Date of Award

2024

Document Type

Doctoral Thesis

Degree Name

Doctor of Philosophy

Department

Biological Sciences

First Advisor

Dr. Eamonn Culligan

Second Advisor

Prof. Roy Sleator

Third Advisor

Dr. Craig Murphy

Abstract

Uropathogenic Escherichia coli (UPEC) is the most common aetiological agent of community and hospital-acquired urinary tract infections (UTIs). UTIs caused by E. coli result in considerable morbidity, mortality, and economic loss worldwide due to increasing resistance to antibiotics. Substantial efforts are being made to develop novel alternatives to conventional antibiotic therapies. One approach is the principle of bacterial interference; using low-virulence, or commensal, bacteria to prevent colonisation of pathogens by competing for nutrients, or producing antimicrobial compounds such as bacteriocins. E. coli isolates inducing asymptomatic bacteriuria (ABU) have been proposed as a therapeutic alternative for UPEC infection. ABU is a carrier state that occurs when bacteria inhabit the urinary microbiome (urobiome) for long periods of time without inducing symptoms of infection. The model ABU strain, E. coli 83972, is known for its ability to outcompete uropathogens and is approved as a prophylactic for recurrent UTIs (rUTIs), however, its mechanism(s) of action remain to be determined.

The aim of this thesis was to identify and characterise bacteriocin-producing ABU E. coli isolates from the urogenital tract. Conventional bacteriocin agar-based screening and in silico screening approaches were used to detect antimicrobial production among eight uncharacterised ABU isolates. This research was further expanded using turbidimetric bioassays with lysogeny broth (LB) and artificial urine to identify additional bacteriocin-producers that were not detected using agar-based methods with the same bank on E. coli strains. Overall, three ABU bacteriocin-producers (PUTS 37, PUTS 58, and SK-106-1) were identified with significant (p > 0.05) antimicrobial activity against UPEC. Moreover, the antimicrobial activity increased when the ABU isolates were analysed against UPEC in an artificial urine medium, a screening analysis which has not previously been conducted to date. Thus, this thesis present novel ABU isolates encoding putative bacteriocins with therapeutic potential against UPEC. Additionally, phenotypic,

genomic and pangenomic characterisation of the ABU isolates was performed and compared to two reference E. coli isolates: the ABU strain E. coli 83972 and the UPEC strain E. coli CFT073. The ABU isolates PUTS 58 and SK-106-1 were described as lowvirulence bacteria containing few virulence and resistance genes. In particular PUTS 58 resembled commensal E. coli as it was part of phylogroup A and encoded no toxins. Finally, in silico screening approaches were used to compare the prevalence and diversity of bacteriocins encoded by E. coli ABU and UPEC strains. Virulence factors among ABU and UPEC strains were also identified and compared, and their association with bacteriocin production was assessed. ABU strains were more diverse with the range of putative bacteriocins they were encoding and were lacking in virulence factors compared to UPEC. A correlation between multi-bacteriocin producers and an increase in toxic virulence factors was detected. Overall, this approach is critical for the identification of ABU strains with low virulence as potential prophylactics or therapeutics for UTIs. In turn, this will aid in enhancing the use of low-virulence ABU isolates as potential biotherapeutics for UTIs.

Access Level

info:eu-repo/semantics/openAccess

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