Waking up with a fever, nausea, and a sense of malaise (feeling of discomfort) is a terrible way to start the day. Before heading to the doctor’s office, a quick Google search tells you that it could be the flu, the common cold, strep throat, COVID-19, or worse, the plague! These symptoms are typical for many infections, making it hard to identify the cause when they appear. A trip to the doctor is now necessary, and they will run some tests. If it’s COVID-19, a PCR test can work. If it’s strep throat, a swab and color-changing test will work. What if it’s neither? What if it’s a bacteria or virus that a test hasn’t been developed for yet?

The lab technicians must now culture the pathogen, which means they must grow the microbe in petri dishes to see how it behaves. For bacteria, they are grown in petri dishes filled with agar, a sugar-rich gel that the bacteria stick to. Different agars contain different nutrients and dyes to indicate what the bacteria can do to determine its identity. For viruses, they need to be grown with cells to mimic infection because viruses cannot survive on their own. When enough viruses have been grown, their genomes can be analyzed to help determine their identity. Other characteristics can help, like how fast infected cells die or are affected by the virus.

Recent advances in genome identification through the PCR test have been very helpful, especially in the case of COVID-19, and DNA sequencing of ribosomes has helped identify bacteria more effectively, too. However, despite these advancements, around 60 percent of pathogens are still unidentified in clinical settings. Because a lot of infections present similar symptoms, clinicians may accidentally take a sample from a nasal swab, thinking that the patient has COVID-19, instead of taking a sample of blood because the patient actually has HIV. Taking a minimum amount of samples from a patient and analyzing them without wasting time through culturing microbes has been a new method for detecting pathogens for more accurate diagnosis.

The rise of metagenomics, the study of genomes from all the microbes and cells within the human body, can provide such a method for analysis to provide accurate diagnosis within less time. Metagenomics was applied in 2021 to identify the pathogen of 109 patients with more accuracy than culturing the microbes and other traditional tests. This study advertised metagenomic analysis as a more effective method of diagnosing patients, but whether doctors and clinics would accept the results as accurate was another story.

From February 2021 to May 2022, another study took over 500 samples from 361 patients, an enlarged version of the previous metagenomic diagnosis study. While the earlier study analyzed blood, lung fluid, and urine, this study analyzed almost everything: blood, lung fluid, urine, joint fluid, cerebral spinal fluid, bile, and pus, and that’s not the complete list. This metagenomics to a new level as almost every part of the human body that could contain a pathogen was analyzed. The latest results confirmed the same thing: metagenomic analysis accurately identified the pathogen in a shorter time than traditional testing. This study also compared the metagenomic results with the results of conventional tests, which matched.

With the comparison, metagenomics has more evidence confirming that it is reliable for diagnosing patients. In the future, patients won’t have to wait for days to get results when metagenomics can be performed within hours and give accurate results. This doesn’t mean the old methods are obsolete, though. They can still be helpful as confirmation. However, metagenomics is a rising star in the biological field and is now making its way into the medical field. Maybe in a few years, it will be able to identify new pathogens we haven’t encountered before they become the next pandemic.