Identification of Pathogenic Islands using Comparative Genomics Based Tools

In the United States alone, more than 2,000,000 people develop antibiotic resistant infections resulting in 23,000 deaths annually. It has been estimated that failure to address this problem will result in more than 10 million deaths annually worldwide by the year 2050 surpassing Ischemic heart disease as the number one leading cause of death. The associated costs will exceed 100 trillion dollars Given this dire prediction, understanding how bacteria acquire antibiotic resistance could help scientists develop new classes of antibiotics, breaking a 27-year dry spell and minimizing the overwhelming number of predicted deaths.
This curriculum unit was created with the purpose of introducing high school students to comparative genomics and the computer based tools that scientists use to identify genomic islands.  Specifically, this unit is meant to guide students to discover virulent genes and proteins found in pathogenicity islands within the genomes of disease causing bacteria.  Explore concepts such as benefits and disadvantages of diversifying the genome; relating
genome diversity to bacterial survival and fitness; modes of gene transfer; the driving forces behind genome diversity; familiarity with common pathogenic factors and the significance of these genes to pathogenesis.  Gain a better understanding of the global impact of disease outbreaks as well as a realistic comprehension of the caveats in pharmaceutical advancements and the significance of the comparative genomics in accelerating identification of targets and drug development.  Facilitate discussion about natural products, cancer research, and pharmaceutical synthesis, and

For any questions, please contact the authors: Jo Marie Bacusmo ( and Kathy Savage (

Download the Full Curriculum

In the introduction you will find tips on using the curriculum, summaries of each lesson, a lesson sequencing guide, pertinent vocabulary, a standards alignment chart (Next Generation Sunshine State Standards), and general background information for the unit.

Introduction: Identification of Pathogenic Islands using Comparative Genomics Based Tools

Lesson 1: Introduction to Virulence Factors  

Students will take a pretest over the content presented in these six lessons. Students will then watch short videos of a pathogenic bacterium invading a host cell to identify the behaviors and biological mechanisms (virulence factors) exhibited by the bacterium that make it successful.

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Lesson 2: Pathogen Prototype


Student groups build a bacterial prototype expressing virulence factors and then compare their prototype to others. Students will assess the potential success of each prototype by voting for the most successful and least successful prototype and justifying their choices.

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Lesson 3: Bacteria Survivor

Students watch a video on horizontal gene transfer and answer three questions. The teacher can choose to discuss the answers to these questions after the worksheet has been collected.  Students team up and play a teacher directed game demonstrating genome diversification via gene transfer, highlighting its impact on bacterial fitness and survival.

Download Lesson 3          Download the Gene Cards



Lesson 4: Meet PATRIC


Students watch videos on the use of comparative genomics as a tool to help scientists focus their research, as well as how comparative genomics facilitates identification genomic islands contributing to pathogenesis of disease outbreak strains.  This lesson also provides a tutorial of PATRIC, a comparative genomics web-based tool.

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Lesson 5: Student Research (a) and Presentations (b)


Students work in groups using PATRIC to research virulent genes and disease outbreaks for an assigned bacteria species, and then present their research to the class and are graded according to a rubric (provided).

Download Lesson 5a          Download Lesson 5b





Developed in the laboratory of Dr. Valerie DeCrecy-Lagard in the Department of Microbiology and Cell Science at the University of Florida.

Funding for this project provided by the National Science Foundation, grant number MCB-1412379.