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