Exploring antimicrobial resistance plasmid diversity at a single hospital network in a 7-year period

Plasmid transmission between bacteria of the same or different species is an important driver of genetic diversity, bacterial adaptation and evolution. In the clinical setting, the transmission of plasmids between hospital pathogens such as Klebsiella pneumoniae plays a critical role in the dissemination of antimicrobial resistance (AMR) genes that can subsequently imbue strains with the ability to cause untreatable infections. Rates of AMR appear to be particularly high within some strains that are known to circulate or cause outbreaks in clinical settings, and of notable concern are strains with resistance to last line antimicrobials such as third generation cephalosporins or carbapenems. The use of DNA sequencing and comparative genomics have provided some important insights into the genetic diversity of strains and plasmids isolated from patients and clinical settings. This project will use techniques within the comparative genomics space to examine how AMR plasmid loads and types vary across Klebsiella strains collected from infections at a single hospital network across a 7 year period. How much diversity is there within the plasmid population? Are there any important strain-AMR plasmid trends across time? These insights will be important for identifying ‘high risk’ lineages or plasmids that have higher plasmid transmission/maintenance rates, and therefore may be important targets in genomic surveillance or transmission intervention strategies. Examples of techniques or approaches that will be used in this project include but are not limited to de novo genome assembly and annotation, DNA sequence alignments and building phylogenetic trees. The work is therefore suitable for students with an interest in computational biology and its application in studying bacterial pathogens and plasmids.