Spatial dynamics of the evolution and spread of antibiotic-resistant Escherichia coli in the United States

Antibiotic resistance is when bacteria acquire the ability to defeat the antibiotics designed to kill them, and it has become a global public health challenge. One of the major drivers of resistance is the overuse of antibiotics. However, the large consumption of antibiotics among livestock and pets makes the issue more complicated. Escherichia coli (E. coli), a bacterium found in both human and animals, is of particular concern because of its common presence and increasing resistance. This dissertation aimed at providing a comprehensive understanding of the spread of antibiotic resistance in E. coli among different host and regions and its potential drivers. We compared the genes that cause different resistance found in E. coli samples from the US, and examined the evolutionary history of a subset of the samples. Our results showed that while the bacteria do not normally directly transmit between humans and livestock, they can both have transmissions with pets. We also found geographic differences of resistance that may be explained by local antibiotic use patterns and animal raising industries. Furthermore, we employed clinical resistance testing data of E. coli found in Midwest veterans and found important risk factors for resistance, including being male, having diabetes and previous usage of antibiotics. Other risk factors such as age and local median household income had different associations for different classes of antibiotics, potentially because they are prescribed in different clinical situations. These findings showed that to mitigate antibiotic resistance, we must consider both human and animal populations and geographic diversity.