Public health researchers need to take advantage of every tool and emerging technology that they can get their hands on in the fight against communicable diseases.
The lives and well-being of millions of people are at stake. According to Genetic Engineering & Biotechnology News, 4.1 million deaths are attributable to diarrheal diseases and infectious lower respiratory diseases (as of 2019, the latest figures available). And with the rise of COVID-19 cases in a global pandemic, the need to rapidly deploy robust testing systems against growing diseases becomes even more crucial.
Challenges of Traditional Diagnostic Methods
Medical researchers have been relying on microbial diagnostic setups that are based on using culture media as well as serological tests for antibodies that are associated with pathogens.
In a relatively more modern approach, they also use polymerase chain reaction (PCR) to detect microbial DNA or RNA sequences. But lab technicians will tell you that such approaches are not able to provide the speed or comprehensive coverage that you can get with more cutting-edge techniques. The goal is to apply a metagenomic approach when it comes time to profile a patient’s sample for DNA or RNA.
Next Generation Sequencing Seen to Improve Metagenomics Efforts
Scientists are currently doing metagenomic analysis with next generation sequencing. They are doing so because NGS allows a higher processing rate than traditional microarray approaches.
With NGS, you can run millions or even billions of reads during each run when conducting analysis in a clinic of patient samples. Not only is this a faster technique, but it also costs less to administer.
How Next Generation Sequencing Works With Metagenomics Tests
Work usually begins with technicians extracting nucleic acid from DNA and RNA. Then, they reverse-transcribe RNA, turning it into complementary cDNA. Using NGS equipment, they sequence the DNA and cDNA sequences, assigning them to the appropriate reference genomes. Doing so enables a lab technician to learn which microbes are in the sample and how big the microbial populations are.
This is a vital first step in understanding the prevalence and spread of various infectious diseases.
A molecular PCR diagnostics test takes about 2 hours to finish, while metagenomic next generation sequencing (mNGS) systems take about 20 hours. But timing is only part of the picture. With mNGS, you can look for and identify a much wider range of potential pathogens in a patient’s sample, from parasites to viruses, fungi, and bacteria. These pathogens can be readily identified by their RNA or DNA sequences.
What’s more, a metagenomic approach with NGS allows scientists to sequence RNA of human hosts to see how people respond to different diseases and treatments.
One recent example of metagenomic tests with next generation sequencing was conducted by researchers at the Chinese People’s Liberation Army General Hospital along with the Vision Medicals Center for Medical Research. They were employing mNGS to look for CAP (community-acquired pneumonia), which can be tricky to address because it can be caused by more than 100 different species of bacteria, fungi, and parasites.
There are not many diagnostic assays to detect uncommon pathogens like this, and culture medium-based approaches to amplify and detect pathogens do not have a good detection rate. Genetic Engineering & Biotechnology News explained that as much as 62% of CAP infections are undetected by doctors.
Using mNGS, scientists were able to detect infections of rare pathogens about 70% more effectively than the control group that didn’t rely on mNGS, illustrating that this is a promising new technique in detecting the public spread of disease.
A Role for Next Generation Sequencing to Address Future Public Health Threats
It’s clear that next generation sequencing is poised to play a vital role in the efforts of scientists and public health researchers in their fight against microbial diseases. The novel coronavirus causing COVID-19 infections is an example of how medical authorities can get caught off guard and will need rapid, comprehensive tests to improve how we monitor the spread of infections.