There is a multitude of possible methods, how I determine a infected/injured kidney vs a healthy kidney is by looking at: 1) significant aggregates of inflammatory cells or possible necrotic tissue. 2) the space between the tubules are much more far apart from one another. And mainly 3) look for tubulointerstitial fibrosis, vascular sclerosis and glomerulosclerosis (this can be done with masson's trichrome staining to identify more extracellular matrix protein, collagen, present within the infected/injured tissue.
There is a multitude of possible methods, how I determine a infected/injured kidney vs a healthy kidney is by looking at: 1) significant aggregates of inflammatory cells or possible necrotic tissue. 2) the space between the tubules are much more far apart from one another. And mainly 3) look for tubulointerstitial fibrosis, vascular sclerosis and glomerulosclerosis (this can be done with masson's trichrome staining to identify more extracellular matrix protein, collagen, present within the infected/injured tissue.
Further to Matthew's very thorough response you may also wish to consider special stains for specific infective agents (Gram stian etc) assuming that this assessment is not post antibiotic therapy.