An integrated approach to ciprofloxacin susceptibility analysis and high-throughput bacterial phenotyping in Salmonella

Abstract

Antimicrobial resistance is a growing threat across the world. Salmonella are Gram-negative, motile, rod-shaped bacteria that are transmitted through the faecal-oral route and invade the small intestine to cause self-limiting gastroenteritis or invasive, systemic disease. Invasive non-typhoidal Salmonella are a significant cause of bacterial infection globally, and the ST313 lineage of Salmonella Typhimurium are responsible for much of the burden of salmonellosis in sub-Saharan Africa. In recent years, there has been a drastic rise in multidrug resistance within this lineage, including fluoroquinolone resistance, a first line antimicrobial against invasive Salmonella species. In this thesis, I have explored the response of Salmonella Typhimurium (S. Typhimurium) to ciprofloxacin, a fluoroquinolone, using a combination of methodologies. In particular, this work was targeted at better understanding ciprofloxacin susceptibility in invasive non-typhoidal S. Typhimurium in sub-Saharan Africa. I began by assessing growth of S. Typhimurium in the presence of ciprofloxacin, finding that S. Typhimurium is capable of growth in concentrations of ciprofloxacin above the minimum inhibitory concentration (MIC). I have developed high-content imaging methodologies to screen Salmonella grown in the presence of ciprofloxacin. These morphological data suggest that there may be heterogeneous subpopulations with differential responses to ciprofloxacin, which was supported by studying the bacterial transcriptional response, and this may influence survival during ciprofloxacin treatment and interactions with host cells. Additionally, ciprofloxacin exposure triggers a bacterial stress response that appears to be distinct from responses generated by other stressors. Finally, I have investigated the genomic and phenotypic differences of a larger set of related S. Typhimurium ST313 isolates with an array of susceptibilities to ciprofloxacin. High-content screening has shown that isolates appear to differ in their morphological signature depending on their genetic makeup. Together these data suggest that the study of the bacterial response to ciprofloxacin and integration of genotyping and phenotyping could significantly enhance our understanding of antimicrobial resistance and help guide appropriate antimicrobial usage.