(CNN) Even after a hurricane's immediate threat of flooding goes away, North Carolina residents could face a host of potential health problems from the water brought by Hurricane Florence -- and from what that water leaves behind . In addition to the usual physical and mental challenges floodwaters can typically bring, there is a potential problem for human health that involves some of the state's key industries: hog farming and coal power generation.

Hog farms flooded out

An earthen dam surrounding a hog lagoon was breached by floodwaters in Duplin County and in Sampson County , according to North Carolina Department of Environmental Quality Secretary Michael Regan . As of Thursday, four other lagoons have structural damage.

Hog or swine lagoons are human-made pits or dugouts that store animal waste. The lagoons are meant to help reduce pollution, and the the North Carolina Pork Council says it's "rare" for lagoons to overflow, but there are reports of at least 30 lagoon "overtops," the department said. There are 21 reports from the Department of Environmental Quality of hog lagoons being inundated by nearby bodies of water as well as of Thursday.

The North Carolina Pork Council said that one of the lagoon breaches in Duplin County was at a small farm and that an on-site inspection showed "that solids remained in the lagoon." There was no mention of whether there were any solids being released from the other lagoons that had structural damage or were inundated by floodwaters. The council said the other 3,300 lagoons in the state are in good shape, and the Department of Environmental Quality will do inspections when it can.

The North Carolina Pork Council said it will also watch the situation closely. About 8.9 million pigs are raised on 2,100 farms across the state, and although farmers "took extraordinary measures" ahead of the storm, including moving thousands of animals to higher ground, they have suffered losses.

The North Carolina Department of Agriculture and Consumer Services says the state has lost about 5,500 hogs. By comparison, North Carolina lost 2,800 swine to Hurricane Matthew in 2016. Farmers have also lost 3.4 million poultry to Florence.

Those numbers are expected to grow inspectors are still unable to access all the farms and rivers haven't crested everywhere, meaning flooding will get worse.

"We know agricultural losses will be significant because the flooding has affected the top six agricultural counties in our state," said Agriculture Commissioner Steve Troxler, who conducted an aerial survey of damage Tuesday.

"We remain concerned about the potential impact of these record-shattering floods," the North Carolina Pork Council said on its website . "We are continuing to assess the impact and expect to provide further updates later."

Hog farmers are required by law to report when a breach happens. Deputy Communications Director Bridget Munger said there may be other problem areas, but the staff has had to gather these reports quickly under difficult circumstances. The department's Wilmington office had no power, and the staff in Fayetteville had to be evacuated due to flooding.

"We are processing the information as quickly as we can, as it is coming in," Munger said. The department will have a larger report out later.

It's unclear how much waste is in the storm water, but the waste pits contain bacteria like E. coli and Salmonella. Exposure to feces can cause kidney problems, vomiting, fatigue, stomach problems , skin infections and other issues.

"The industrial farming and hog farms use a lot of antibiotics. It's how you get growth hormones and get lots of animals fat quickly," said Winifred Hamilton , who has studied the health consequences of flooding and is director of the Environmental Health Service at the Baylor College of Medicine. She said antibiotic-resistant bacteria levels were 250 times higher in sediment left in houses by floodwater from Hurricane Harvey in Texas last year.

"When people are in their homes in the muck stage, they really need to be protected," Hamilton said. Bring masks and protective gear. "You don't want to touch the floodwater at all."

It may be hard to avoid contaminated water. Duplin and Sampson counties make up some of the most concentrated area for swine farms in the world, and the area had problems with health concerns related to pollution before the flooding. The waters could certainly compound those issues. An immunocompromised person, like someone with a chronic health condition, can face a salmonella infection, although that is rare . Bacteria and viruses could also be a problem.

Cape Fear Riverkeeper Kemp Burdette has been watching the storm with great concern. The area has seen record flood levels that are expected to increase even more. The farms that are built on flood plains -- and there are dozens -- will be in serious trouble, he said, and he expects that more hog lagoons will breach before the storm is over.

The dirt in fields that were sprayed with manure before the storm will also mix with storm water, and Burdette said the state will probably see some of the barns flooded out, meaning animals in those barns will probably die and further contaminate the floodwater.

Compounding North Carolina's troubles, Environmental Protection Agency spokeswoman Maggie Sauerhage says, the state has reported that seven of its wastewater treatment facilities are "in nonoperational status."

"This is looking kind of like a worst-case scenario situation," Burdette said.

His own home has been flooded, and his family is safe, but he's concerned for the residents who stayed behind and the ones who will rush in to clean up and in doing so will get the usual cuts and scrapes and get exposed to this water.

"There will be ample opportunity to get sick," he said. "To be really blunt and honest, there are a lot of these farms upstream from homes that are flooded or will be flooded, and it will wash through people's homes and cover their belongings. Recovering from a flood is difficult. How do you come back from this? I don't know. It's pretty terrible."

Burdette questions why so many farms are built in flood plains. "There is no way to prevent this kind of catastrophe in a hurricane like this with the way we do animal agriculture in North Carolina," he said.

Coal ash in floodwaters

Hamilton is also concerned about the health threat of coal ash in the floodwaters. "Coal ash will end up in everyone's homes" near those areas. It "will end up in the air and as they clean up," she said.

Coal ash is industrial waster created by coal-burning power plants. It contains heavy metals including arsenic, lead and mercury, which can can carry health risks.

There was a failure at one of the landfills containing coal ash at the Sutton Plant in Wilmington, according to the Department of Environmental Quality's Regan. He said his agency was inspecting the area. Duke Energy, which owns the property, is also on site doing an analysis.

Duke Energy spokeswoman Erin Culbert said the company calculates that about 2,000 cubic yards of ash material was displaced from the landfill. It is unclear how much water came into contact with the coal ash.

"We don't have any indication that the ash has gone to the cooling pond," Culbert said, adding that the company will continue to perform water testing. A small amount of ash and water made it outside the landfill perimeter into an adjacent industrial site, and Duke Energy is working with the property owner to clean up. It also detected multiple areas of erosion and is doing the initial repair work.

A breach at the L.V. Sutton Power Station outside Wilmington, North Carolina.

Culbert said that coal ash itself is non-hazardous, and the company does not believe the incident is a threat to human health. It is also watching two other locations: the retired HF Lee Power Plant in Wake County, which is OK for now but has low-lying ash basins that are forested and have flooded in the past; and the retired Weatherspoon Plant near Lumberton , where the nearby Jacob swamp had risen into the cooling pond, but the water has now receded, and the company said it will do some additional inspections there.

"We believe this will not have an impact on the public," Culbert said, but Duke will monitor the situation.

Flooding with coal ash can make its way into streams that contaminate the fish people eat and the water they drink.

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Wilma Subra, a chemist and environmental health scientist in Louisiana, said people should be concerned about the coal ash being dispersed in yards and homes. She cautioned people to use protective gear when cleaning up, as even health threats common in other hurricanes like exposure to sewage could be a problem.

"That's what happened after Katrina. They went back and got boils on their legs" from exposure to sewage, Subra said. Toxic chemicals can also settle into the soil. "And if you go back and find two inches of yuck on your property, so you handle your house, and the grass starts growing, and you never remove it from your yard. Then, every time you mow your grass, the sludge dried out will cause a dust and re-exposure over and over."