The rise of the superbugs - and why industrial farming is to blame

Over the past few months we’ve been inundated with alarming new evidence on how our industrial society is wreaking havoc upon other species and the rest of the natural environment. Not a week goes by without the emergence of a new report that stresses how the human-induced climate crisis is accelerating far beyond what scientists were predicting just a year or two ago. In April this year, a team of scientists published a report documenting that 40 percent of all insect species are in decline and could die out in the coming decades with catastrophic consequences for the natural ecosystems they are part of and the food crops they pollinate. As a partial consequence of this, the bird populations in France have collapsed by one third in the last decade and a half, according to another report. Now a UN-backed global study - compiled by 145 expert authors from 50 countries- found that we’re driving over one million plant and animal species into extinction; that is one out of every eight currently in existence – a process that is also accelerating.

In the midst of all this destruction, little is known about what is happening to the invisible microorganisms and the role they play in maintaining and balancing ecosystems. It transpires that they might be fighting back in a way that could have disastrous consequences for humanity. In April, a report submitted to the UN Secretary General drew attention to the escalating crisis involving new ‘superbugs’ that are building up resistance against commonly used medicines. The risk of death from what are currently considered easily treatable common diseases is becoming a real threat as medicines like antibiotics simply stop working when microbes become resistant to them. Today, some 700,000 people die every year because of antimicrobial resistance but the report warns that by 2050 over 10 million people could die annually, more than the amount of people that currently die of cancer.

The development of antimicrobial resistance to commonly used medicines has been worrying scientist and policymakers for a number of years now. The demand for antimicrobial medicines is on the rise, and with it are the superbugs. The global market for antibiotics stood at some $42 billion in 2017, but is projected to reach $50 billion by 2025. The United States is a key consumer, accounting for more than one-fifth of the global market but, according to one study, nearly one in three antibiotics prescriptions given to people in that country are unnecessary. Analyses from the OECD show that inappropriate use may account for up to 50% of all antimicrobials consumed in human health care. To make a bad situation worse, there are hardly any new types of antibiotics in the pipeline as pharmaceutical companies claim a lack of return on investment. Some have described the situation as a ‘silent tsunami’ in waiting as more and more people will become exposed to diseases that cannot be cured.

The main driver behind the increased use of antibiotics is not humans, but animals reared for food in factory farms. Currently, in the EU and the US, over 75% of all antibiotics are used in agriculture, while BRICS countries are projected to experience a 99% growth in antimicrobial consumption by 2030, largely due to the continued expansion of factory farming. Total global consumption of antibiotics in animal food production is projected to grow by almost 70% between 2010 and 2030.

This escalation is largely caused by factory farms that use massive amounts of antibiotics to promote growth and prevent diseases on healthy animals. The use of antibiotics in industrial livestock for growth enhancement has been banned in Europe since the 1990s, and in the US only as recently as 2017. But in many countries in the world this is still a common and growing practice. On the other hand, their non-therapeutic use on healthy animals from birth to slaughter, especially in poultry and pigs, is growing everywhere. This is needed due to the crowded conditions in which the animals in factory farms are being raised, as it is impractical to diagnose and treat the animals individually. These crowded conditions also make for a perfect breeding ground for the bacteria to develop resistance. The situation in industrial aquaculture, in which antibiotics are used from egg to adult, is similar or worse.

Antibiotics are not fully digested and processed in the gut of animals, leading to a situation where up to 90% of the ingested antibiotics becoming excreted in the animal’s urine and/or feces which is often used as fertiliser on crop fields and thus contaminates soils and groundwater. The drug-resistant bacteria can also find their way into humans through both direct contact with the animals and through the consumption of meat and dairy which contains the resistant bacteria. Humans and farm animals share many of the same microbes in their systems and thus similar antibiotics too. The OECD reminds us that of the 27 classes of antibiotics currently available, only seven of them are used exclusively in agriculture; the remainder are used also for human health. With no new antibiotics having been developed for over 40 years, factory farming and its massive use of antibiotics is a clear threat to the antibiotics that humans use as they contribute to the build-up of antibiotic resistance everywhere.

The issue goes beyond the indiscriminate use of antibiotics in factory farming. In April this year, the New York Times published a disturbing article about a man in New York who had died from a newly discovered germ as deadly as it was mysterious. The germ, a fungus called Candida auris, preys on people with weakened immune systems and is quietly spreading across the globe. The man died after 90 days in the hospital, but C. auris did not. Tests showed it was everywhere in his hospital room, “so invasive that the hospital needed special cleaning equipment and had to rip out some of the ceiling and floor tiles to eradicate it.” The fungus, which was first discovered in 2009 in Japan is resistant to all the major antifungal medications we have at our disposal and has now spread across the globe. Nearly half of the people that contract it die within three months.

The NYT article establishes a possible link between the emergence of this deadly fungus and usage of a type of agricultural fungicide: triazoles, the same chemical used to treat fungal diseases in humans. Globally, triazoles have become the most used fungicide in agriculture, being sprayed on everything from begonias to beans to bananas. But its widespread use in farming is possibly connected to the emerging resistance of human fungal diseases to medicines. While the link to the resistance of C. auris is still speculative, it has been clearly documented in the case of another fungus that affects both humans and crops: Aspergillus fumigatus. In humans it can cause fatal infections for immune-compromised patients, and it has become resistant to triazoles. A team of Dutch researchers found that this resistance has built up within the Dutch flower farm industry that sprays triazoles routinely and intensively on their fields. From soil samples it was found that 30% of the Aspergillus present in them were resistant to the fungicide, the same resistance as the one in the human medicine.

Another threat that undermines our capacity to combat deadly diseases in humans comes from a more unexpected culprit: weedkillers. Herbicides like Roundup and Camba are used across the world to kill weeds. The amounts used have substantially increased over the last few decades as agrochemical companies have genetically modified crops to become more tolerant to them, meaning that farmers can apply herbicides as much as they like without harming the crops. Now, a New Zealand research team found that these weedkillers affect bacteria too. Their study, published in October last year, shows that when bacteria are simultaneously exposed to herbicides and antibiotics, mutants with higher levels of resistance can evolve. “In some cases, resistance evolved 100,000 times faster,” the researchers claimed. How and why this happens is not exactly clear yet. What is clear is that, in industrial farming, antibiotic and herbicide residues are bound to meet often.  Jack Heinemann, one of the authors of the study, warns the countries that are growing GM crops at scale: “[they] may wish to include these unanticipated effects on microbes in their evaluations.” Referring to herbicide-antibiotic combinations, Heinemann adds that “such combinations can be like trying to put out the raging fire of antibiotic resistance with gasoline.”

Massive use of antibiotics, fungicides and herbicides in industrial farming is contributing to the undermining of live-saving human medicines. Governments and intergovernmental agencies have created task forces, working groups and guidelines to deal with the rise of antimicrobial resistance. But none seem to want to confront one of the root causes. Is this not further evidence that it is time to move away from industrial farming and turn to agroecology and food sovereignty instead? This would also help to eliminate one of the key causes behind the collapse of species populations across the world, as well as one of the central culprits behind the climate crisis.