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Modelling an outbreak of an emerging pathogen

Nature Reviews Microbiology volume 5, pages 700–709 (2007)Cite this article

Key Points

  • We show how mathematical models of infectious diseases can be used to understand the dynamics of outbreaks and epidemics, design effective interventions and make informed health policy decisions. To illustrate the usefulness of mathematical models to the microbiology and medical communities, the construction and application of a simple transmission model of an emerging pathogen — community-acquired meticillin-resistant Staphylococcus aureus (CA-MRSA) — is explained.

  • We show how to construct a model of a large (>8,000 reported cases) on-going outbreak of CA-MRSA in the Los Angeles County Jail (LACJ). We explain how to parameterize the model and reconstruct the outbreak. We then demonstrate how to use the model to assess the severity of the outbreak, predict the epidemiological consequences of a catastrophic outbreak and design effective interventions for outbreak control.

  • By using the model it was determined that the within-jail transmission was not high enough to sustain the outbreak, and that it was only sustained because of the continuous inflow of colonized and infected individuals from the community.

  • The modelling also revealed that the LACJ outbreak, although large, is not catastrophic, but would have become catastrophic if inmates had been incarcerated for more than a couple of months. In a worst-case scenario, the prevalence of infection within the jail would have increased to approximately 40%, and several thousand colonized and infected inmates would have been released into the community each month.

  • These analyses revealed that the outbreak could have been controlled if a large-scale highly effective screening programme of entering inmates had been set up to identify both colonized individuals and infected individuals.

  • The development of more complex transmission models, using the simple model as a platform, is discussed. This would allow investigators to gain additional quantitative insights into outbreak dynamics.

Abstract

To illustrate the usefulness of mathematical models to the microbiology and medical communities, we explain how to construct and apply a simple transmission model of an emerging pathogen. We chose to model, as a case study, a large (>8,000 reported cases) on-going outbreak of community-acquired meticillin-resistant Staphylococcus aureus (CA-MRSA) in the Los Angeles County Jail. A major risk factor for CA-MRSA infection is incarceration. Here, we show how to design a within-jail transmission model of CA-MRSA, parameterize the model and reconstruct the outbreak. The model is then used to assess the severity of the outbreak, predict the epidemiological consequences of a catastrophic outbreak and design effective interventions for outbreak control.

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Figure 1
Figure 2: Graphical depiction, and equations for, the within-jail community-acquired meticillin-resistant Staphylococcus aureus transmission model.
Figure 3: Model Parameters.
Figure 4: Results from the stochastic within-jail transmission model.
Figure 5: R0 analysis.
Figure 6: Results from the deterministic and stochastic versions of the within-jail transmission model.

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Acknowledgements

The authors acknowledge J. Boscardin, R. Breban, N. Freimer, V. Supervie, R. Vardavas, D. Wilson and all the staff at the Los Angeles County Jail and the Los Angeles County Department of Public Health. T. Pylko is also acknowledged for helpful clinical discussions during the course of this research. Financial support was received from the National Institute of Allergy and Infectious Diseases in the National Institutes of Health (R01 AI04 935).

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Authors and Affiliations

  1. Semel Institute of Neuroscience & Human Behavior & Department of Psychiatry, UCLA AIDS Institute, David Geffen School of Medicine at UCLA, 1100 Glendon Avenue PH2, Los Angeles, 90024, California, USA

    Emily Kajita, Justin T. Okano, Erin N. Bodine & Sally Blower

  2. Department of Epidemiology, School of Public Health, UCLA, Los Angeles, 90024, California, USA

    Emily Kajita & Scott P. Layne

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Correspondence to Sally Blower.

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Glossary

Catastrophic outbreak

An extremely large outbreak in a confined population that may be caused by the synergistic interaction of two processes: a high level of transmission and a large inflow of infectious individuals into the transmission site.

Prevalence

The number of infected individuals at a specific time.

Nurse cohorting

Reducing the contact of nurses with a large group of patients by assigning specific groups of nurses to the care of only a subset of patients. This intervention reduces the interaction of nurses with patients and is therefore expected to reduce nurse–patient transmission.

Title 15

Title 15 deals with “Miscellaneous Crimes” and is part of the California Penal Code.

Incidence

The number of newly infected individuals per unit of time.

Uncertainty analysis

An analysis in which the variation in the value of an outcome variable is determined. The variability that is observed in the outcome variable is due to the uncertainty in estimating the exact value of each parameter in the model.

Simulation

An analysis of a model that is carried out with a computer. The model is programmed using a computer language and then run using specific parameter values. Each run of the model is called a simulation, or a scenario.

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Kajita, E., Okano, J., Bodine, E. et al. Modelling an outbreak of an emerging pathogen. Nat Rev Microbiol 5, 700–709 (2007). https://doi.org/10.1038/nrmicro1660

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