Updated

As tens of thousands of refugees streamed into emergency medical centers, shelters and hospitals outside the devastated New Orleans area on Friday, health workers struggling around the clock to treat critical patients and prevent a public health catastrophe said facilities were already overwhelmed and in crisis.

"We're going through a medical crisis in Baton Rouge," FOX News medical contributor Dr. Manny Alvarez said. "These health workers have been working around the clock, but it is running thin now. Something needs to be done urgently."

Alvarez, the only physician working with the medical staff at the emergency shelter set up at the Baton Rouge convention center, said many of the patients there have chronic conditions like diabetes and hypertension and had not had their medication in days. Others were recent surgical patients.

"One of the things we've noticed, most of the folks don't know what kind of medication they are on, and all of the medical records have been washed away," Alvarez said.

Some of the patients were diabetics with open sores that had become infected from being exposed to the polluted flood waters in New Orleans.

In Houston, 60 doctors and nurses worked in a makeshift clinic in a hangar at Ellington Field, quickly examining evacuees from Gulf Coast cities before sending them to hospitals or releasing them to family members.

"We've seen patients who've recently had transplants, were on ventilators, had serious infections, nursing home patients, patients with pneumonia, patients who've not had kidney dialysis for a week," said Dr. J. Kalavar, director of the patient reception team at Ellington. "Everyone of them is anxious and exhausted."

Click in the video box to the right for more coverage of the hurricane-related health crisis in New Orleans.

Theadore Hunter and his mother, Henrietta, spent two days on the roof of their flooded apartment complex before they were rescued Wednesday by a helicopter from New Orleans and brought to Houston on a military cargo plane.

"I didn't know where we were being taken. All we knew is we were getting out of the storm, getting away from the flood. Now I don't know what we are going to do but we are alive," Hunter said.

With one hand he hugged his crying daughter, Tracy, who had fled New Orleans for Houston days earlier. In his other hand, he clutched a brown leather bag with his mother's medicines, the only thing he could save from his flooded apartment.

Inside the Houston Astrodome, where refugees had been sent from New Orleans, doctors were having trouble keeping up with everyone needing treatment.

"Many people might think there are enough people here, and there are not. We just need help," said Dr. Steven Glorsky, who had treated evacuees for heart attacks, open wounds and diabetes. "We have a crisis in there."

Health care workers were also expressing concern Friday about what they saw as a looming mental health crisis.

"People don't know where there families are. There is a mental health crisis here," Dr. Alvarez said. "These people need counseling and medication," he said.

In more encouraging news, Alvarez said that the children who had made it to Baton Rouge were doing well.

"Everybody's working very hard to make sure the children are in good shape," he said. "They're children, they have no idea of the mental impact," he said.

Help Reaches Hospitals

Meanwhile, in New Orleans, evacuations resumed Friday at some of the city's most troubled hospitals, where desperate doctors were being forced to make tough choices about which patients got dwindling supplies of food, water and medicine.

Rescuers finally made it into Charity Hospital, the largest public hospital and trauma center in the city, where gunshots prevented efforts on Thursday to evacuate more than 220 patients.

"We moved all of the babies out of Charity this morning," said Keith Simon, spokesman for Acadian Ambulance Service Inc.

Late Thursday afternoon, the U.S. Surgeon General's office said five private helicopters had attempted to take patients out of Charity. One doctor said a sniper had opened fire outside Charity as National Guard vehicles prepared to evacuate patients.

After waiting all day, hospital officials loaded some people onto boats, but some were returning because transportation anticipated at higher ground wasn't available, according to Dr. Ruth Berggren.

Richard Zuschlag, the ambulance company's president, said Friday that the military was now handling the evacuation of Charity and other hospitals in the flooded downtown.

The hospitals were desperate for help. On Thursday, doctors from Charity and University, the city's other public hospital, had called the Associated Press pleading for rescue, saying they were nearly out of food and power and had been forced to move patients to higher floors to escape looters.

Charity Hospital is across the street from Tulane University Medical Center, a private facility that had almost completed evacuating more than 1,000 patients and family members Thursday.

On Thursday, Dr. Lee Hamm, chairman of medicine at Tulane University, had taken a canoe from Tulane to check on conditions at the two public hospitals and had described a harrowing situation.

"The physicians and nurses are doing an incredible job, but there are patients laying on stretchers on the floor, the halls were dark, the stairwells are dark. Of course, there's no elevators. There's no communication with the outside world," he said. "We're afraid that somehow these two hospitals have been left off ... that somehow somebody has either forgotten it or ignored it or something, because there is no evidence anything is being done."

Hamm said it was "demoralizing" when rescue failed to show up this week.

Relatives of Dr. Hamm reported that they received a text message from him around midday Friday, confirming that evacuations were taking place at Charity and nearby University Hospital, where more than 1,000 patients, family members, staff and people from the community had huddled.

Toxic Water in New Orleans

Four days after Hurricane Katrina hit the Gulf Coast, nearly 80 percent of New Orleans remained steeped in a putrid stew of standing floodwater contaminated with raw sewage, human and animal corpses, human waste, fuel and toxic chemicals, posing the potential for outbreaks of typhoid, cholera, tuberculosis and bacterial infections.

The standing water and pressing heat, officials warned, were also setting the stage for an increasing threat of mosquito-borne diseases like West Nile virus, dengue fever and malaria.

Calling the situation a "remarkable human tragedy," Health and Human Services Secretary Mike Leavitt said Friday that officials were focused on preventing a "second wave" of disaster in the form of a public health crisis from sweeping the city.

"We are very concerned about the public health issues," Leavitt told FOX News.

He said 24 teams of health workers had been dispatched to the area to combat the crisis, including sanitation and mosquito abatement.

Removal of the standing floodwater, officials said, is expected to take weeks. Meanwhile, for the victims who remained trapped in the city, the filthy water is the only route to safety.

"These are highly contagious diseases, and as people begin to experience the diarrhea and vomiting, it'll spread because we have people in very close quarters now in the Astrodome or wherever they are," said Dr. Steven Garner, a FOX News medical analyst. "Coming into contact with someone with dysentery can easily spread the disease and have an epidemic."

So far, there has not been an outbreak of disease, other than individual cases of diarrhea, U.S. Surgeon General Richard Carmona told FOX News on Friday.

Other experts have said that outbreaks of diseases such as cholera and typhoid are unlikely, and that dead bodies do not pose that great of a disease threat. But Carmona said health officials were most concerned about mosquitoes.

"When a disaster like this occurs, mosquitoes have the chance to grow and harvest," he said. "It's a very real threat."

In Baton Rouge, Dr. Alvarez said they had so far not seen disease outbreaks.

Louisiana Lt. Gov. Mitch Landrieu, who has been working with search and rescue, confirmed that 30 people died at a nursing home in St. Bernard Parish and 30 others were being evacuated. He did not give any further details.

Officials at the Centers for Disease Control and Prevention said they had deployed more than 30 people to Gulf Coast states to assess health conditions. The agency also will send six 20-person teams to help local and state public health and medical personnel.

FOX News' Todd Connor and the Associated Press contributed to this report.