Clinical standardization of metagenomic next generation sequencing (mNGS) in the pathogen diagnosis

Abstract

Background With the development and advancement of gene sequencing technologies, next generation sequencing, especially metagenomic next generation sequencing (mNGS), has been explored in infectious disease diagnosis. Aims To first introduce the standardization of each step of mNGS, the interpretation of positive and negative results and their clinic application in pathogen diagnosis. Methods A typical workflow of mNGS includes six main steps: sample collection, nucleic acid extraction, library construction, sequencing ,data analysis and report writing. Results Based on our previous work, we introduce the standardization of steps of mNGS in pathogen diagnosis and summarize the interpretation of positve and negative results and their application in clinic settings. Conclusion It is believed that this clinical standardization of mNGS could be a routine diagnostic tool for infectious diseases in coming future.

Detection of pathogens and antimicrobial resistant genes from urine within 5 hours using Nanopore sequencing

“…Metagenomic next-generation sequencing (mNGS) has the potential for rapid unbiased identification of pathogens at the strain level and their corresponding antimicrobial resistance genes, which overcome the limitations of the current diagnostics methods (16). mNGS is also superior for its ability to identify microbes that are difficult to culture and detect AMR genes directly without needing a targeted assay.…”

“…While many commercially available sequencing technologies exist, the MinION sequencer (Oxford Nanopore Technologies, UK) exhibits excellent potential for rapid point-of-care testing. This is a pocket-sized USB-connectable, portable device capable of real-time long-read sequencing and data analysis (16,17). Previous studies have shown the feasibility of using MinION to detect bacterial pathogens and antimicrobial resistance genes from urine samples (16,(18)(19)(20).…”

“…This is a pocket-sized USB-connectable, portable device capable of real-time long-read sequencing and data analysis (16,17). Previous studies have shown the feasibility of using MinION to detect bacterial pathogens and antimicrobial resistance genes from urine samples (16,(18)(19)(20). Schmidt et al detected pathogens and their corresponding antibiotic-resistance genes (ARGs) among clinical and spiked urine samples with a turnaround time of 4 -6 hours (19).…”

“Smart markets”: harnessing the potential of new technologies for endemic and emerging infectious disease surveillance in traditional food markets

“…Likewise, as there is an increase in metagenomic information acquired from TFMs, the development and implementation of a metagenomic viral surveillance matrix are envisioned to outline details on viral movement between livestock and humans ( 52 ). To aid in the visualization and parsing of the vast amount of data generated from the metagenomic analysis of environmental samples, we envision the use of advanced bioinformatic pipelines capable of analyzing large data sets and producing clean and easily visualized summary reports ( 53 – 58 ). Importantly, the relative speed of these surveillance pipelines is only as fast as their rate-limiting step.…”