Presentation Authors: George Coba*, Timothy Koo, Saif Zaman, Tampa, FL, Maria Stefil, Matthew Dixon, Norwich, United Kingdom, Liqiang Ni, Orlando, FL, Michael McDonald, Celebration, FL, Vladimir Mouraviev, Orlando, FL
Introduction: The fast implementation of next generation sequence (NGS) technology in the field of urological infection may facilitate the comprehensive individual signature of most prevalent bacteria causing chronic UTI. Standard urine culture and sensitivity (C&S), although remaining as the gold standard of microbe identification, cannot detect a potentially aggressive microbial association of urinary microbiome in patients with UTI. This study aims to compare the accuracy of C&S versus (vs.) NGS.
Methods: A prospective, feasibility, bi-institutional study was performed in 69 patients with chronic UTI. Urine samples were obtained trough mid-stream catch and shipped to local lab for C&S and core lab of MicroGenDX for NGS test. Comparisons were performed for number of pathogens detected by both techniques and antibiotics resistance on standard blood agar vs. resistance genes using polymerase chain reaction (PCR). The correlation was sub-stratified in 3 degrees such as a complete match (CM), partial match (PM) and mismatch (MM).
Results: Analysis revealed significant difference between the accuracy of C&S vs. NGS. In 19 culture-negative cases the NGS detected microbes in 17 patients. In total NGS identified a causative bugs for UTI in 67 of 69 patients. The only 2 cases otherwise were that NGS detected 0 and 1 pathogen while C&S detect 1 and 2 micro-organisms, respectively. While in 32 culture-positive cases only 1 pathogen was found in 21 patients and 2 microbes in 11 cases respectively, NGS was able to detect a microbial association of median 3 pathogens (range:1-12). There was a MM in 34 of 49 patients (p = .0013). In contrast, 6- PM and 9 CM between the testing methods. In 16 of the MM-cases, NGS was able to identify bacteria after C&S reveal no a low bacterial load with colony-forming units (CFU) < 50,000/ml. Regarding antibiotic resistance genes, of the 69 cases there had 44 MM, 10- PM and 15-CM between the testing methodologies (p = .0001).
Conclusions: Our results indicate that NGS provides more accurate data for determining the etiology of UTI. NGS sequencing is superior to C&S in terms of pathogen detection being a highly sensitive tool to detect a few pathogens in every urine sample. This sometimes remained unclear which one contributes to the ensuing flare-up of UTI and thus more aggressive in each case. Although, the defining of resistance genes to different groups of antibiotics seems promising in antibiotic stewardship but warrant more robust clinical trials to prove.