Evaluation of Ordering Practices, Microbial Yield, and Clinical Utility of Urinary Stone Cultures

Abstract

Abstract Urinary stones are a global problem. While it has been established that microorganisms can be associated with urinary stone formation, data on best practices for microbial culture and clinical interpretation of microbial culture of urinary stone specimens are limited. Our objective was to investigate the microorganisms present in urinary stone cultures (usc) and companion urine cultures. We conducted a retrospective study at a tertiry hospital examining cultures submitted between October 2018 and October 2021. We collected data from electronic medical records of patients who had at least at least one usc performed. As part of routine clinical workup, all urinary stone specimens submitted for culture were ground using a disposable tissue grinder and inoculated on a tryptic soy agar with 5% sheep blood agar plate (BAP), a chocolate agar plate (CHOC), and a MacConkey agar plate (MAC), streaked for isolation and incubated in 5% CO2 at 35°C for up to three days. Urine cultures were performed using the Kiestra TLA system with 10 µL of inoculum onto each of a BAP and MAC, and plates were examined at 16 and 24 hours of incubation. For urine specimens submitted from a straight or “in and out” catheter, 10,000 CFU/mL was the threshold for workup. From clean-voided, midstream, ileostomy, nephrostomy, or indwelling/Foley catheter specimens, 100,000 CFU/mL was the threshold for workup. The final clinical significance of cultures is determined by evaluating the culture result in light of the patient’s clinical presentation. For usc and urine cultures, clinically insignificant growth was considered no growth or when no pathogens were recovered in culture. Urine cultures with more than 3 species over threshold were considered contaminated. A total of 1,049 usc were performed from 854 patients (55.3% female). The median patient age was 61 years (IQR 49-70). The most frequent microorganisms reported in usc cultures were Proteus mirabilis (N=98), Enterococcus faecalis (N=75), and Escherichia coli (N=73). No pathogen was identified from 57% of usc. 441 usc were performed in a context of urine culture (+/-2 days) in 336 (39.3%) patients. In addition, 138 patients (16.1%) had more than 1 usc, being the maximum as 11 usc performed in one patient. The most common urine/USC concordant result was no growth in 165 of 441 cultures (37.4%), followed by coagulase negative Staphylococcus. Cohen’s kappa obtained from usc and urine culture results was 0.45, which is not the minimum acceptable agreement. A pathogen was identified from usc in 43% of cases. Usc and urine cultures rarely resulted in concordant results, but the most common concordant result was no growth in culture. Additional studies are warranted to evaluate the impact of usc results on patient care, including antimicrobial use and correlation of microbes isolated with stone chemical composition.