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Title: The genomic basis of preservative resistance
Author: Cunningham-Oakes, Edward
ISNI:       0000 0005 0285 3856
Awarding Body: Cardiff University
Current Institution: Cardiff University
Date of Award: 2020
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Antimicrobial resistance (AMR) is of increasing global concern, especially in the face of a stagnant antibiotic pipeline. As such, accurate global microbiological surveillance is more important than ever. This global crisis has been extensively highlighted in the nosocomial setting, where ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) are responsible for persistent infections, which bolster patient morbidity and mortality. In these settings, vigilant tracking and identification has been invaluable in limiting further outbreaks and infection. However, intrinsically resistant microorganisms are also problematic in manufacturing settings, where they can overcome antimicrobial preservatives present in food and cosmetics and enrich due to the presence of proteins and formulation additives. Therefore, the accurate identification of these organisms and understanding the mechanisms underpinning preservative tolerant phenotypes is essential for both the billion-dollar revenue of the HPCP industry, and consumer health. In this study, we first highlight that 49% of organisms responsible for non-food product recalls recorded in public recall databases remain unidentified, whilst the predominant identified organisms for recall are the Gram-negative bacteria, P. aeruginosa, Pseudomonas spp. and Enterobacteriaeceae. We then taxonomically characterise bacteria and fungi in the factory environment and demonstrate that the predominant identified microorganisms do not mirror those responsible for non-food product recalls. Utilising genomics and whole genome sequencing, we then illustrate that the use of historical taxonomic classification techniques such as multi locus sequence typing is insufficient for the accurate species-level identification of intrinsically preservative-tolerant Burkholderia cepacia complex spp. Finally, we use genomics to unveil the unique genome organisation of the problematic organisms P. aeruginosa and Pluralibacter gergoviae, revealing the presence of unique large extrachromosomal elements known as megaplasmids in bacteria from the industrial environment, before characterising these megaplasmids in the context of related megaplasmids from a variety of other stressful environments.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: Q Science (General)