During the COVID-19 pandemic, disinfectants became our shield. Hand sanitizers, disinfectant wipes and antimicrobial sprays became part of daily life. They made us feel safe. Today, they are still everywhere: in homes, hospitals and public spaces.
But there’s a hidden cost. The chemicals we trust to protect us may also inadvertently help microbes evolve resistance and protect themselves against antibiotics.
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QACs: The chemicals in most disinfectants
Among the most common active ingredients in disinfectants are quaternary ammonium compounds (QACs). They are found not only in the wipes, sprays and liquids we use to clean surfaces at home and in hospitals, but also in everyday products like fabric softeners and personal care products.
Roughly half of the products on the U.S. Environmental Protection Agency’s (EPA) List N of disinfectants effective against SARS-CoV-2 and List Q for emerging viral pathogens contain QACs.
Due to their widespread use, QACs enter wastewater treatment plants in substantial amounts, with effluents and sewage sludge being the main pathways through which QACs are released into the environment.
Within wastewater treatment plants, more than 90 per cent of QACs are typically removed, but small amounts remain in the effluents and reach rivers and lakes, where they accumulate.
Once QACs enter the environment, they meet microbial communities, networks of bacteria, archaea and fungi that recycle nutrients, purify water and support food webs.
Given that QACs are designed to kill microbes, it is no surprise that they can affect environmental ones. Yet microbial communities are remarkably adaptable; some die, but others survive and evolve resistance.
THE CANADIAN PRESS/Jonathan Hayward
The paradox of protection
Unlike antibiotics, which target specific cellular processes, QACs attack microbes and viruses in many ways, damaging cell walls, proteins and lipids. This broad attack makes QACs powerful disinfectants.
However, microbes are resourceful. Faced with these chemicals, some strengthen their cell membranes, pump toxins out or form protective biofilms. These adaptations don’t just help them survive QACs, but increasing evidence shows they can also boost antibiotic resistance.
At the genetic level, QAC resistance genes are often carried on mobile DNA, segments of genetic material that can move between different bacteria. When these elements carry both QAC and antibiotic resistance genes, the resistances travel together and can spread across bacterial communities, a phenomenon called co-resistance.
In other cases, a single defence mechanism protects against both QACs and antibiotics, a process known as cross-resistance. The widespread and increasing use of QACs amplifies these mechanisms, creating more opportunities for resistance to spread. This, in turn, establishes pathways through which antimicrobial resistance can reach human pathogens, contributing to the global rise of antibiotic-resistant infections.
According to a new World Health Organization (WHO) report, antimicrobial resistance is “critically high and rising” globally: In 2023, one in six laboratory-confirmed bacterial infections responsible for common illnesses worldwide were resistant to antibiotic treatment. Between 2018 and 2023, resistance increased in more than 40 per cent of the pathogen-antibiotic combinations that are monitored, with an average annual rise of five to 15 per cent.
(Unsplash/NIAID)
The WHO estimates that in 2019, bacterial antimicrobial resistance directly caused 1.27 million deaths and contributed to nearly five million more worldwide. What begins as a household cleaning choice can ripple outward, connecting our everyday habits to one of the most pressing public health challenges of our time.
Antimicrobial resistance is often seen as a clinical problem caused by antibiotic misuse, but it begins much earlier, in households, wastewater, rivers, lakes and soils. These are battlegrounds where microbes share resistance traits and adapt to human-made chemical pressures. Once resistance arises, it can make its way back to us.
At its core, the disinfectant dilemma is a feedback loop: we disinfect to prevent disease, but the chemicals we rely on may quietly make microbes harder to control.
Rethinking clean
This doesn’t mean we should stop disinfecting. Disinfectants play an essential role in infection control, especially in hospitals and high-risk settings where their benefits far outweigh their risks. The issue lies in their overuse in everyday life, where “clean” is often equated with “microbe-free”, regardless of necessity or consequence.
What we rarely consider is that cleaning doesn’t end when the surface looks hygienic. Some disinfectants remain active long after use, continuing to shape microbial communities well beyond their intended moment of control. QACs are a clear example: they persist in the environment, exposing microbes to low, chronic selective pressures that can favour the development of resistance.
Other disinfectants, such as alcohol and bleach, may carry different, but still meaningful environmental risks, underscoring the need for risk assessments that more explicitly integrate long-term ecological consequences.
Ultimately, the disinfectant dilemma reminds us that managing microbes is as much about ecology as it is about chemistry. To clean responsibly, we need to think beyond what kills microbes today and consider how our choices shape the microbial world we will face tomorrow.
