BLOG: Disease outbreaks and mass killings are the predictable consequences of industrial factory farming

August 12, 2025

By Sylvie Boucher, Communications and Fund Development Associate

When a major disease outbreak occurs on a factory farm and is suspected to be zoonotic in origin, terms like “depopulation,” “mass animal mortality management,” and “decontamination capabilities” begin to circulate. These sanitized phrases obscure a harsh reality: a large-scale, systematic killing of farmed animals is underway to contain the disease. This practice, often framed as a necessary response to prevent further transmission, is not random, nor the fault of animals being “dirty” or “disease-ridden.” Instead, it is a direct and predictable consequence of the industrial farming model. The blame lies not with the animals but with the corporate-driven industrial animal agriculture system that depends on the conditions that cause just such a crisis. 

Factory Farming and the Spread of Disease 

Modern industrial farms rely on extreme density by packing thousands of animals into confined, unsanitary spaces where they are forced to live in close proximity to their waste and each other. This environment is a perfect breeding ground for infectious disease, allowing viruses to spread rapidly across herds and flocks. 

When a contagious disease such as Highly Pathogenic Avian Influenza (HPAI) or African Swine Fever is detected, agencies like the USDA implement a “stamping out” policy. This approach mandates the killing of entire herds or flocks (potentially millions of animals) regardless of how many are actually infected. 

The scale is staggering. During the 2014–2015 HPAI outbreak, the largest animal health emergency in U.S. history at that point, nearly 50 million birds were killed or died. Similarly, during COVID-19, slaughterhouse disruptions led to the killing of millions of birds and hundreds of thousands of pigs. The most recent HPAI outbreak has cost the lives of over 280 million birds across the globe since 2021.

But instead of addressing the root causes that facilitate the rampant spread of disease in densely confined factory farms, the animal agriculture industry has developed training programs and infrastructure for mass animal depopulation, carcass disposal, and decontamination, all intended to kill and dispose of animals more efficiently. The industry is aware that the scale of industrial animal agriculture will inevitably induce public health crises. However, instead of trying to prevent outbreaks at the source, the industry's growth-driven mindset prioritizes preparing to efficiently suppress them once they occur.

Funded Training for Mass Mortality Events at Clemson University  

Two such training programs were recently funded by USDA’s Animal and Plant Health Inspection Service 2023 National Animal Disease Preparedness and Response Program. The first, titled South Carolina Subject Matter Expert Mass Animal Mortality Management Training, ran from March 2023 to February 2025 and received $85,648 in funding. The second, Enhance the Capacity and Capability of Responding to Depopulation Events in South Carolina and Southeastern States, spans from September 2023 to August 2025 and was awarded $482,498. Both are being implemented by Clemson University Livestock-Poultry Health which serves as South Carolina's animal health authority, responsible for disease control, meat and poultry inspection, and emergency preparedness for mass animal killing events. 

These trainings were designed for scenarios where “a large number of poultry and swine may die or require depopulation” during infectious disease outbreaks. A USDA APHIS report obtained by Animal Partisan details one of these projects: training up to 25 responders as carcass disposal subject matter experts (SMEs). With $85,648 in funding, trainees learned how to compost poultry carcasses, measure the temperatures needed to inactivate pathogens, and troubleshoot decomposition processes. Photos from the training showed decomposing chickens and coyotes scavenging near compost piles at night. 

The rationale for these trainings is economic protection. When asked to justify the need for these projects, the response was: “The impact and value of this project will help SC or a regional state respond rapidly and effectively to stop the spread of disease to other farms, which could save millions of dollars.” In other words, animals are treated as disposable commodities of a profit-driven machine. 

The Methods of Mass Killing 

The depopulation methods outlined in one of the trainings are efficient, brutal, and designed for scale: 

• Foaming: A water-based foam is used to suffocate birds kept on floors in confined spaces. As they inhale the foam, the birds suffer from “terminal convulsions, and altered terminal cardiac activity.” (E.R. Benson, et al. 2012).  

• CO₂ Gassing: Carbon dioxide chambers are used to render animals unconscious before death. To maximize efficiency, animals may be gassed and then manually killed via neck-breaking or decapitation. For large numbers of pigs, specially designed chambers are required to ensure lethal gas levels, making pigs unconscious in two minutes and dead in ten (AVMA Guidelines). 

• Captive Bolt: A captive bolt device delivers a concussive blow that instantly destroys an animal’s brain. This method, used across species, is praised for its “efficiency” in mass killing (AVMA Guidelines).  

These are not methods of mercy or welfare. They are tools of expedience, developed not to minimize suffering, but to maximize speed in an emergency of the industry’s own making. The trainings extend to carcass management, composting, and other disposal strategies which reveals the industry’s chilling preparedness for recurring mass death events. 

This is not merely a disease problem, it is a structural failure. The animals trapped in factory farms are often selectively bred for rapid growth, which compromises their immune systems. Their extreme confinement ensures that when disease strikes, it spreads rapidly and widely. The “stamping out” policy is not a solution but a symptom of an industrial coping mechanism for a system designed to implode. 

Animals should never be in these conditions to begin with. They are living, breathing sentient beings who deserve respect, compassion, and a life free from suffering. 

The recent training in South Carolina was deemed a success. Instructors called it the “best Compost SME training to date,” and trainees found value in digging through month-old carcass piles to study decomposition. These are the outcomes celebrated in a system that not only creates its own emergencies but hones its ability to manage the aftermath, just in time for the next emergency.  

We don’t need more efficient ways to kill and compost animals. We need to question and dismantle the system that makes this so routine.

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