Superbugs and farming: Unchecked use of anti-fungals in modern agriculture is responsible for rise of deadly germs
Candida auris is a dangerous fungal infection that emerged in 2009 in Japan and, in just a few years, has spread round the world.
One reason for its superbug status is the indiscriminate doling out of antifungals by the medical community.
But even more harmful is the use of antifungals in modern agriculture/animal husbandry.
Global sales of fungicides have tripled since 2005, from $8 billion to $21 billion in 2017.
Candida auris is a dangerous fungal infection that emerged in 2009 in Japan and, in just a few years, has spread round the world, especially in hospitals. It is a superbug: a germ that has evolved defences against common medicines and cannot be treated by the fungal medications currently available, such as fluconazole, the standard anti-fungal drug in many countries, and echinocandins.
Once the germ embeds itself, it is hard to eradicate it from a facility. Some hospitals have had to bring in special cleaning equipment, and even rip out floor and ceiling tiles, to get rid of it.
Candida auris is a life-threatening fungus with a high mortality rate. It has been identified in Japan, South Korea, India, Pakistan, South Africa, Kenya, Kuwait, Israel, Venezuela, Colombia, the United Kingdom, Canada, and the United States. It is probably present in other countries as well, but scientists have not been able to identify the fungi in the absence of the specialised laboratory methods needed to do so.
People with weakened immune systems are the most vulnerable to this fungus — newborns, the elderly, people who are sick with other infections, diabetics, and people who have undergone broad-spectrum antibiotic or anti-fungal therapy. The rise of C auris has received little publicity because it is relatively recent. Outbreaks have been played down, or kept confidential, by hospitals and even governments, as publicising an outbreak would scare people into not going to hospitals. In America, even the Centre for Disease Control is not allowed to make public the location or name of hospitals that have seen C auris outbreaks.
The initial symptoms of C auris — fever, aches, fatigue — are not unusual, so it is hard to identify the infection without testing. The next step is blood poisoning/sepsis, coma, organ failure and ultimately, death. The fungus can colonise on human skin, or surfaces, and stay alive for a long period, allowing it to spread to new patients.
One reason for its superbug status is the indiscriminate doling out of anti-fungals by the medical community. But even more harmful is the use of anti-fungals in modern agriculture/animal husbandry.
It is clear that Candida auris’s resistance can be traced to industrial agriculture’s mass application of fungicides that are similar in molecular structure to human anti-fungal drugs.
Wheat, banana, barley, apple, potatoes, soya bean, grapes, corn, stone fruit are some of the varied crops on which fungicides are used.
Before 2007, six main classes of fungicides were rarely used: azoles, morpholines, benzimidazoles, strobilurins, succinate dehydrogenase inhibitors and anilinopyrimidines. Now their use is common, with azoles leading the pack. Azoles, used in both crop protection and medicine, are broad-spectrum fungicides, annihilating a wide range of fungi.
It cannot be mere coincidence that C auris has developed resistance to the azole anti-fungals, including fluconazole, amphotericin B, and echinocandins. C auris has probably been fought off for centuries by the human system. It is only now that it has become immune to human intervention, and succeeded in entering the bloodstream.
In an effort to identify the source of the infection, an international team collected fungal germs from hospitals across Pakistan, India, South Africa, and Venezuela in 2012–2015.
They found azole resistance in all – but the strains were varied and related to the fungicide that was used in that country. In response to wide exposure to fungicides in the field, each strain evolved its own unique solution to the problem. This fungus spread and diversified because patients and crops (through agricultural trade) migrate.
In 2015, scientists discovered that the C auris genome had several genes of a superfamily (MFS). An MFS effectively destroys broad classes of drugs. It permits C auris to survive an onslaught of anti-fungal drugs. They also found that the C auris genome also had many genes that increased its virulence.
Candida auris is not the only fungus on the cusp of a multidrug resistance. Many more, which affect both plants and humans, are becoming resistant to medication.
One fungus, Aspergillus fumigatus, causes infection in the lungs and is a major cause of mortality. Azole anti-fungals, itraconazole, voriconazole, and posaconazole have long been used to treat pulmonary aspergillosis. In the last decade, the fungus has developed resistance to these drugs, causing the death of lakhs of people worldwide every year.
