Towards ultra-rapid microbial cfDNA nanopore sequencing for the identification of sepsis-causing pathogens
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Bloodstream infections lead to long hospitalisations and create severe socioeconomic burden globally, but most critically, in developing nations. The current standard for pathogen identification for diagnosis is through blood culture, which lacks specificity, sensitivity, and has time to results often exceeding three to five days, or longer. Microbial cell-free DNA (cfDNA), released from lysed pathogens in the infected human circulation, has been shown to have high sensitivity for detection. Nanopore sequencing could offer a culture-free, sensitive and specific diagnosis while being quicker and more cost-effective than current proposed solutions. For such a system to become a reality, however, current methodologies must be updated to accommodate for cfDNA fragment size: nanopore-based devices are long-read sequencers with methodologies specialising on long DNA fragments, while cfDNA peaks at 167bp and rarely exceed 500bp.
