A highly accurate nanopore-based sequencing workflow for culture and PCR-free microbial metagenomic profiling of biological samples.

Current clinical methods for microbial detection are largely culture based and, due to limitations of accuracy, bias and sensitivity, hamper efforts to adequately diagnose and treat urogenital infections leading to frequent instances of prolonged and recurrent suffering for women. We report a new method that utilises 3rd generation long-read nanopore sequencing to produce fast, accurate and fully quantitated microbiome profiles appropriate for clinical use that can be immediately utilised to aid diagnosis and focus treatments in cases of recurrent or chronic urinary tract infection, rUTI, cUTI and persistent bacterial vaginosis, BV. Here, as proof of principle, we apply this methodology to reassess the healthy urogenital microbiomes of asymptomatic female and male samples.