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MRSA in the NICU

Outbreak or Coincidence?


Maria P. Chadiarakou
National Center for Genome Resources
Anitha Sundararajan
National Center for Genome Resources
Ingrid E. Lindquist
Health Sciences Center
University of New Mexico
Gabriella A. DeFrancesca

Desert Academy
Madeline Kwicklis

The Masters Program
Drew A. Lighthall

Tierra Encantada
Michèle I. Shuster
Department of Biology
New Mexico State University
Joann Mudge
National Center for Genome Resources


DNA sequencing and analysis (bioinformatics) is an increasingly important tool for understanding biological data, including medical data. In this case study, students will be exposed to DNA sequencing to quickly identify how an outbreak of methicillin-resistant Staphylococcus aureus spreads through a neonatal intensive care unit (NICU). This PowerPoint-driven case is based on an actual outbreak described in the New England Journal of Medicine and students will use the actual DNA sequences from the outbreak that were used by scientists. A handout (Supplemental Materials) provides background and instructions that guide students in how to create and read a phylogenetic tree and use to it identify which organisms are part of the outbreak and which are independent MRSA infections. They will then use this data to assess the containment strategies used at the hospital during the outbreak. Students will learn how DNA sequencing can inform epidemiology to identify outbreak cases, track trajectories of the spreading disease, and quickly put containment measures into place. This case study is especially suited for high school and introductory undergraduate biology classes.


  • Generate two phylogenetic trees, one based on antibiotic resistance (phenotype), and the other based on DNA sequences from patient infections.
  • Interpret the two phylogenetic trees to analyze an outbreak in a hospital environment.
  • Analyze the strengths and weaknesses of phenotype (antibiotic resistance profile) vs. genotype-based (DNA sequencing) phylogenetic trees for analyzing a hospital-based outbreak.
  • Develop a fuller understanding of evolution by natural selection, phylogenetic trees, bioinformatics tools, and medical applications of bioinformatics tools and information.


NICU; outbreak; MRSA; antibiotic resistance; phylogeny; DNA sequencing; bioinformatics

Topical Areas


Educational Level

High school, Undergraduate lower division, Undergraduate upper division, Clinical education, General public & informal education


PDF, PowerPoint

Type / Methods

Analysis (Issues), Directed, Discussion, Journal Article



Subject Headings

Biology (General)  |   Epidemiology  |   Genetics / Heredity  |   Medicine (General)  |   Evolutionary Biology  |   Public Health  |   Science (General)  |  

Date Posted


Teaching Notes

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Teaching notes are intended to help teachers select and adopt a case. They typically include a summary of the case, teaching objectives, information about the intended audience, details about how the case may be taught, and a list of references and resources.

Supplemental Materials

The following handout and datasets are used in this case study.

  Case Study Handout
  Genetic (sequencing) data in phylip interleaved format
  Phenotypic (antibiotic resistance) data in binary format (sensitive or resistant)

Answer Key

Answer keys for the cases in our collection are password-protected and access to them is limited to paid subscribed instructors. To become a paid subscriber, begin the process by registering.