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Urologists Should Consider Routine Antifungal Prophylaxis in High Sepsis Risk Patients Undergoing Percutaneous Nephrolithotomy
Architha Sudhakar, MD, Erin Santos, MS, Evelyn James, MS, David W. Sobel, MD.
Maine Medical Center, Portland, ME, USA.

Background: Current AUA guidelines do not recommend routine antifungal prophylaxis for patients undergoing percutaneous nephrolithotomy (PCNL), and only recommend single dose prophylaxis for patients with asymptomatic funguria detected on preoperative urine culture (PUC) prior to surgery. Previous research demonstrates that PUCs and renal stone cultures (RSCs) obtained during PCNL are often discordant, with RSCs sometimes isolating atypical pathogens. We examined the role for routine antifungal prophylaxis in "high sepsis risk patients," defined at our institution as patients with chronic indwelling catheters (foley, SPT, nephrostomy tube), staghorn stones, limited body mobility due to neurologic conditions, or history of sepsis of urinary origin within three months. Methods: A systematic retrospective review of all PCNL procedures performed at a single academic institution from October 2016 through February 2023 was conducted. Procedures were included if RSC was obtained and sent during PCNL. Other variables such as PUC and incidence of postoperative sepsis (measured by qSOFA score) were recorded. The association between positive PUC and RSC speciation and postoperative sepsis was analyzed. Results: Of 263 procedures included, 86 (33%) had positive RSC (Table 1). Within the positive RSC group, 21 (24%) stone cultures grew yeast. Yeast was the second most common pathogen speciated. Other dominant species in positive RSC included Enterococcus (29%), Proteus (23%), Pseudomonas (13%), and E. coli (13%). Of the patients with yeast-growing RSC, 16 (76%) patients in the yeast-growing RSC group were considered "high sepsis risk" according to our institutional criteria. 5 (24%) developed postoperative sepsis and only one of these received antifungals preoperatively. All 5 patients were classified as high sepsis risk. The overall incidence of patients with positive RSC and concordant positive PUC was 70% (Table 2). Only 5/21 (24%) patients with RSC demonstrating yeast had a concordant PUC with yeast growth. Yeast was the fifth most common pathogen speciated in PUCs. The overall incidence of postoperative sepsis was 7%. Conclusions: Routine antifungal prophylaxis should be considered for any patient with high risk for sepsis undergoing PCNL regardless of preoperative urine culture. Yeast was found to be present in a high proportion of renal stone cultures which was not apparent on corresponding preoperative urine cultures. Our institution has implemented a high sepsis risk protocol utilizing a routine preoperative course of three days of fluconazole in addition to targeted antibiotics and antifungals with broad spectrum antibiotics perioperatively. Studies are ongoing to evaluate infectious outcomes following initiation of this protocol. We encourage other urologists to study their institutional stone culture antibiogram as this may inform augmented antimicrobial prophylaxis to reduce sepsis in these high risk patients.
Table 1: Speciation of positive renal stone cultures (RSC)

Positive renal stone culture86 (32.7%)
Enterococcus spp.25 (29.1%)
Yeast21 (24.4%)
Proteus spp.20 (23.3%)
Pseudomonas spp.11 (12.8%)
Escherichia coli11 (12.8%)
Staphylococcus (non-staph aureus)10 (11.6%)
Klebsiella spp.7 (8.1%)
Providencia spp.5 (5.8%)
Enterobacter spp.3 (3.5%)
Morganella spp.3 (3.5%)
Staphylococcus aureus3 (3.5%)
Streptococci spp.1 (1.2%)
Other8 (9.3%)

Table 2: Speciation of preoperative urine culture (PUC) in those with positive renal stone culture (RSC)
Positive preoperative urine culture59 (70.2%)
Klebsiella spp.9 (10.5%)
Enterococcus spp.7 (8.1%)
Escherichia coli7 (8.1%)
Proteus spp.7 (8.1%)
Yeast5 (5.8%)
Enterobacter spp.4 (4.7%)
Pseudomonas spp.4 (4.7%)
Staphylococcus (non-staph aureus)2 (2.3%)
Citrobacter spp.2 (2.3%)
Acinetobacter spp.1 (1.2%)
Morganella spp.1 (1.2%)
Corynebacterium1 (1.2%)
Staphylococcus aureus1 (1.2%)
Streptococci spp.1 (1.2%)
Other16 (18.6%)

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