Because of this diagnostic difficulty, there is a need for novel techniques that can help differentiate between the specific etiologies causing interstitial inflammation in the kidney. Extensive efforts have been made to develop less-invasive tools such as blood and urine biomarkers. Interferon gamma-controlled chemokines (CXCL9, CXCL10) and cytotoxic T-lymphocyte granule contents (Granzyme B, perforin) have been shown to be highly expressed in acute rejection. CXCL10 has been shown to be a candidate urinary biomarker for acute rejection [38, 39]. Our recent pilot study explored the utility of miRNA profiling (microRNA) by Nanostring technology using kidney allograft biopsy tissue [26]. This study by Oghumu et al. selected a group of 49 patients who had a transplant biopsy within the first 24 months after transplantation with interstitial inflammation characteristic of acute pyelonephritis. As described above 16/49 patients had concomitant positive urine cultures at biopsy, 14/49 patients had positive urine culture but it did not coincide with the biopsy (had positive culture beyond 10 days before or after biopsy), and in 19/49 patients, urine cultures were negative. Based on urine culture results at the time of the biopsy these patients were subdivided into groups of ‘highly likely,’ ‘possible,’ and ‘equivocal’ for pyelonephritis. Eleven patients representing these groups were selected for the miRNA testing and compared to five patients with unequivocal AR and four patients with normal (preimplantation) biopsies as controls. miRNAs profiles were analyzed using top 100 miRNAs and found that there was good intra-group clustering within the AR and the normal groups. Amongst the pyelonephritis group intra-group clustering was poor. Several biopsies of graft pyelonephritis clustered with AR. We did, however, find a small group of miRs that showed statistical differences between the biopsies with AR and the cases of unequivocal graft pyelonephritis (miR-145, miR-99b, let-7b-5p, miR23b, and miR-30a). A follow-up study looking at gene expression (mRNA transcripts) was performed using Nanostring platform [29]. For this study we also added a group of biopsies with native kidney pyelonephritis. Gene transcripts for CXCL1, CXCL2, and lactoferrin (LTF) were found to be higher in pyelonephritis (both native kidney and graft pyelonephritis). CXCL1 and CXCL2 are known to be neutrophil chemoattractants [35]. LTF is an iron-binding glycoprotein in secondary granules of polymorphonuclear leukocytes, found in various body secretions such as saliva, tears, and milk. It has antimicrobial activity. Conversely, interferon gamma-controlled chemokine genes—CXCL9, CXCL10, and CXCL11 (and also metabolic enzyme IDO1) are expressed significantly higher in acute rejection biopsies as compared to pyelonephritis (both native kidney and graft pyelonephritis). These are CXCR3 ligands and potent T-lymphocyte chemoattractants, universally induced during cell-mediated immune responses [36, 37]. CXCL10 has been shown to be a candidate urinary biomarker for acute rejection [38, 39]. Surprisingly though, we found that gene expression in graft pyelonephritis does not exactly resemble that in native kidney pyelonephritis. In fact, CXCL9, CXCL10, and CXCL11 transcript levels in graft pyelonephritis are significantly higher than in native kidney pyelonephritis (albeit lower than AR). In silico functional pathway analysis using Ingenuity software was also performed. Pathway analysis showed similarities between graft pyelonephritis and acute rejection. The T cell dominant upstream regulatory molecules (IFNγ, IFNα, IL-18, IL-12) are predicted to be activated in both AR and APN (culture positive and culture negative), but not in native kidney pyelonephritis. Differences between MAP kinase subfamilies (ERK1/2 and p38) were also seen between APN and native kidney pyelonephritis. Therefore, ineffective bacterial phagocytosis in APN resulting in lack of response to antibiotics in some cases may be speculated. Whether it is an effect of the immunosuppressive treatment is not known but is certainly a possibility. Also there is no predicted activation of TNF and NFĸ-B in native kidney pyelonephritis as compared to graft APN and AR, probably suggesting a more controlled inflammatory reaction in NP as compared to AR and APN. Thus, the pathogenesis of allograft APN and native kidney pyelonephritis may not be exactly the same. We, therefore, think that graft pyelonephritis may also have a component of alloimmunity (in addition to antimicrobial immune response). Some cases of graft pyelonephritis do not completely recover with antibiotics alone. Selected cases may show some benefit with addition of steroids [29]. But since this method needs further validation and optimization the authors recommend using a ‘gestalt’ approach including clinical history, biopsy findings, culture results, immunosuppressive drug levels, C4d staining, and donor-specific antibody results in arriving at the best possible clinical diagnosis.

