by Peter Stephens, Head of R&D, Microbiology Division, Thermo Fisher Scientific
Microorganisms are everywhere—in, on and around us. These tiny living organisms—bacteria, viruses and fungi—are invisible to the naked eye and can help keep us healthy or, alternatively, make us very sick. For centuries, society has had a foundational understanding of how microorganisms influence health. For example, ancient Egyptians would apply moldy bread to infected wounds to help heal them. In recent years, through scientific innovations, we are able to access more information than ever about these microscopic organisms that can have such a significant impact on us and the world we live in.
With an increasingly global food supply, there’s a growing risk of treatment-resistant bacteria and emerging pathogens that can spread quickly and with devastating impact. We need to be able to gain deeper insights to better understand and, therefore, fight against potentially dangerous microbes. It’s important to prioritize technological and diagnostic improvements in order to fully enter a new era of microbiology.
The past and present of microbiology
Despite the centuries of finding ways to treat and prevent infections, the actual discipline of microbiology is only around 150 years old. In that time, how we study microbes, diagnose illnesses and treat infections has changed dramatically. For almost 100 years, culture media was the most used diagnostic tool. Culture media are nutrient-rich formulations that provide microorganisms with what they need to multiply so labs can grow enough of the microbe being studied to undertake experiments. Although still critical to microbiology workflows, there has been a focus on advanced diagnostic solutions that produce faster results.
One of the first generations of new tests to be introduced was the immunoassay. One version of immunoassay that transformed microbiology diagnostics was the enzyme-linked immunosorbent assay (ELISA) test, which began being used widely in the 1980s. ELISA tests use antibodies to determine the presence of a target hormone, protein or antigen, like a bacteria or virus, and how much of it is present. It is one of the first immunoassay formats and remains an important test in detecting HIV, as well as in diagnosing other conditions like pregnancy. Some years later, in the early 1990s, lateral flow tests rose in prominence. Lateral flow tests operate on the same principles as ELISA tests but are simpler to use. This means they can be used in many settings, including the lab or point-of-care, like at-home tests. For example, many at-home covid-19 tests used during the pandemic were lateral flow tests. Lateral flow tests helped democratize clinical microbiology technology and provided rapid and reliable results.
At around the same time, polymerase chain reaction (PCR) tests were also being developed. PCR tests work by amplifying specific segments of DNA from a small sample. This is critical when testing clinical and food samples for the presence of pathogens because a small sample can yield critical results relatively quickly. PCR tests are also helpful in several applications outside of microbiology, including forensics, agricultural biotechnology and other clinical diagnostics. Each of these new tests has helped revolutionize microbiology, allowing us to improve efficiency and access to diagnostics to help treat and manage illnesses more effectively.
However, recent bacterial outbreaks linked to contaminated food, along with public health crises caused by fast-spreading viruses, have made it clear that we must do more to improve our ability to detect, understand and treat harmful microbes.
The future of microbiology
In addition to the bacteria and viruses that make us sick, our understanding of how we interact with microorganisms more broadly is expanding rapidly. Recent studies have revealed that the gut microbiome can affect personalities and even the lifespan of offspring in mice, expanding how we think about its impact on our health and well-being. By continuing to advance the technology used in microbiology research, we can unlock even deeper insights into the microbes we study.
One form of testing that has the power to change the way we approach microbiology is genetic testing. Genetic testing allows us to study organisms at the nucleic acid level. This detailed information can help us understand how microorganisms function and how we can treat the ones that can cause harm. Where genetic testing can have a profound impact is on antimicrobial resistance (AMR), a growing global public health concern. AMR occurs when microbes become resistant to the medicines designed to kill them. This makes infections incredibly difficult to treat, increasing the possibility for diseases to spread and the risk of severe illness and death.
The World Health Organization (WHO) estimates that bacterial AMR was directly responsible for 1.27 million global deaths in 2019 and contributed to 4.95 million deaths. Molecular testing, however, including genetic testing, can help determine the spread and evolution of AMR and therefore provide us with deeper insights to slow its growth. Although microbes naturally evolve to survive and multiply, the misuse and overuse of broad-spectrum antibiotics are major drivers of AMR.
Gaining a deeper understanding of microbial mechanisms will help ensure that patients receive targeted treatments for their specific infections, reducing the risk of further increasing AMR. Understanding bacteria and other microbes at the DNA level can also help in outbreak analysis by improving variant detection.
Like most—if not all—industries, the future of microbiology will also be shaped by artificial intelligence (AI) and a need for greater automation. A trend across laboratory research in recent years is a decline in available skilled labor. AI has the potential to help fill the knowledge gaps in skilled labor that are increasing in the lab by helping interpret test results and helping lab technicians feel confident in their results. It may also be able to help improve the accuracy and speed of diagnostic results.
I see a future where AI can efficiently analyze test results in combination with additional details it has access to, like patient history or current symptoms, to diagnose and determine a path for treatment for pathogens. This could be revolutionary in areas like sepsis testing, where quick, accurate results can help save a person’s life. However, AI doesn’t have to be limited to supporting clinical microbiology.
AI could improve areas like food safety testing, where customers need easy-to-use, rapid and accurate tests. Much in the same way that ELISA, lateral flow and PCR tests changed how we approached microbiology testing, genetic sequencing and AI will help us gain even more insights into the microbes we’re studying. Of course, these are just the technologies we’re aware of. It’s likely that new technologies will emerge in the coming years that we couldn’t even dream of now.
Each scientific advancement in microbiology has been due in part to new technologies, and now the field must evolve even more rapidly. We have come so far from the origins of microbiology as a practice, in our knowledge of microbes and ability to diagnose illness and treatment options. And yet, we continue to discover just how much further we have to go to truly understand the microorganisms around us and how we interact with them. But with access to innovations and technological advancements, the future of microbiology is bright.
About the author
Peter Stephens is head of R&D for Thermo Fisher Scientific’s Microbiology Division. In this role he is responsible for tracking technology development across the world of microbiology diagnostics as well as driving forward internal product development programs. Peter has worked in the microbiology diagnostics industry for over 30 years, starting initially with his PhD into the resuscitation and growth of individual cells of sub-lethally injured Salmonella. His research has taken him through the development and evolution of culture media formulations, immunoassays, molecular amplification technologies, cytometry and spectrometry through to whole genome sequencing. He has been fortunate to have worked alongside some of the pioneers of microbiology diagnostics of the last few decades and has a natural fascination with tailoring powerful technologies to deliver rapid, accurate, meaningful and affordable diagnostic solutions.