Studies comparing long-term azole users and patients just beginning to take the drug have shown that drug-resistant A fumigatus was to be present in both groups, suggesting that resistance came from the food that they ate and the anti-fungals used in fields, rather than in the medicine administered to them. Agricultural rather than medical reasons are at the root of the malaise.
Scientists have found, in several field studies, prevalence of fungicide-resistant A fumigatus in the soil and crops across the world. In simple terms, due to agricultural practices, Aspergillus is entering hospitals already adapted to the slew of anti-fungal cocktails designed to check its spread. By using azoles to control fungi on fruit and grain, conditions have been laid to accelerate drug resistance in human patients.
Interestingly, Aspergillus fumigatus and Candida auris share similar geographical distributions. One would have thought that the spread of these two fungi would have been enough for governments to acknowledge the acute danger people were in, and to phase out all fungicides.
Instead, government policy has actively promoted the expansion of fungicide use. Agricultural azole fungicides comprise a third of the total fungicide market. Twenty-five different forms of agricultural azole fungicides are being used in millions of tonnes, compared to just three forms of medical azoles. Fungicides use to control soyabean rust have quadrupled between 2002 and 2006. Thirty percent of corn and wheat crops had fungicides applied in 2009; now, it is more than 50 percent. Boscalid fungicide is now commonly used in fruit and vegetables. As many as thirty-three different fungicides are used on potatoes.
Global sales of fungicides have tripled since 2005, from $8 billion to $21 billion in 2017, expanding not only in the quantity sold, but also in their geographic distribution.
And, of course, all the fungicide leaches into ground water, and you drink it.
Climate change brings heavy unseasonal rains and droughts and higher temperatures. This means more fungi. And more fungicides. Unless the government finds a more organic way forward.
Instead of blaming hospitals and hospital workers for contamination, we should be looking at ban of anti-biotics and fungicides in agricultural use. Several Indian agriculture ministers, and prime ministers, have promised in Parliament to do so – but have gone on to do the exact opposite. As time passes, companies will propose more genetically modified crops to, supposedly, combat fungi, and these will prove to be as deadly as GM Cotton and require even more deadly fungicides in time. As I see it, large chemical companies run governments and the world. And you and I are the victims.
There is so much empirical evidence that simply rotating crops and putting different crops together, like soya bean and flax, can effectively remove fungi. In California, strawberry producers have found that planting broccoli, between rotations of strawberry crops, removes fungus.
Scientists have discovered that rather than using azole fungicides to control blight in potatoes, silica is much better.
Organic farming supports good fungi, which crowd out pathogenic fungi. Reducing chemical fertilisers and limiting tillage creates strains of fungi that form beneficial relationships with plant roots. Crop rotations, the incorporation of legumes, and the cultivation of soil aggregates, instead of burning, create good conditions for soil microbiota.
Leaving small wild areas in cultivated land also removes fungal depredation. For instance, a study done by University of Michigan and Vandemeer, on agroecological fungal control in coffee in Mexico and Puerto Rico, found Mycodiplosis fly larvae, from nearby wild areas, feed on the coffee rust.
What we are doing to our farmers is giving them absolutely the wrong information and tools – of which fungicides are one. Monocultures need fungicides and both cause disease. Agribusiness, and their governments, views nature as their enemy. So wiping out local ecologies and the benefits these offer in helping farmers enrich their soils, clean their water, pollinate their plants, feed their livestock, and control pests — pathogenic fungi among them — means the largest companies can now sell their poisons to a captive market.
There must be some reason that successive Indian governments have refused to train agricultural scientists, and are happy to have totally ignorant people working in Krishi Vigyan Kendras. Could it be a business plan? Financed not just by pesticide companies but by hospitals and the medical industry as well? Is there any difference between the rich and poor if neither has food safety?
Long before climate change finally does us in, it is catastrophic superbug outbreaks which would have wiped out millions. While data is available, it is rarely taken seriously by politicians. In the US alone, two million illnesses and thousands of deaths are caused by drug-resistant infections. In India, it would be at least a crore, because we use medicines indiscriminately on animals grown for food and on crops.
An intelligent, far-sighted and humane government is the need of the hour.
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