Urinary tract infections (UTI) are common and affect half of women and 5% of men during their lifetime. Most infections are caused by uropathogenic Escherichia coli (UPEC) and are limited to the lower urinary tract (cystitis), but ascending infection (pyelonephritis) can lead to fibrosis and the development of chronic kidney disease. A complex network of tissue-resident immune cells exists throughout the urinary tract that are vital for initiating and propagating local immune responses, however our understanding of their nature and function remains incomplete. In this thesis, we aim to understand two broad areas of tissue immunology: (i) the role of group 3 innate lymphoid cells (ILC3s) in bacterial cystitis and (ii) macrophage-derived amphiregulin (AREG) in acute pyelonephritis and infection-mediated scarring.

Here, we identify type 17 immune response genes amongst the most up-regulated networks in the mouse bladder following UPEC challenge and identified ILC3s as a major source of these cytokines. Depletion of ILCs in Rag2-/- mice resulted in increased bladder bacterial load, identifying them as important players in bladder defence. Furthermore, we describe evidence of reciprocal cross talk between ILC3s and macrophages, with IL17 shaping bladder macrophage activation and polarisation. Together our findings reveal important insights into the orchestration and execution of type 17 immunity in bladder defence.

AREG, is an epidermal growth factor receptor (EGFR) ligand that is expressed by a variety of activated immune cells, including macrophages and is a vital mediator of immune responses in infection and tissue repair. Using microarray analysis, we found AREG expression was higher in the renal medulla and augmented following UPEC stimulation. In vivo, in vitro and in silico experiments found renal macrophages to be a major source of AREG and mice globally deficient in Areg demonstrated increased susceptibility to pyelonephritis with impaired monocyte recruitment. Provisional findings in our haematopoietic- and myeloid-specific Areg knockout mice, also confirmed greater susceptibility to pyelonephritis. Furthermore, we describe accelerated repair of epithelial cells in vitro following the addition of recombinant AREG and conditioned medium from UPEC stimulated macrophages. Our data reveal a novel mechanism by which kidney MNPs interact with renal tubular cells to promote host-defence, organ integrity and repair in UTI.

To study the role of AREG in infection-mediated kidney scarring we successfully developed a robust and reproducible in vivo murine model of chronic pyelonephritis. These experiments have found AREG expression to be highest in the medulla of kidneys with chronic pyelonephritis, and similarly enriched in medulla-derived macrophages. We found mice globally deficient in Areg were protected against kidney scarring and in 100% bone marrow chimeras, loss of AREG from the hematopoietic compartment offered greatest protection. Finally, using single-cell RNA sequencing we generate the first detailed atlas of the human kidney in chronic pyelonephritis and in conjunction with our murine data, offer insight into cellular mechanisms driving fibrosis, with the potential to inform strategies to reduce the development in CKD with patients with recurrent pyelonephritis.