Introduction: The changing face of current infection phenotypes from planktonic to biofilm type has been developed implicating bacterial biofilms in recurrent infection. To date, no specific medical treatment exists to specifically target biofilms in the human host. Similarly, the identification of a biofilm has relied upon the analysis of tissue samples with electron microscopy or DNA identification with polymerase chain reaction (PCR) and sequencing. Standard culture and sensitivity test is not able to detect a presence of biofilms. Materials and methods: Two types of molecular microbial diagnostic testing "levels" are performed as noted below. In both types of analysis, the microbial DNA is extracted from the patient's sample. The patient report contains information about the pathogenic bacterial and fungal microorganisms detected, bacterial load and resistance genes to different antibiotics. Once the bacteria have been identified antibiotic recommendations are made based on research confirming the effectiveness of treatment. The technique was tested in 112 patients in different areas of urology for prevention and treatment purpose. Results: The clinical application of next generation sequence in different clinical phase I-II trials (acute cystitis in 56 patients, rectal swabs before transrectal prostate biopsy in 32 men, neurogenic bladder in 13 patients, chronic bacterial prostatitis in 17 men) demonstrated that this novel approach extends our knowledge about the microbiome of the urogenital tract in both men and women. DNA sequence has a high sensitivity to detect a bacterial and fungal association with resistant genes to antibiotics revealed allowing to implement a targeted and individual prevention and treatment of urinary tract infection (UTI) with improved efficacy compared to standard culture and sensitivity technique. Conclusion: The next generation DNA sequence technology enables the discovery of new concepts regarding the role of microorganisms in diseases of the urinary tract with an individualized approach for a more accurate diagnosis, prevention, prophylaxis and treatment of UTI.