Intensive farming, superbugs + antimicrobial resistance

Wicked Leeks explores the alarming rise in AMR and joins the dots between food, farming and environment

We use vast amounts of antibiotics. Our natural environment is awash with them. The more antibiotics in our water courses, soil, manure and sewage, the more antimicrobial resistant (AMR) bugs we will see. And the harder it becomes to treat sick people in hospital. It’s a growing and deadly issue. Take the MRSA superbug which kills 2,200 British people and 33,000 in Europe a year. 

That’s because the drugs we use to treat or prevent infection aren’t fully absorbed by farm animals or humans. They wash out in urine and faeces, which can then be applied to land as fertiliser or spill out from water treatment plants. In a recent study in Scotland, genes resistant to common antibiotics were found to be present in every single soil sample that was tested.

Climate change is making AMR worse. Higher temperatures and moisture levels accelerate bacterial growth rates and the transfer of resistant genes. At the same time, there’s a push for the reuse of resources deploying more human and animal waste to farm fields. AMR is also compounded by microplastics, which are increasingly found, even in organic waste. Sadly, resistant microbes are even present in the humble earthworm.   

“Nobody is really aware that pharmaceuticals are there, because you can’t see them. People get angry at plastic or human waste in water because you can spot it with the naked eye,” explains Laura Carter, Associate Professor in Soil and Environmental Chemistry at the University of Leeds. “Yes, resistance occurs naturally, but when there’s excess pressure in the environment from antibiotics this speeds up the process. We need to do something about this, but there’s little public awareness.” 

The numbers are stark. A new United Nations Environment Programme (UNEP) report estimates that by 2050, ten million people a year globally could die because of antimicrobial resistance, this would make it as fatal as cancer. So what’s the chance of a new Covid-level, global infection coming from the very soil, water and nutrient cycles that nurture our crops and livestock? 

The consensus amongst scientists interviewed by Wicked Leeks is that we don’t yet have enough data, which isn’t helped by the fact that there are no agreed international reporting standards for AMR. Recently, post-Brexit regulations on antibiotic use on farms have also watered down tighter EU laws

This is a growing issue, flanked by emerging science, and scientists are only now beginning to invest in studies, collect more data and trace antimicrobial resistance genes more frequently in the natural environment. The early signs don’t look good. The scale of the issue is put into perspective when you realise that 7,600 deaths a year in the UK are directly attributed to antibiotic resistance, while 35,200 deaths are associated with it.  

The effects could be devastating

Take fungal diseases for instance. Aspergillosis causes millions of deaths every year. The mould mainly affects people with lung diseases, those with asthma, cystic fibrosis, even Covid. Certain strains of this fungus have now become resistant to anti-fungal treatments called azoles. This is why researchers have had up their game. 

An exciting new anti-fungal treatment, Olorofim is now showing great promise in clinical trials. This new class of antifungals, developed in the UK, has cost over £250 million to develop over two decades. It could be a lifesaver in hospitals across the globe. 

However, in parallel to this, a novel crop spray called ipflufenoquin is also being developed. This farm-applied fungicide deploys the same chemistry as Olorofim. It’s used to treat fungal infections in apples, pears, strawberries and blueberries. Now approved in the U.S. and Australia for spraying on farms, it’s also raising alarm bells. 

Scientists at the University of Manchester are worried about the use of this new fungicide. At some point in the future it could be used in the UK, where farmers have the potential to drive an outbreak of a super-resistant form of aspergillosis in humans by applying this chemical in the field. 

Sprayed composting waste from farms could cause the fungicide to accumulate in dark, damp conditions where the mould Aspergillus is likely to grow. Drug resistant spores are easily spread by the wind, ending up in urban areas and peoples’ houses. Its effects could be ‘devastating,’ according to scientists.   

Joining the dots between humans and the environment

Farm animals consume about 30% of all antibiotics in the UK and about 65% of antibiotics worldwide The Soil Association

“We need to have some sort of strategy and risk management in place that aligns both human and farm health. At the moment, the indirect effects of using fungicides, which might lead to soil microbes getting antimicrobial resistance are not within the remit of UK legislation,” states Norman van Rhijn, a research fellow at the University of Manchester who’s presently working on this issue. 

There’s certainly a need to join up the dots on AMR. A so-called ‘One Health’ approach is slowly gaining traction. This recognises the extensive links between the health of ecosystems, animals, farms and humans. Such an approach could eventually benefit farmers who are willing to reduce the use of antibiotics in livestock, fungicide applications or tackle AMR head-on, and it is being led by the World Health Organisation (WHO).

