The “Pathogenic Islands” module consists of six lessons formatted into
50-minute sessions (Table 1). It was developed by a science teacher/
science researcher team to align with Florida’s Next Generation Sunshine State Standards for Science. It also embraces three-dimensional
learning as espoused by the National Research Council (2012), which
calls for students to be actively engaged in the practices of science
while exploring disciplinary core ideas and crosscutting concepts.
The major learning goals of the module are as follows:
1. List and describe virulence genes that cause the different
modes of pathogenicity.
2. Describe the various modes of gene transfer.
3. Demonstrate the concept of gene transfer applied in the process of selection and evolution.
4. Use genome comparison tools such as PATRIC and Island
Viewer to identify genomic islands.
5. Apply knowledge of virulence genes and horizontal gene transfer to identify the source of virulence in pathogenic strains.
6. Perform independent research on a set of pathogens and
present the location of pathogenic islands on the genome,
identify the virulence genes contained in the pathogenic
islands and their function, and provide a brief history on
the epidemiology of the disease caused by the pathogen.
Lesson 1: Introduction
Lesson 1 introduces the real-life issue of diseases caused by pathogenic microorganisms, such as typhoid fever and bubonic
plague, to stimulate student thinking. Students are presented with
the various modes by which a pathogen can cause a disease. The
main objective of this lesson is to equip students with the foundational knowledge and vocabulary to initiate learning and embark
on this six-day journey we have set them on. Lesson 1 begins with
a video of Salmonella invading the gut ( https://youtu.be/gpLUQ-
za4uWw), followed by a whole-class discussion of the video.
The instructor prompts students to suggest features of the pathogen that contribute to its successful invasion of the host. Specific
vocabulary is then introduced, and students are encouraged to
help classify the virulence factors as either offensive or defensive
After recording initial ideas and introducing new vocabulary,
the instructor replays the video, pausing at each virulence factor
presented and discussing it with the class. Once the class is familiar
with a few of these virulence factors, students perform independent
research on a list of virulence factors. Students are provided with a
website as a starting point and invited to use additional web or text
resources for answers. This information will be used in the next
Table 1. Lesson sequencing guide and summaries. All lessons are based on a 50-minute class period and
24 students per class.
Day 1 Lesson 1 Students take a pretest over the content presented in these six lessons. They 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.
Day 2 Lesson 2 Student groups build a bacterial prototype expressing virulence factors and then compare
their prototype to those created by the other groups. Students assess the potential success of
each prototype by voting for the most successful and least successful prototype and
justifying their choices.
Day 3 Lesson 3,
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 (“Pathogen Survivor”) demonstrating
genome diversification via gene transfer, highlighting its impact on bacterial fitness and
Day 4 Lesson 4,
The video “The Power of Comparative Genomics” (7:07; https://www.youtube.com/watch?
v=mU9ROpm6d70) introduces comparative genomics as a tool to help scientists focus their
The video “Comparison of Genomes of Eight Enteroaggregative E.coli O104:H4 Isolates” (2:07;
https://youtu.be/6VTxmnZQXgU) shows how comparative genomics facilitates identification
of genomic islands that contribute to the pathogenicity of disease outbreak strains.
Students complete video tutorials on the Pathosystems Resource Integration Center (PATRIC),
a web-based comparative genomics tool.
Day 5 Lesson 5,
Students work in groups, using PATRIC to research virulent genes and disease outbreaks for
an assigned bacterial species.
Day 6 Lesson 5,
Students present their research to the class and are graded according to a rubric (Figure 4).