Examining the role of Klebsiella pneumoniae in the dissemination of antibiotic resistance genes in the gut microbiome

For nearly a century, antibiotics have been the primary treatment for bacterial infections. However, with the global rise of antibiotic resistant bacteria, these treatments are becoming ineffective and some bacteria are now resistant to many types of antibiotics. Every year, around 700,000 people die from antibiotic resistant bacterial infections making it vital to better understand how these bacteria become resistant. Bacteria are able to transfer genetic material to other neighbouring bacteria via small circular strands of DNA called plasmids. These plasmids often contain antibiotic resistant genes(ARGs) and, upon transfer, confer resistance to the recipient bacteria. This occurs frequently in the human digestive tract due to its diverse bacterial population, containing trillions of bacteria, and is a key factor in spreading antibiotic resistance. Klebsiella pneumoniae, a bacterial species commonly found in the gut, is known to contain numerous plasmids and likely aids in the dissemination of ARGs. However, the exact role that K. pneumoniae plays in distributing ARGs to other bacteria in the gut has not been well studied. I propose to use computational methods and publicly available DNA samples from the gut to study ARG transfer between K. pneumoniae and other bacteria. I will evaluate the best computational tools for identifying plasmids, examine which bacteria contain what ARGs, and lastly, track ARG transfer between K. pneumoniae and other bacteria. Understanding the movement of ARGs can influence public health strategies to reduce the transmission of ARGs as well as inform future bacterial outbreak investigations.