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Investigating plasmids in the bacterial pathogen Klebsiella pneumoniae

Description 
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 K. pneumoniae plays a critical role in the dissemination of virulence and antimicrobial resistance (AMR) genes that can subsequently imbue strains with the ability to cause invasive and untreatable infections. Outside of the clinical setting, bacterial samples from animal and environmental sources are also enriched with plasmids, and alongside the occasional detection of AMR genes, also encode for other lifestyle-enhancing traits such as heavy metal resistance or virulence. Differences in plasmid distributions across the bacterial population and within different sampling niches highlight complexities in both the transmission dynamics of different plasmids and the varying ability of bacterial strains to uptake and maintain plasmids. For example, the AMR plasmids are detected at higher frequencies in the bacterial populations that circulate and cause outbreaks in hospitals. While comparative genomics and experimental evolution experiments have so far provided some insights into both bacterial and plasmid mechanisms responsible for this variation in transmission, many questions remain unanswered. This project will use techniques within the comparative genomics space to examine how plasmid loads and types vary across Klebsiella strains from different sampling origins (i.e. clinical vs non-clinical) and genetically distinct lineages. These insights will be important for identifying ‘high risk’ species, lineages or plasmids that have higher plasmid transmission/maintenance rates, and therefore may be important targets in genomic surveillance or transmission intervention strategies. This project will largely utilise techniques in the genomics space including but not limited to de novo genome assembly and annotation, DNA sequence alignments, building phylogenetic trees and BLAST. The work is therefore suitable for students with an interest in computational biology and its application in studying bacterial pathogens.
Essential criteria: 
Minimum entry requirements can be found here: https://www.monash.edu/admissions/entry-requirements/minimum
Keywords 
plasmids, antimicrobial resistance, AMR, nosocomial pathogens, bacterial genomics, bacterial pathogen, Klebsiella pneumoniae, comparative genomics, plasmid transmission
Available options 
PhD/Doctorate
Masters by research
Honours
BMedSc(Hons)
Time commitment 
Full-time
Top-up scholarship funding available 
No
Physical location 
Burnet Institute with Monash University in Melbourne, Australia.
Co-supervisors 
Dr 
Jane Hawkey

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