The pathogen Xanthomonas citripv. Malvacearum (Xcm) is widely known as the causal agent of Cotton Bacterial Blight (CBB), which causes millions of dollars of crop loss in the United States annually. Understanding the molecular mechanism underlying this disease is vital for engineering resistant cotton varieties and preventing crop failures worldwide. In 2011, novel virulent strains of Xcm appeared in the southwestern United States which lacked previously identified key virulence factors but could infect varieties of cotton which were resistant to historical strains of Xcm, suggesting that the pathogen had evolved a new mechanism for effecting virulence. This thesis describes an efficient method of quantifying this bacteria’s proliferation in planta in a laboratory setting and utilizes this method to test this pathogen for a primary mode of virulence through systematic gene knockouts. The data from this study suggests that light emission can be used to efficiently track bacterial populations in planta, and that novel strains of Xcm may be using a new type III effector named Tal7b as a primary virulence factor. Development of a method to track bacterial infections enables a more precise understanding of how bacteria proliferate during the infection process, which can be used to understand with more depth how this pathogen causes disease. Additionally, laboratory studies of Tal7b may yield potential routes for future crop editing and resistance to these emergent strains.