Death rates for female pigs (sows) in the U.S. are rising fast and alerts are up throughout the farming industry. The mortality rate rose from 5.8 percent to 10.2 percent on farms owning more than 125 sows between 2013 and 2016, according to The Guardian.

The numbers have been linked to a rise in prolapse — the collapse of the animal’s rectum, vagina or uterus — which can be fatal. While the deaths of the animals may not be rising industrywide, some farms are seeing prolapse causing as many as 25 percent to 50 percent of sow deaths. In response, the American Association of Swine Veterinarians has created a sow prolapse working group to investigate.

In April, the National Pork Board announced a multi-year research collaboration with Iowa State University’s Iowa Pork Industry Center, designed to get a broad overview of the problem. Iowa is the nation’s top pork producer.

The study will collect data from 400,000 sows — or about 13 percent of the nation’s 3 million working sows — on more than 100 farms across 16 states.

A number of possible causes have been suggested, including vitamin deficiency, mycotoxins in feed and high-density diets. The result might be nothing related to diet, but instead confinement systems in which the breeding sows spend most of their lives in gestation and farrowing crates. The animals are not allow to move or turn around.

A blunt fact unknown to most is that about 97 percent of the U.S.’ 73 million hogs are raised in closed barns or confined feeding operations. In this system, the USDA says that the average sow produces more than 23 piglets per year.

Mary Temple Grandin, professor of animal science at Colorado State University and consultant on the design of livestock-handling facilities, told The Guardian that “highly focused breeding across the industry has led to unintended consequences” and that one side effect “is an increased tendency toward lameness.”

Iowa leads the nation in pork production and is experiencing a rise in large hog operations. According to the most recent U.S. Department of Agriculture census, as of 2012, total hog production in in the state rose from 14.3 million a year to 20.5 million, but the number of farmers producing hogs dropped from 45,768 to 6,266 since the early 1980s.

The increased hog production means the remaining pig farm owners have built large-scale facilities that keep the animals indoors where their food and waste can be controlled, and the animals can remain constantly bred. These high-breed facilities also are leading to the rising number of sow deaths, and an increase in environmental pollution.

According to Civil Eats, these operations also fall under the Environmental Protection Agency’s Clean Water Act. Concentrating animals in one location requires more strict manure management than animals raised on pasture.

Large farms produce millions of gallons of manure a year, which is more fecal waste than is produced in some American cities, according to the National Association of Local Boards of Health. The manure in most hog facilities falls through slatted floors into holding tanks. Then it’s hauled off and spread as fertilizer for crops.

Manure from these organizations can contain E. coli, MRSA, antibiotics and animal growth hormones. When the manure is not spread properly, these contaminants pollute waterways and private wells, as well as contribute to the rise of antibiotic-resistant bacteria.

According to Local Boards of Health group, “states with high concentrations of CAFOs experience on average 20 to 30 serious water quality problems per year as a result of manure management problems.” And, all manure lagoons leak, the EPA says.

Founded in early 2017, an agency called Northeast Iowans for Clean Air and Water is lobbying and fighting for changes to the breeding organizations, advocating and supporting legislation to stop the construction. Water quality is a chief concern for members of Northeast Iowans for Clean Air and Water and is something its members say they cannot necessarily protect. Some hog facilities are near rivers, where manure runs off when a tank leaks or heavy rains fall.

Individuals and organizations in opposition to these large-scale facilities say they should be treated like the factories and corporations instead of being given pollution tax exemptions and land zoned for agriculture and are free from many of the environmental and public health regulations other operations generating similar amounts of waste must follow.

The EPA’s Clean Water Act only regulates confinements of more than 2,500 hogs. Otherwise, the EPA does not regulate the confinements unless they dump waste directly into a waterway.

A study from Iowa State University and the University of Iowa determined air emissions from concentrated animal feeding operation (CAFOs) “constitute a public health hazard.”

About one in four CAFO workers in the U.S. suffers from a respiratory disease, such as bronchitis and asthma-like symptoms. A study of North Carolina residents found people living near CAFOs faced an increase in the same respiratory diseases suffered by CAFO workers.

Many advocates point out failures in the design of the state’s master matrix, which guides the siting of proposed operations. The process awards points depending on the building’s distance from homes, schools, and water sources; the overall point score determines whether a project is approved and where it’s sited. A 2018 study found the DNR approved 97 percent of requested building permits.

Confinements of up to 1,249 hogs do not need to create a manure management plan or file a construction permit. Confinements of up to 2,499 hogs do not need a construction permit.

According to DNR data, 3,745 sites in Iowa have fewer than 2,499 hogs, but a 2017 report using satellite imagery identified more than 5,000 hog and cattle lots in Iowa the DNR did not know about; more than 1,000 of them believed to require state oversight.

Iowa isn’t the only state with a growing CAFO presence. Trouble with CAFOs and environmental damages got national attention in 2016 in North Carolina when Hurricane Matthew flooded manure lagoons into waterways and the Atlantic Ocean; Hurricane Florence has flooded manure lagoons again. Similar issues are arising in Kansas, Wisconsin, Michigan, Arkansas, Illinois and Minnesota.

According to the USDA, the United States has more than 45,000 CAFOs.

The high incidence of animal loss in confinement systems is one of the main reasons that Paul Willis, co-founder of Niman Ranch — a subsidiary of Perdue Farms — has focused on smaller, alternative hog farming practices where the pigs are free to roam and wallow. “I have a neighbor that has been raising pigs [in a confinement system] … and they have a dumpster, and I can go by there almost any time of the day or week and it’s full of dead hogs,” Willis told The Guardian.

When he was raising hogs at a smaller scale, perhaps 200 to 300 at a time, and allowing them to spend time outside, engaging in behaviors that are typical for hogs, such as wallowing and building nests out of straw, Willis said he’d lose just “a few animals a year.”

Under this system, pigs only produce about half as many offspring a year as they do in industrial systems. Operations like these also don’t produce the pollution and environmental issues as their bog breeding, high population counterparts.