Drug-resistant fungus could be lurking in your compost, but you can reduce the risk

A pile of food scraps and compost materials.

A compost bin reduces waste and your carbon footprint. But it could also be making you sick. Ben_Kerckz / Pixabay

Collecting compost is a common practice in any environmentally-conscious home. Not only is creating this natural fertilizer an easy way to reduce household waste, but the organic matter also adds valuable nutrients to the soil and has even been shown to suppress harmful pathogens that can thrive underground. However, a new study published in Nature Microbiology reveals that a drug-resistant fungus may grow in compost and infect humans that inhale its spores. 

The culprit, Aspergillus fumigatus, is a common fungal pathogen that has infected people all over the world, including over 2 million in the European Union alone. But the drugs typically used to treat A. fumigatus have become less effective in recent years, and this drug resistance puts at-risk populations like leukemia patients in even greater danger.

Similar to how some bacteria can become drug-resistant after encountering antibiotics, antifungal resistance may result from exposure to agricultural fungicides, the study says.

With that in mind, it’s important for eco-friendly gardeners to keep themselves safe.

Know what’s compostable and what’s not

One easy way to maintain a clean compost bin is by adhering to a strict list of compostable goods. The Environmental Protection Agency recommends adding equal amounts of “greens” and “browns” to compost, and the proper amount of water. Only composting the recommended items will help keep your compost bin efficient and clean.


Fruits, vegetables, coffee grounds, grass clippings, tea bags, eggshells, houseplants, leaves, hair, and yard trimmings all fall into this category. They provide nitrogen that will fuel photosynthesis and plant growth.


Consider these your compost’s carbon source. As the building block for cells, carbon is an energy source in soil. Dead leaves, branches, nut shells, shredded newspaper, shredded cardboard, hay, straw, sawdust, and wood ash all satisfy this need.

What not to compost

However, there are several items the EPA warns against composting. Never compost any part of a black walnut tree, as their leaves, twigs, and branches can release toxic substances that may hurt your garden. And while wood ash is a good source of carbon in compost, coal and charcoal ash is potentially harmful to plants. Dairy products, fats, animal and fish scraps, and eggs all smell bad and risk attracting rodents and flies. Pet waste and diseased plants both risk introducing illness and parasites into previously healthy compost. In addition, yard trimmings treated with chemical pesticides could kill the beneficial microorganisms that help compost organic materials. 

Satisfy your compost’s need for speed

To help your compost… compost, you should chop and shred all your materials. This creates more surface area on your scraps for microorganisms to latch onto and helps them decompose the natural materials faster. Papers and branches can be shredded, and food scraps can be chopped or crushed. 

The volume of your container can also help move microbes along. Cornell’s Waste Management Institute says containers between 3 and 5 feet cubed (27 to 135 cubic feet) will create the fastest compost. Smaller containers struggle to hold in the heat generated during composting, and larger containers make it difficult for air to reach the internal microbes. During dry periods, adding water will also help the decomposition process by sustaining microbes.

[Related: How to start composting at home]

To determine if your compost is breaking down quickly, just take its temperature. Microorganisms produce heat when they decompose organic material, and high heat is associated with fast decomposition.

High temperatures also help keep compost safe. The EPA says that to significantly reduce pathogen numbers, compost should be kept at 104 degrees Fahrenheit for at least five days, and over 131 degrees for at least four hours within that same timeframe. This time helps destroy fly larvae, weed seeds, and some pathogens sensitive to temperature. However, most microorganisms cannot survive in temperatures above 140 degrees, so if your compost starts to approach that benchmark, you should mix it up to cool it down.

After this stage of rapid decomposition and high temperatures, which may take weeks or months, decomposition will slow and your compost’s temperature will drop. The final stages of composting help stabilize the stuff so you can use it in your garden.

How to keep mold out of your compost bin

Unfortunately, you simply cannot clear all microorganisms and fungi out of your compost bin. Compost needs microorganisms and fungi to turn waste into fertile compost. In addition, A. fumigatus is so common that people inhale its spores repeatedly throughout the day. Most people can breathe in the spores with no reaction. But when it infects immunocompromised patients, they face severe health risks, including death. With so many spores around, Cornell recommends several key safety measures beyond proper composting materials and temperature control.

  • Good hygiene: Washing your hands, avoiding touching your face, and other childhood cleanliness skills are still useful. By practicing basic hygiene, composters can mitigate the risks of compost microorganisms.
  • Mask up: Don’t throw away your masks quite yet (for several reasons). N95 respirators are approved by the National Institute for Occupational Safety and Health to prevent inhaling small mold particles. Gloves can also keep mold spores off your hands.
  • A breath of fresh air: If A. fumigatus spores are introduced to the home, there are several ways to prevent a build-up. Fix leaks, keep humidity levels low, and clean bathrooms with products that kill mold. The easiest method, however, is to keep your windows open. Maximized airflow will help avoid a build-up of the airborne spores.
  • Know your limits: Immunocompromised individuals are at the greatest risk for infection by drug-resistant A. fumigatus. The latest study indicates a risk to humans due to these evolving spores, and the Centers for Disease Control and Prevention notes that drug-resistant fungi have severely limited treatment options. High-risk gardeners may be advised to avoid composting, and Cornell recommends using caution when handling compost.

Fungi, of course, have existed for nearly 1 billion years on Earth, and they are an unavoidable part of composting. But if you take time to maintain a clean compost bin, pay attention to compost temperatures, and stay hygenic, you mitigate the risk that the bad microorganisms will outweigh the good.