CA-MRSA intro final version (presentation)

Report
MRSA in the Community: A Serious New Drug
Resistant Bacteria
Supercomputing Challenge Kickoff
New Mexico Tech
October 12, 2013
Beginning NetLogo 1 strand
Irene Lee, Santa Fe Institute
Maureen Psaila-Dombrowski, NM-CSforAll
with Diane Lauderdale, University of Chicago
1
Today’s Workshop
1. Slide show introduction to MRSA
2. Hands-on activity (Toss Up) to learn about how infectious
diseases spread
3. View and deconstruct a NetLogo model for disease spread
4. Run experiments on NetLogo version of Toss Up
--- SUNDAY --5. Construct a simple contagion model in NetLogo
6. Run experiments, collect data, look for patterns.
Your role:
Listen, learn about and modify code, run experiments, and
give us feedback.
2
What is MRSA?
(Methicillin-resistant Staphylococcus aureus)
3
The History of MRSA
1880 Staphylococcus aureus first identified in
Scotland
1959 Methicillin licensed in England to treat S.
aureus infections
1961 S. aureus infections acquire resistance to
Methicillin.
1961-1990s MRSA infections in hospitals increased
Before 1990s, almost all MRSA cases were among
sick patients in the healthcare setting.
4
New Community-Associated MRSA
(CA-MRSA)
1990s Scattered reports of MRSA cases and
outbreaks among persons w/o healthcare risk factors
Outbreaks in sports teams, daycare centers, army bases and other groups
2000s MRSA becomes the most common type of skin
infection in the USA
CA-MRSA strains are genetically different from
the older healthcare strains, affect healthy
people and are more likely to cause skin
infections.
5
Typical Skin Infections
Often appear as pustules or boils that are red, swollen, painful,
and have pus. They may look like spider bites at first.
6
How does CA-MRSA spread?
• Individuals may be colonized with MRSA on their skin or in their nose.
• People have no idea whether or not they are colonized, and most
colonized people will not develop an infection. Colonization may last a few
days or months.
• Direct physical contact (such as hugging, holding hands, child care or
contact sports) with a colonized or infected person can spread MRSA.
• Uncovered skin infections are more likely than colonizations to spread to
another person.
• In some cases, a skin infection develops where there was an obvious cut
or bruise, but not always.
• We believe that colonization always precedes infection (although the
colonization phase before infection may be quick).
• MRSA can also linger on surfaces and spread from person to person if they
touch the same item, such as a towel.
7
How are CA-MRSA Infections Treated?
• MRSA-like skin infections should be seen by a health
professional
• The infection is usually drained, cleaned and covered
• Patients are told how to reduce risk of transmission to
others (keep it covered and don’t share personal items)
• May be treated with an appropriate antibiotic
depending on several factors
• Without medical care, would in almost all cases still
recover, but would take longer and be more likely to
infect others
8
Can you get a CA-MRSA infection more than once?
• Some diseases, like measles, give you lifelong
immunity so you only can get them once.
– Individuals develop resistance
• CA-MRSA does not give lifelong immunity and
repeat infections are possible.
– Individuals remain susceptible
9
MRSA Transmission
SUSCEPTIBLE
(HEALTHY)
COLONIZED
INFECTED
10
How do we study MRSA?
• Lab studies of the bacteria
– Determine strain and genetic features
– Determine nature of antibiotic resistance
• Studies of People
– Clinical Trials are experiments that assign people
to prevention measures or treatments
– Epidemiologic Studies collect data to learn about
the distribution and risk factors for disease
11
Types of Epidemiologic Studies
• Compare individuals who become colonized or
infected to those who do not
– To determine risk factors for MRSA
• Track an outbreak
– Figure out what happened
• Characterize the “natural history” of colonization
or infection
– How long do individuals remain colonized/infected?
– What types of infections?
– Risk factors and frequency of repeat infections.
12
Computer Models to Study MRSA
• Carry out experiments that are not practical
• Can estimate population-wide impact of
changes in risk factors, behaviors or
treatments
13
Next, Toss Up paper based game
• We will look at a simple model of contagion.
• First, we will consider a model in which
infection leads to lifelong immunity.
• This is called an SIR model
– susceptible-infected-recovered
SUSCEPTIBLE
(HEALTHY)
INFECTED
RECOVERED
14
Let’s look at some code
• Show interface of NetLogo Toss Up SIR.
• Hand out code
• Take a few minutes to decipher the code
thinking back on the Toss Up Game and then
we will share out.
• Then we will run experiments with the
NetLogo SIR model.
15
SIR -> SIS
• Moving from SIR to SIS
• What do you remember about SIS? What’s an
example?
• What would need to change in code?
• How is that change implemented?
• Make a prediction – what is the dynamics of an
SIS disease transmission?
• Next, we will run experiments with the NetLogo
SIS model.
16
Wrap Up
• Diseases become resistant to antibiotics.
• Antibiotic resistant bacteria pose a global
threat.
• Direct analogy between Participatory
Simulations and Computer Simulations
• Modeling and Simulation can be used to study
dynamics of disease spread.
17
End of first hour.
18
Modeling and Computational Science
• A model is a representation of the interaction of
real-world objects in a complex system.
• The goal is to gain an understanding of how the
model’s results relate to real-world phenomena.
• Random factors built into the model and
variables changed by the user cause different
results to be generated when the model is run
repeatedly.
Agent-based modeling in NetLogo



The “Observer”– sets up and runs the world
The “Turtles”– the agents in the world
The “Patches” – the places in the world
Agent based modeling phases



Setup– setting up the world
Go / Runtime Loop– the agents put into motion.
Exit



Agent-based modeling
Abstractions
Agents with rules
Environment or space in which they exist
Time

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