The use of antibiotics in conventional livestock production has made meat cheap and abundant, but it has also contributed to the spread of antibiotic-resistant bacterias like E. Coli and Salmonella.
Now, a new drug-resistant pathogen is spreading rapidly through hospitals and nursing homes around the world that might also be linked to the overuse of agricultural chemicals. But in this case, the pathogen is not a bacteria. It’s a fungus: Candida Auris.
People don’t often think about fungi when they think about pesticides. But for many farmers, fungus is as big a threat to their crops as bugs or weeds. This is especially true for 1) farmers in high-rainfall areas and 2) orchard and vineyard crop growers. These farmers often apply more fungicides to their crops each year than insecticides (bug killers).
Farmers in any area where it rains frequently during the growing season simply could not produce many crops without extensive use of fungicides. Rain — especially warm rain — creates an ideal environment for fungus to grow on many crops. Climate change is likely to increase overall humidity and rainfall in many growing areas, leading to higher fungal pressures.
But even in relatively dry environments like California, tree and vine crops normally require treatment with fungicides. Powdery mildew is an extremely pervasive fungus that exists all over the world. It doesn’t affect only grapes, but for grape growers, it is the biggest threat to their crop. Most grapes are sprayed several times every season for mildew, including organic ones. Almonds, which are now the most valuable crop in California, bloom in late winter when brown rot fungus can infect the trees and kill the crop before it even gets started. The trees must be sprayed with fungicides during this period; the same goes for peaches, pistachios, walnuts and other deciduous tree crops.
How could use of fungicides to kill agricultural infections cause antibiotic resistant human pathogens? Well, farmers use many of the same types of chemicals to control fungi on their crops that doctors use to control them when they infect humans. The Candida fungus that is causing alarm among doctors appears to have become resistant to almost every known anti-fungal medication (aka fungicide). It can’t have developed that resistance from overuse of drugs to treat it, since it is a relatively “new” human pathogen.
Nor is the Candida fungus an agricultural pest. But it might have been an innocent bystander in an ecosystem that was being regularly sprayed with fungicides to kill a different pathogen. Where other fungi died, it survived and thrived. And once it found its way into a fairly sterile environment like a hospital or nursing home, it would have little competition from other pathogens that are killed by sterilants. In the facilities it has infected, it has been found in every nook and cranny of every imaginable surface. And it has mutated into a form that makes people sick.
For many years organic farmers had a very limited number of fungicides available, including elemental sulfur and copper. But in recent years, a number of “biological” fungicides have been introduced. Many of them are so-called “beneficial” fungi that either parasitize the bad fungi, or simply out-compete them for space on the plants.  Because of how they work, they are very unlikely to cause “bad fungus” to mutate.
The main downside to biological fungicides is financial. Because they are living organisms, it is more expensive to produce them and they have to be applied more frequently than systemic chemicals. Organic growers can pass these expenses onto their customers; conventional farmers cannot.
The development of drug-resistant fungi like Candida Auris could very easily cause a public outcry that will lead to calls for restrictions or bans on the use of many fungicides in agriculture. Any effort to take such an action would have to very carefully consider the impact on the world’s food supply to ensure that actual alternatives exist to whatever chemicals were targeted.
Thanks to organic agriculture and the demand for its products, there are a number of effective and safe alternative fungicides. But unless and until conventional farmers switch to them, buying organic is the best way for consumers to avoid contributing to the development and spread of fungal “superbugs”.