The effect of antibiotic resistance genes (ARGs) on the dynamics of diverse bacterial populations : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Biological Sciences at Massey University, Albany, New Zealand

Abstract

Antibiotic resistance genes (ARGs) represent a significant threat to global public health by compromising the effectiveness of antibiotics. Understanding how ARGs affect the dynamics of bacterial communities is essential for predicting how resistance may persist and spread, especially in environments without antibiotic selection pressure. This study examines how ARGs influence bacterial fitness across various genetic backgrounds and community structures, providing insights into the complex interactions driving antibiotic resistance. In this study, six distinct bacterial strains—Escherichia coli REL606 and five natural isolates— were first genetically tagged with unique chromosomal barcodes, enabling precise identification and tracking using high-throughput nanopore sequencing. Then, the barcoded sub-derivative strains were paired with plasmids carrying one of six ARGs (aadA, blaTEM-116*, blaCTX-M-15, blaSHV-12, cat, dfrA5) or a control vector. This approach allowed for a detailed analysis of the fitness effects associated with different ARGs across multiple strains and competitive contexts. Experimental results demonstrated clear fitness costs linked to the carriage of ARGs, although these costs varied significantly depending on the bacterial strain and the specific ARG involved. From the six ARGs tested, four (aadA, blaCTX-M-15, cat, dfrA5) consistently imposed significant fitness burdens on their bacterial hosts. It is worth mentioning that the interactions between ARGs and host genetic backgrounds played an important role, underscoring the strain-specific nature of resistance. Furthermore, the composition of bacterial communities had a strong influence on the fitness effects of ARGs. Experiments ranging from simple pairwise competitions to more complex multi-strain interactions highlighted the significant role of community context in determining the persistence of ARGs and competitive bacterial success. Overall, this research provides valuable new insights into the intricate relationships between ARGs, bacterial genetic diversity, and community composition context, offering valuable insights for developing targeted strategies to manage and mitigate antibiotic resistance.