Acute Uncomplicated and Complicated Cystitis: From Empiric Treatment to Antibiogram-Based Tailored Treatment

Introduction: Any new diagnostic test must meet a threshold that surpasses the gold standard of established routinely used techniques. This includes the laboratory diagnosis of organisms in urine and its accuracy. It is also important to establish the bacterial load present and to improve the speed of diagnosis. The correlation with clinical outcomes for each patient based on objective scoring should be evaluated in this setting. The aim of our study was to conduct a head-to-head comparative phase II trial of standard urine culture and sensitivity versus deoxyribonucleic acid (DNA) next generation sequencing testing for the diagnosis and treatment efficacy in patients with urinary tract infections based on short-term outcomes. Materials and methods: Between January 2016 and December 2016, 56 patients were entered into this study with symptoms of an acute cystitis, and 44 patients completed the study. Twenty-two volunteers were entered as controls in this study without symptoms of a urinary tract infection. The Level 1 Panel is a quantitative real-time polymerase chain reaction (PCR) test for bacteria and fungi. It can also assess for genetic factors conferring resistance to bacteria. The Level 2 test can detect virtually all microbial organisms and fungal pathogens by the use of primers to detect the 16S rRNA gene and its target sequence in each sample. We compared this with standard urine culture and sensitivity tests. Results: Based on a head-to-head comparison, symptom scores were statistically significantly better for those patients whose treatment was based on metagenomics results versus traditional culture studies. For instance, all 44 patients showed positive results in DNA sequencing tests, while only 13/44 patients had positive urine culture tests. In the cohort of patients with a positive DNA test and negative urine cultures, the treatment outcomes were improved with respect to symptom scores when they started treatment on day 8. That ultimately improved recovery time and decreased the cost of treatment. Another possible advantage of the DNA test is an increased sensitivity to diagnose anaerobic flora noted in 20/44 patients with symptoms of a UTI. Conclusions: In this study DNA next generation sequencing testing demonstrated a more accurate diagnosis of UTI than the standard urine culture and sensitivity test. In addition, the DNA test allowed us to achieve better treatment outcomes in patients treated with antibiotics for primary anaerobic, aerobic, or a combination of bacteria. Therefore, DNA testing may help diagnosing and treating symptoms of a UTI especially when urine cultures are negative.