Molecular Analysis of Asymptomatic Bacteriuria Escherichia coli Strain VR50 Reveals Adaptation to the Urinary Tract by Gene Acquisition

Scott A. Beatson, Nouri L. Ben Zakour, Makrina Totsika, Brian M. Forde, Rebecca E. Watts, Amanda N. Mabbett, Jan M. Szubert, Sohinee Sarkar, Minh-Duy Phan, Kate M. Peters, Nicola K. Petty, Nabil-Fareed Alikhan, Mitchell J. Sullivan, Jayde A. Gawthorne, Mitchell Stanton-Cook, Nguyen Thi Khanh Nhu, Teik Min Chong, Wai-Fong Yin, Kok-Gan Chan, Viktoria Hancock, David W. Ussery, Glen C. Ulett, Mark A. Schembri

Urinary tract infections (UTIs) are among the most common infectious diseases of humans, with Escherichia coli responsible for >80% of all cases. One extreme of UTI is asymptomatic bacteriuria (ABU), which occurs as an asymptomatic carrier state that resembles commensalism. To understand the evolution and molecular mechanisms that underpin ABU, the genome of the ABU E. coli strain VR50 was sequenced. Analysis of the complete genome indicated it most resembles E. coli K-12, with the addition of a 94 kb genomic island (GI-VR50-pheV), eight prophages and multiple plasmids. GI-VR50-pheV has a mosaic structure and contains a number of UTI-associated virulence factors, namely genes encoding Afa (afimbrial adhesin), two autotransporter proteins (Ag43 and Sat) and aerobactin. We demonstrated that the presence of this island in VR50 confers its ability to colonise the murine bladder, as a VR50 mutant deleted for GI-VR50-pheV was attenuated in a mouse model of UTI in vivo. We established that Afa is the island-encoded factor responsible for this phenotype using two independent deletion mutants (Afa operon and AfaE adhesin). E. coli VR50afa and VR50afaE displayed significantly decreased ability to adhere to human bladder epithelial cells. In the mouse model of UTI, VR50afa and VR50afaE displayed reduced bladder colonization compared to wild-type VR50, similar to the colonization level of the GI-VR50-pheV mutant. Our study suggests that E. coli VR50 is a commensal-like strain that has acquired fitness factors which facilitate colonization of the human bladder.