Understanding the mechanism and cost of bacteriophage resistance in the Enterobacteriaceae

Bacteriophages are viruses able to kill bacteria, forcing bacteria to adapt to survive phage attack and helping drive microbial evolution. Little is known about specificity of the interactions or how phages shape bacterial ecological traits. The aim of this thesis is to investigate how Enterobacteriacae gain resistance to bacteriophage infection, and to evaluate how different bacteriophages predating on a bacterial species can alter adaptation mechanisms utilised by the bacteria. It is known that multiple bacteriophage families can infect the same bacterial species, but how different bacterial species respond to these different phages is poorly understood. The adaptations that occur in different species of bacteria within the Enterobacteriacae when exposed to the same bacteriophage species was compared.

A diverse panel of six bacteriophage species was used to create a collection of 123 phage resistant mutants in E. coli and 20 in Salmonella enterica Typhimurium. The costs of resistance in the bacteria were measured, with no fitness cost as well as decreased or increased fitness observed. Putative genes involved in bacteriophage resistance were identified by whole genome sequencing and identification of SNPs and INDELs, with 118 genes found to contain mutations. Using gene knock-out mutants, the contribution of individual genes to phage resistance was evaluated for 18 genes. Only three of these genes (btuB, sdaC, dcrB) could be confirmed to confer a phage resistance phenotype.

Furthermore, fhuA which was one of the most commonly mutated genes, did not confer phage resistance when gene knockouts were created. The results demonstrate the complexity in understanding phage resistance mechanisms.