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ItemPhylogeny and virulence factor genes of canine urinary Escherichia coli in relation to clinical disease and antimicrobial resistanceTeh, Helsa Binti Hisyam ( 2018)Traditionally, urinary tract infections (UTIs) have been categorised as either uncomplicated or complicated in veterinary medicine, with treatment differing for the two categories. In human medicine, there is an additional category: asymptomatic bacteriuria, which is the presence of bacteriuria without symptoms of infection. Escherichia coli is the most common bacterial species involved in UTIs in dogs. Clinical signs can be absent in dogs with complicated UTIs, and this has been likened to asymptomatic bacteriuria in people and has been termed subclinical bacteriuria (SBU). Treatment recommendations for SBU in dogs have been adapted from human recommendations. Many E. coli strains are resistant to multiple antibiotics and uropathogenic E. coli possess virulence factor genes that facilitate overcoming host defence mechanisms. These E. coli commonly belong to phylogenetic groups B2 and D. Some studies suggest that human E. coli isolated from asymptomatic bacteriuria differ from those causing clinical UTI. While the virulence factor genes and phylogeny of canine urinary E. coli isolated from UTIs are well characterised, little is known about virulence factor genes and phylogeny in E. coli isolated from SBU. Furthermore, these genomic characteristics have not been studied in detail in multi-drug resistant (MDR) canine urinary E. coli. Thus, the pathogenic potential of canine urinary E. coli is not well described and the benefit of antibiotic therapy in SBU and MDR infections is unknown. This study used whole genome sequencing to characterise 47 E. coli isolated from dogs with SBU and 67 E.coli from dogs with clinical UTI in terms of their phylogeny and virulence factor gene profile. From those strains, the 15 MDR strains were characterised. When the phylogeny and virulence factor gene profile of E. coli isolated from dogs with SBU were compared with clinical UTIs, results showed that most clinical UTI and SBU E. coli belonged to phylogenetic group B2. The virulence factor gene profile was similar between the two groups, and no association was found between them and the 83 virulence factor genes analysed. Many of the MDR E. coli belonged to phylogenetic group B1 and these isolates possessed fewer virulence factor genes than non-MDR E. coli. Based on the results of this study, it was concluded that phylogeny and the presence of virulence factor genes do not influence the manifestation of clinical disease. Host immunity and rather than presence and the expression of or mutations of virulence factor genes may have a role in the development of clinical disease. ii MDR E. coli have fewer virulence factor genes than non-MDR isolates, with MDR isolates commonly belonging to commensal phylogenetic groups. This suggests that treatment of MDR isolates is not always indicated because they tend to have commensal bacterial phylogeny, which can have implications for reducing the development of antimicrobial resistance. While whole genome sequencing is an accurate method for determining phylogeny and the presence of virulence factors, it is unable to easily differentiate the pathogenicity potential of urinary E. coli and therefore treatment recommendations cannot be made based on this technique.