It uses the techniques of metagenomics to identify and characterize the genome of bacteria, fungi, parasites, and viruses without the need for a prior knowledge of a specific pathogen directly from clinical specimens.
The capacity to detect all the potential pathogens in a sample makes metagenomic next generation sequencing a potent tool in the diagnosis of infectious disease especially when other more directed assays, such as PCR, fail.
[2] Next-generation sequencing uses the techniques of metagenomics to identify and characterize the genome of bacteria, fungi, parasites, and viruses without the need for a prior knowledge of a specific pathogen directly from clinical specimens.
[3] The capacity to detect all the potential pathogens in a sample makes metagenomic next generation sequencing a potent tool in the diagnosis of infectious disease especially when other more directed assays, such as PCR, fail.
[8][7] The traditional method consists on formulating a differential diagnosis on the basis of the patient's history, a clinical presentation, imaging findings and laboratory testing.
But here it is suggested a different way of diagnosis; metagenomic next-generation sequencing (NGS) is a promising method because a comprehensive spectrum of a potential causes (viral, bacterial; fungus and parasitic) can be identify by a single assay.
[10] It is important to incorporate not only the antimicrobial resistance gene sequence and mechanism but also the genomic context, host bacterial species and geographic location (metagenome).
Its role in the future of pandemic preparedness is anticipated and could exist as the earliest surveillance system we may have to detect outbreaks of unknown etiology and to respond in an opportune manner.
[12] The use of mNGS to characterize the microbiome has made possible the development of bacterial probiotics to be administrated as pills, for example, as a treatment of Clostridioides difficile-associated diseases.
[citation needed] RNAseq analysis have a lot of other purposes and applications such as to identify novel or under appreciated host–microbial interactions directly from clinical samples, to make indirect diagnosis on the basis of a pathogen specific human host response and to discriminate infectious versus noninfectious causes of acute illness.
[13] Accordingly, there is an overall lack of penetration of this approach into the clinical microbiology laboratory, as making a diagnosis with metagenomics is still basically only useful in the context of case report but not for a true daily diagnostic purpose.
A potential exception to the 16S/ITS testing is blood, given the huge amount of 16S sequence available, making clean cutoffs for diagnostic purposes problematic.
[13] In addition to issues with interfering substances, specially in the diagnosis area, accurate quantitation and sensitivities are essential as a confusion in the results can affect to a third person, the patient.