Antibiotic Resistance and Directed Evolution

research project for the Summer Science Program in Genomics

Antibiotic resistance in bacteria is a serious public health problem. At the Summer Science Program in Genomics, teams will stimulate the evolution of antibiotic resistance in a safe, controlled culture, then sequence its genome and analyze the acquired mutations. They will gain hands-on experience with the molecular biology, genomics, and bioinformatics needed to address this and other complex, real-world life science problems.

Each team of three participants use a custom chemostat to maintain constant growth of a non-disease-causing ocean microbe called Vibrio natriegens under moderate antibiotic selection pressure. The chemostat includes components for mixing and aeration of the growth media, optical monitoring of growth rate, and feedback control of antibiotic delivery to the culture. Teams will then map the genetic mutations that arise as a result of incomplete growth suppression.

photo credit: C. Rusnac,
photo credit: C. Rusnac,

Following the SSP philosophy of “no black boxes,” faculty will teach the underlying science and engineering that teams will use in their research:

  • Genetics: genetic evolution, DNA manipulation, PCR and sequence analysis
  • Microbiology: bacterial life cycle and growth dynamics
  • Mathematics: rate equations, linear and non-linear curve fitting, biostatistics
  • Instrumentation: optical measurement, integral feedback control
  • Bioinformatics: read trimming, genome assembly (de novo and from reference genomes), Gene annotation, SNP calling

Genomics Project FAQ

A: The health and safety of participants is our highest priority at SSP. This research is carefully designed and conducted to be safe. These are marine bacteria, harmless to humans. They will evolve resistance to one specific antibiotic. They can still be killed by exposure to different antibiotics, or to heat. They never leave the lab, and at the end of the project, they are thoroughly and completely destroyed.

A: Vibrio natriegens is a common marine (ocean) bacterium. It grows easily in a lab culture, and is not capable of causing disease in humans or animals.

A: When any living thing reproduces, its DNA is copied, a process subject to random copying errors. Those are called “mutations.” In this research, these specific bacteria will be exposed to a specific antibiotic, creating evolutionary pressure favoring survival of bacteria with mutations for resisting the effects of that antibiotic. Studying those mutations enables us to better understand antibiotic resistance in general, which is a major public health problem worldwide.

A: Purdue University imposes strict safety protocols on its teaching laboratories. These protocols have been approved by Purdue’s Institutional Biosafety Committee in accordance with guidelines from the National Institute of Health and the Centers for Disease Control. Participants wear appropriate gear, are trained in laboratory safety, and are supervised by faculty in the lab at all times. At the end of the experiment, the bacteria cultures, chemostat, and other equipment will be thoroughly and completely sterilized and/or properly disposed of.