Searching for cures for antibiotic resistance on the road to scientific and personal discovery

The hybrid course began in late December, before the holidays - the students met online, learned about the global health crisis of antibiotic resistance, explored various scientific techniques available to them, and developed their research question and hypothesis.

While previous classes had analyzed soil, this cohort focused on water. Their professor and two teaching assistants prepared 16 test samples, which consisted of water collected from rural and urban ponds, rivers and puddles in Rhode Island, Massachusetts and Connecticut.

Most antibiotics used in medicine today are molecules produced by soil bacteria and fungi, used as a defense mechanism to promote their own survival, Achilli explained. The students were participating in a global antibiotic discovery effort organized by the Tiny Earth Network based at the University of Wisconsin and involving student researchers at over 540 institutions.

Over three weeks, the students would culture and grow bacteria from the samples, isolate the different strains, extract DNA from the bacteria and send it to an external lab to be analyzed. Next, students would design an experiment to see if their newly discovered bacteria had antibiotic activity against "safe-relatives" of pathogens that are resistant to common antibiotics. The strains that that did would be analyzed using biochemical techniques to extract the molecules with antibiotic activity.

The students worked in the lab every weekday, learning to properly perform the techniques of polymerase chain reaction (PCR), gel electrophoresis and DNA sequencing.

"I tell the students that they really get to do everything, including microbiology, molecular biology, bioinformatics - when the samples come back from the external lab - and even organic chemistry, which they're doing as they extract metabolites from the samples," Achilli said.

Scientific and personal discovery

The bacteria on the lab plates looked like art projects: smears of different colors on clear disks. Hattie Grant, a senior concentrating in neurobiology, had missed class due to illness when it was time to choose a plate, so she ended up with one that had only white streaks - surely a disappointing sign of a lack of diversity in the sample, everyone assumed - but it ended up that the sample had a highly promising and active bacterial isolate.

Grant enrolled in the class both to fulfill a research requirement and because she had taken a class with Achilli before and looked forward to learning with her in a course that promised an abundance of hands-on activity. Grant said she appreciated learning about scientific techniques, like working with bacteria and performing PCR and gel electrophoresis.

"Now I feel like I can perform these techniques on my own, with success," Grant said. "It's a really nice feeling."

She also valued being part of a community of scientists: being able to connect with fellow students, work independently yet also as part of a small group, and having the direct support of the professor, teaching assistants and staff laboratory technicians. The technicians had come to the Biomedical Center over the holidays to set up equipment and prepare the work stations, and they regularly attended the lab sessions. The course would not be possible without their knowledge, dedication and skills, Achilli said.