Recurrent UTI: This is reported as highly variable, 2.6–27% [40], based on several retrospective studies. A CT scan with contrast to study the native kidneys, transplant kidney, ureters, and the bladder will identify strictures, obstruction, abscesses, stones, or complex cysts. For instance, if the native kidney appears to harbor a persistent reservoir of infection and transmitting the infection to the transplanted kidney, a native nephrectomy would be potentially curative. A post-void ultrasonogram of the urinary bladder would diagnose inadequate emptying and patients may respond to bladder training, medical therapy or frequent self-catheterization. In cases without an obvious etiology, a referral to the Urology department is appropriate to investigate urinary tract anomalies. Fiberoptic cystoscopy to diagnose urethral and bladder lesions, voiding cystourethrogram to diagnose ureteral reflux, urodynamic studies to diagnose detrusor dysfunction, and functional outflow problems are all appropriate tests. In cases with all negative results but with suspicion for an infected nidus in one of the kidneys, the urologists at our institution have performed a selective ureteral urine sampling from each of the two native ureters and the transplant ureter via cystoscopy after sterilizing the bladder. A positive culture would then identify the culprit kidney allowing a selective treatment approach, such as native nephrectomy or prolonged antibiotic therapy. Among men rare causes for UTI are prostatitis and epididymitis and in women weak pelvic floor muscles causing urogenital prolapse and atrophic vaginitis from post-menopausal estrogen deficiency.

Etiology: Many retrospective studies reported that the most common pathogens causing UTI are enteric gram-negative bacilli such as Escherichia coli, Klebsiella sp., Pseudomonas sp., and Enterococcus faecalis. Resistant strains are more common than in the general population, up to 17.2% reported by Valera et al. [41]. A prospective, randomized study from 1990 comparing trimethoprim/sulfamethoxazole (TMP/SMX) to placebo, a significantly higher proportion of UTIs in the treatment group, was due to multi-drug-resistant bacteria (62% vs. 18%) [42]. Similarly, Samra et al., from a large tertiary care center, reported that from an outbreak of carbapenem-resistant Klebsiella pneumoniae producing KPC-3 (carbapenemase producing K. pneumoniae type 3), 11% of all the isolates were from RTRs [43]. Green et al. did a meta-analysis of all the prophylaxis studies and concluded that no significant reduction was found in the all-cause mortality and adverse events rates [44]. In this analysis, prophylaxis significantly reduced bacteriuria and sepsis with bacteremia but impact on graft survival could not be demonstrated. Maillard et al. reported the emergence of ampicillin-resistant Enterococcus faecium strains (ARE) in a kidney transplant ward and noted that prior cephalosporin use and patient-to-patient transmission were associated with the emergence of ARE [45]. This strain has the potential for clonal dissemination and further outbreaks but also is thought to represent an important step in the emergence of vancomycin resistance, which is highly prevalent as a nosocomial infection today [46]. In summary, even though antibiotic prophylaxis appears to be an important factor in the emergence of resistant bacteria it is difficult to prove this conclusively based on the retrospective, single-center studies that used a variety of regimens for prophylaxis.

Pathogenesis is similar to that in native kidney pyelonephritis. Ascending infections from the lower urinary tract are more common. Shorter ureter due to pelvic location of the transplanted kidney, absence of the natural anti-reflux mechanisms at the junction of the urinary bladder and surgically implanted ureter, post-surgical tissue injury, ureteral edema and stenosis, and suppressed immune system all together contribute to the ease of bacterial attachment to the urothelium, survival, and spread through the urinary tract.

In general, as is the case with the general population, initial treatment of UTI is decided based on the clinical context, risk factors, and severity of the presentation. Results of the urine and blood cultures will ultimately decide the specific antibiotic regimen, the duration, and follow-up. There have been no prospective, randomized clinical trials comparing antibiotic choice or duration and therefore, the treatment should be individualized and must take into account the local center’s bacterial culture profiles and patient’s risk factors.

Asymptomatic bacteriuria: Treatment of patients with incidental positive bacterial cultures but without symptoms remains controversial. As described before, the incidence of asymptomatic bacteriuria is very high in the early post-transplant period and continues to be a significant event even in the long-term. The clinical outcomes appear to be worse with antibiotic treatment if not the same. El Amari et al. [47] showed in a retrospective study that 45% of the asymptomatic bacteriuria patients treated with antibiotics had persistent bacteriuria and 35% of them with emergence of antibiotic-resistant strains. Among cases not treated with antibiotics 59% cases had spontaneous resolution of the bacteriuria. Similarly, Green et al. [44] showed that treating asymptomatic bacteriuria resulted in a three times higher risk for symptomatic UTI. This evidence, along with the risk for emergence of antibiotic resistance strains as well as the significant adverse effects of antibiotic exposure, e.g., Clostridium difficile, Candida infections question the efficacy of routine antibiotic treatment of asymptomatic bacteriuria.