“It is particularly important to prevent, predict, detect, and respond to global health threats such as the COVID-19 pandemic,” state the WHO. “The approach mobilises multiple sectors, disciplines and communities at varying levels of society to work together. This way, new and better ideas are developed that address root causes and create long-term, sustainable solutions.”

“We’ve argued in a think tank situation, that if we are going to reduce AMR by, for example, reducing fungicide use, then farmers might get less profit,” continues van Rhijn. “But they could then be compensated from a single pot of health money. At the moment farming and human health are not matched up. Yet this is all related to the same pot when it comes to health and expenditure. It is actually one system that we are working with.”

Alarm bells over intensive farming  

Going organic could also help, since it does not allow the spread of human sewage on to land, nor permit chemicals such as fungicides to be used. This limits the potential to spread AMR in the natural environment; Soil Association certified organic farms that include livestock also have much lower levels of antibiotic use. 

Another potential hotspot for AMR is intensive livestock farming involving poultry, pigs and cattle. Stressed animals kept in highly intensive conditions face a significant risk of infection, since this is where bacteria thrive. 

“Farm animals consume about 30 per cent of all antibiotics in the UK and about 65 per cent of antibiotics worldwide. It is intensive farming systems that use drugs at unnecessarily high levels, putting human health at risk,” says the Soil Association. “Intensively reared pigs and poultry account for 79 per cent of UK farming antibiotic use, and there are a number of “critically important” antibiotics that are restricted in Soil Association’s higher standards. These antibiotics play a critical role in treating infections in humans and animals and if bacteria becomes resistant then the impact would be catastrophic.”

Unlike the EU, the UK government has refused to ban the practice of feeding prophylactic or preventative antibiotics to groups of animals, even when they’re not sick. It means they can still be used as a general, prophylactic treatment at low levels. In many cases it’s an easy vet’s sign off. 

About 75 per cent of UK farm antibiotic use is still for group treatments of animals, rather than treating individual sick animals. To put it into perspective, in Sweden group treatments account for only 10 per cent. Alarmingly there are no direct figures on the volumes actually deployed. It means we’ve still no real picture of the amounts being released into the natural environment. We still rely on the figures the industry reports on. It’s a challenge. 

For instance, when you think of industrial scale chicken farming in the River Wye area, where some 24 million birds are reared each year, highlighted by Wicked Leeks, then you realise that AMR could become an issue. Two years ago, UK rivers near livestock farms, including the Wye were found to be awash with superbugs and antibiotic residues, according to the Bureau of Investigative Journalism

New laws don’t go far enough  

Despite new UK laws passed in May, banning the routine use of farm antibiotics, there are loopholes. They can be used in exceptional circumstances as preventative treatments, because some farms will need to make ‘improvements to farm infrastructure and management practices’ to reduce or eliminate disease, and this can take time. 

The Alliance to Save our Antibiotics believes some farmers could therefore continue to pump animals with drugs to compensate for poor farm management practices. “Any farm that needs to treat their groups of animals prophylactically is, by definition, poorly run, which is due to poor animal husbandry,” states Coílín Nunan, scientist adviser at the Alliance.

“The growth of intensive farming in the UK is a major factor. So is excessive meat eating. If we had less intensive agriculture, we would have much lower antibiotic use. One of the issues that we’ve argued for many years is that we need better data, a statutory data collection system, which the UK is refusing to do. If there is a change of government, it will be interesting to see whether they will change their position on that.”

Unwittingly, that cheap chicken drumstick or pork shoulder joint on the supermarket shelves could eventually fuel the death of a hospital patient that’s succumbed to a superbug-induced infection after a vital operation. Or that pesticide-drenched, value punnet of strawberries, might just push that chronic asthma sufferer over the edge, when that fungal lung infection becomes untreatable.

Covid has shown us how quickly a killer pathogen can devastate humankind. Are we still ‘eyes wide shut’ as to the next pandemic? Are we unsuspectingly creating the ideal conditions through our food and farming systems that will create a new superbug? As Laura Carter says, it’s not obvious to the naked eye. Maybe it should be. With better data, better regulation, better antibiotic use and better agriculture, we can do better. 


Leave a Reply

  1. That is a frightening and quite shocking report that needs to feature in headline news bulletins. Only by informing the wider public and making the use of fungicide, pesticides and antibiotics a “plastic” type issue; will pressure be brought to bear on producers to change practices and government to legislate.

    1. The Mace and Knight Dec 2023 paper ‘Influenza risks arising from mixed intensive pig and poultry farms, with a spotlight on the United Kingdom’ highlights the specific zoonotic risk involved.

  2. There must be so much pressure from those in the industry to prevent concerned ministers doing something about this quite scary situation.


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