patients' ward at Antoni Infectious Disease Hospital in Kabul.

The US defeated Kabul superbugs in its military, but locals still struggle

Updated 12:14 AM ET, Tue November 6, 2018

This story was investigated by the Bureau of Investigative Journalism and edited and published in partnership with CNN.

Kandahar, Afghanistan (CNN)As the conflicts in Afghanistan and Iraq evolved, military doctors grappling to treat soldiers maimed by roadside bombs began facing another challenge: Their patients were developing almost incurable, multidrug-resistant infections in their wounds. They couldn't be treated with the usual antibiotics the doctors had on hand.

US Army Col. Clinton Murray, 48, an infectious-diseases doctor, was deployed to the region four times between 2003 and 2015, working in military hospitals and clinics across the country.
He said that drug-resistant or "superbug" infections meant some soldiers had problems for years after their initial life-altering injuries. When common antibiotics failed, higher doses of antibiotics, new drug combinations or alternative drugs with severe side effects were tried, but many had repeat and prolonged infections. Others had to undergo extra surgeries or amputations to stop the bacteria from spreading further.
The US Army soon realized that drug resistance was a serious problem and, from 2009, introduced programs to reduce drug resistance in its military hospitals -- but the problem was just as bad, if not worse, in nearby civilian hospitals.
When things got really bad for the Army, soldiers were evacuated to two US hospitals. One was Brooke Army Medical Center in Texas, where Murray also ran the infectious-diseases department.
Civilians, however, had fewer resources and no way out.
Afghan citizens are dying because of the war, and drug resistance will mean even more deaths, said Dr. Nasimullah Bawar, head of health programme at BRAC Afghanistan, a nongovernmental organization providing drugs and maternity, child health, immunization, nutrition, mental health and malaria and TB-control services in four provinces.
Bawar compares superbugs to another scourge, the Islamic State or Daesh, because it will disrupt the country and kill many citizens: "This is going to be another Daesh, I can say."
Making the situation even tougher is 40 years of conflict.

A military struggle against 'Iraqibacter'

Military doctors started noticing an influx of patients with multidrug-resistant infections from 2003, two years after the Afghanistan war started, but it was years before the Army identified the scope of the problem.
Infections from a resistant form of one type of bacteria, Acinetobacter baumannii, became so common in Iraq and then Afghanistan that the soldiers gave it a nickname: "Iraqibacter." The bug had usually been a problem in older or very sick patients who had spent months in the hospital, but doctors were now seeing it in young, fit soldiers, commonly in blast wounds.
At the peak of the problem, between 2004 and 2006, the budget for one class of last-resort antibiotics called carbapenems, used for severe and multidrug-resistant infections, went up more than 400%.
The use of another drug, colistin, called the "last hope" drug because of its use on critically ill patients, became so common that the Army had to restrict it.
Something had to change.
Targeted control programs were introduced in 2009 and included guidelines on antibiotic use, better surveillance of drug resistance, improved record-keeping and better infection control. Resistance was reduced to pre-war levels within six years.
"I have folks I've been following for 10 to 15 years," Murray said. "First couple of years, we wrestled with infection. Then, for the next 11, they've done great. They live functional lives."
Specialist care meant soldiers were being saved from superbug infections.
Murray recalls one patient who lost both his legs after being hit by a roadside bomb in Iraq. Three weeks after the blast, after evacuation to the US, infections developed in his stumps.
Doctors swabbed the wounds and found a plethora of dangerous organisms, including three types of multidrug-resistant bacteria: Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae, as well as Staphylococcus aureus. To stem these infections, they had to give him antibiotics that caused kidney failure, though his organs recovered after the drug therapy was stopped a few days later.
But the patient went on to develop more infections.
On one occasion, the antibiotics poisoned his bone marrow, which affects the body's immunity and clotting. He was given a different antibiotic that cleared the infection in that stump, and fortunately, the poisoning did not turn out to be permanent. However, he soon developed an infection in his other stump.
Doctors suggested more surgery to cut away the infected part of his leg, but he opted instead to take antibiotics long-term to quash the infection.
Now, 12 years after being hit, he still has to take antibiotics to keep the infection at bay, but he lives a normal life with prosthetic legs. "His kids and my kids knew each other, and now they're in college and doing great," Murray said.
But the gains made in military hospitals were not transferred to public facilities, which still struggle with drug-resistant infections.
The health system in Afghanistan has been fragmented by decades of war. Civilian hospitals are understaffed, underfunded and overburdened, and superbugs made the civilian population in war zones an object of fear, said Dr. Christian Haggenmiller, a former senior NATO medical officer in Afghanistan.
Though Army staff were prioritized at military hospitals, some Afghan citizens were also treated there because so many were injured in the conflict and local hospitals were often inaccessible or in poor condition. Many military facilities carried out life-saving treatment on locals but then referred them to public hospitals for rehabilitation.
Military medical facilities sometimes rejected civilian patients because of fear that they carried resistant bacteria that could infect the intensive care unit for military personnel, Haggenmiller said. As a result, they were often treated separately in isolation tents, away from the main medical facilities.
"It's your worst nightmare, having a drug-resistant strain in your health facility that you can't control. It's like a new disease," Haggenmiller said.

Antibiotic addiction

Afghanistan has some of the worst health outcomes in the world. One woman dies every two hours from pregnancy-related causes, according to conservative estimates by Medecins Sans Frontieres (Doctors Without Borders), and one in 25 newborn babies dies, the third highest neonatal death rate in the world, UNICEF figures show.
Life expectancy at birth is 64, compared with 79 in the US and a global average of 72. There is a shortage of doctors, especially in rural areas, and infection control is poor.
Drug resistance has become one of the world's greatest public health crises, estimated to cause 700,000 deaths worldwide and expected to kill 10 million by 2050 if no action is taken.
Fueling the superbug problem in Afghanistan is the unregulated sale of antibiotics in human medicine and in agriculture. Drugs are advertised on television and available to buy over the counter from pharmacies without a prescription or diagnos