Culture-independent long read metagenomic diagnostics for genomic surveillance and infection control of pathogenic bacteria in clinical settings

Metagenomics allows construction of accurate representations of microbial communities directly from mixed samples. Thereby eliminating biases introduced by culture or gene-centric diagnostic techniques. Culture based methods of pathogen detection are limited due to several factors, the most predominant being diversity loss and difficulty in culturing particular pathogens, followed by time consumption. Culture-independent processes eliminate bias, diversity loss, time and resource waste and difficulties involved in culturing some pathogens. It is currently not replicable and reliable to perform molecular techniques straight from clinical samples, as metagenomic assembled genomes (MAGs) remain fragmented, incomplete andprone to contamination, limiting their use for clinical diagnostics. Long read metagenomics constitutes a potential paradigm shift in how we diagnose and respond to hospital associated infections, offering the potential to recover complete genomes from each organism within a polymicrobial community.