How Circulating Microbial DNA is Changing the Face of Infectious Disease Diagnosis????

Infectious diseases are a major burden on the global health system.

In 2019 alone, around 7.7 million people lost their lives due to infections, accounting for about 14% of all global deaths that year.

Diseases like respiratory infections, diarrheal infections, tuberculosis, HIV/AIDS, and malaria continue to take a toll on human lives.

Not to mention, there is always the looming threat of new pathogens like SARS-CoV-2, which has already claimed over 5 million lives since its emergence.

In response to the COVID-19 pandemic, scientists developed highly sensitive diagnostic tests to target the SARS-CoV-2 virus. These tests, which rely on the detectability of nucleic acids, have been a crucial tool in identifying infected individuals quickly.

However, there are certain infections that pose greater challenges when it comes to sample collection, and they may even go undiagnosed.

One potential solution lies in the detection of circulating microbial DNA, which can serve as a biomarker for infections deep within the body.

This approach bypasses the need for invasive techniques like biopsies and offers a more accessible method for diagnosis.

While blood-based nucleic acid tests have been successful in detecting viral infections such as HIV and hepatitis C, they have limited effectiveness when it comes to non-viral infections caused by bacteria.

A very small amount of circulating DNA originates from pathogenic components - microbial cell-free DNA (mcfDNA).

These have shown potential as infectious disease biomarkers in fields like gynecology, oncology, and transplantology.

Advancements in PCR and NGS, have made it possible to detect pathogen nucleic acids in cell-free DNA (cfDNA) present in the blood.

Researchers have identified fragments of cfDNA originating from pathogens in purified plasma, leading to investigations into their potential for diagnosis. Unlike host nuclear cfDNA, microbial cfDNA makes up a smaller fraction of cfDNA (<1%) and has a smaller size due to its lack of organization and protection provided by the mammalian nucleosome structure.

As of today, there is only one commercially available, test for cfDNA-based medical disease diagnosis, developed by Karius , Inc. (USA) in 2018.

The Karius??Test (KT) is an assay utilizing metagenomic NGS (mNGS) for microbial cfDNA detection in patient blood samples during infections diagnosis, based on a clinical-grade database limited to around 1,200 from more than 1,400 species of all known human pathogens.

Following a set of custom-designed methods, including specific artificial intelligence algorithms, KT allows for efficient isolation, purification, sequencing, and taxonomic origin determination of identifiable, blood-circulating extracellular mcfDNA fragments, derived from non-viable microbes present in either healthy, diseased, or vulnerable individuals.

The non-invasive nature of cfDNA testing makes it an attractive option for population-wide screening programs, particularly in resource-limited settings. By simplifying the sample collection process and eliminating the need for invasive procedures, cfDNA-based tests have the potential to reach a larger portion of the population, facilitating early detection and intervention.