Genomic and phenotypic characterisation of bacteriophages for the biocontrol of klebsiella spp.

Elek, Claire Karen Anita (2024) Genomic and phenotypic characterisation of bacteriophages for the biocontrol of klebsiella spp. Doctoral thesis, University of East Anglia.

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Abstract

Klebsiella spp. represent a major threat to human health due to their ability to cause a wide range of infections, particularly in healthcare settings, and the prevalence of antimicrobial resistance determinants amongst them. The use of bacteriophages (phages) as an alternative or adjuvant to antibiotics has recently seen a resurgence and this thesis aimed to investigate the use of phages against Klebsiella. This project identified 26 genetically distinct phages infecting a range of well-characterised Klebsiella spp., with phage isolates spanning five known genera and two new genera within four families in the class Caudoviricetes. Phage time-kill assays revealed two- and three-phage combinations were more efficacious at killing and suppressing bacterial regrowth, particularly when the phages were from distinct genetic lineages. Synergy was observed between phage and antibiotics but was highly dependent on the phage-antibiotic combination. The implementation and optimisation of phage amplification and purification protocols revealed challenges in generating high-quality, high-titre phage stocks. Phage therapy also requires complete, accurate, high-quality phage genomes, and previous work has found traditional phage assembly methods to be error-prone. The work here describes the development of a new workflow: HYPPA – a HYbrid and Poly-polish Phage Assembly to improve phage genomics. This methodology utilises long-read assemblies in combination with short-read sequencing for resolving phage genomes and correcting assembly errors, negating the need for extensive manual curation. Lastly, a transposon mutant library was generated in a Klebsiella michiganensis strain to investigate phage resistance and susceptibility genes in a functional genomics screen. This work provides new insights into understanding the phenotype-genotype link through functional assays and genomics, and the important role complete, accurate, high-quality phage genomes play for regulatory approval of phages as therapeutics in the UK.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Zoe White
Date Deposited:	09 Jul 2024 14:34
Last Modified:	09 Jul 2024 14:34
URI:	https://ueaeprints.uea.ac.uk/id/eprint/95845
DOI:

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