Vehicles (e.g., injection) 6 Vector-borne
7 Soil & debris 7 Vertical (mom-child)

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 15 / 33
 Controlling microbial threats Transmission mechanisms

Chain modelThe 7 Habits of Uninfected People

The 7 Habits of
Uninfected People D) Portal F) Portal
of Exit of Entry
E) Mode of
1 Safe consumption Transmission

2 Personal hygiene
A) Microbial Agent in
G) Susceptible
3 Covering your cough B) Reservoir or
Host
C) Source

4 Getting vaccinated
5 Using protection
Reservoir / Source
1 Air
6 Reducing special risks 2 Water
3 Food
4 People
7 Basic infection control 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

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 16 / 33
 Controlling microbial threats Transmission mechanisms

Good infection control starts with common sense:

Cover the source!

Source: American Society of Microbiology

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 17 / 33
 Controlling microbial threats Transmission mechanisms

Disease scare at San Jose airport: 5 on flight from Asia

examinednone 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
Kongthree Southeast Asian hot spots for SARS.
There were four fire trucks and eight police cars and four or five
ambulances, she recalled. I couldnt believe it. I thought, Wow! Whats
going on here? Little did I know that we were to be the victims.

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 18 / 33
 Controlling microbial threats Transmission mechanisms

Disease scare at San Jose airport: 5 on flight from Asia

examinednone 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, were 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.

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 19 / 33
 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].
Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 20 / 33
 Controlling microbial threats Transmission mechanisms

Public-devised infection control, SARS outbreak, 2003

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 21 / 33
 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 Indias first case of the disease in a marine engineer from
the western coastal state of Goa on Friday, April 18, 2003.

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 22 / 33
 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

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 23 / 33
 Controlling microbial threats Transmission mechanisms

Natural history of infection and infectiousness (A vs. B)

A Time of Symptomatic,
infection Not infectious

Susceptible Latent period Infectious period Non-infectious

Incubation period Symptomatic period Non-diseased

B Time of No symptoms,
infection Infectious

Susceptible Latent period Infectious period Non-infectious

Incubation period Symptomatic period Non-diseased

When the latent period is shorter than the incubation period (B), an infected person becomes
infectious before symptom onset.
Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 24 / 33
 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
Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 25 / 33
 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
Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 26 / 33
 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
Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 27 / 33
 Controlling microbial threats Transmission dynamics

In Contagion, Dr. Erin Mears (Kate Winslet) explains R0

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
Contagion is a 2011 public health thriller control measures. Source (figure): PMID:
directed by Steven Soderbergh. 19620267
Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 28 / 33
 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)
Tomas J. Aragon, MD, DrPH (SFDPH)
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
Preparing for Microbial Threats to Health July 24, 2014 29 / 33
 Controlling microbial threats Transmission dynamics

Reproductive number vs. Infection rate in susceptibles

Control strategies are derived from control points

Parameter control points D) Portal F) Portal

of Exit of Entry
d = duration of infectiousness E) Mode of
Transmission
c = contact rate
p = transmission probability Transmission
A) Microbial Agent in probability (p)
x = fraction of population G) Susceptible
B) Reservoir or
Host
that is susceptible C) Source

P = fraction of population
that is infectious Contact
rate (c)
Fraction of population Fraction of population
Design control strategies that is infectious (P) that is susceptible (x)

All communicable disease Duration of

control strategies are designed infectiousness (d)

to affect the five control

points.

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 30 / 33
 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.)

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 31 / 33
 Integrated model for controlling microbial threats

SFDPH PHD Controlling Infectious Diseases (CID) Model

Transmission mechanisms, dynamics, and containment (Tomas J. Aragon, 2014)

D) Portal F) Portal
of Exit of Entry
The PHD CID Model
E) Mode of
The PHD CID model is an Transmission

integrated model for

preventing and controlling A) Microbial Agent in
G) Susceptible
B) Reservoir or
infectious diseases. Also Host
C) Source
consider the following: (1)
Is there asymptomatic
infectiousness? (latent
Reservoir / Source Modes of transmission The 7 Habits of Uninfected People
period is shorter than 1 Air 1 Contact - direct 1 Safe consumption
2 Water 2 Contact - indirect 2 Personal hygiene
incubation period), (2) 3 Food 3 Droplets 3 Covering your cough
4 People 4 Airborne 4 Getting vaccinated
What is the generation 5 Animals & vectors 5 Vehicle-borne 5 Using protection
time?, (3) What are the 6 Vehicles (e.g., injection) 6 Vector-borne 6 Reducing special risks
7 Soil & debris 7 Vertical (mom-child) 7 Basic infection control
ethical considerations?,
and (4) Do you have the Transmission Containment Strategies
1 Reduce contact rate 4 Reduce biological susceptibility
political and logistical 2 Reduce fraction of population that is infectious 5 Interrupt transmission (physical, chemical)
3 Reduce biological infectiousness 6 Reduce fraction of population that is susceptible
support to be successful?
Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 32 / 33
 Integrated model for controlling microbial threats

Thank you! Any questions?

Tomas J. Aragon, MD, DrPH (SFDPH) Preparing for Microbial Threats to Health July 24, 2014 33 / 33