CA-MRSA intro final version (presentation)
CA-MRSA intro final version (presentation)
MRSA in the Community: A Serious New Drug
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. Slide show introduction to MRSA
2. Hands-on activity (Toss Up) to learn about how infectious
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.
Listen, learn about and modify code, run experiments, and
give us feedback.
What is MRSA?
(Methicillin-resistant Staphylococcus aureus)
The History of MRSA
1880 Staphylococcus aureus first identified in
1959 Methicillin licensed in England to treat S.
1961 S. aureus infections acquire resistance to
1961-1990s MRSA infections in hospitals increased
Before 1990s, almost all MRSA cases were among
sick patients in the healthcare setting.
New Community-Associated 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
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.
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
• 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.
How are CA-MRSA Infections Treated?
• MRSA-like skin infections should be seen by a health
• 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
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
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
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
– How long do individuals remain colonized/infected?
– What types of infections?
– Risk factors and frequency of repeat infections.
Computer Models to Study MRSA
• Carry out experiments that are not practical
• Can estimate population-wide impact of
changes in risk factors, behaviors or
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
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.
SIR -> SIS
• Moving from SIR to SIS
• What do you remember about SIS? What’s an
• 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
• Diseases become resistant to antibiotics.
• Antibiotic resistant bacteria pose a global
• Direct analogy between Participatory
Simulations and Computer Simulations
• Modeling and Simulation can be used to study
dynamics of disease spread.
End of first hour.
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
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.
Agents with rules
Environment or space in which they exist