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

Malawi (CNN) In a sweltering room in the corner of the Chatinkha nursery in Queen Elizabeth Central Hospital in Blantyre, Malawi, Lilian Matchaya is expressing milk.

Her daughter, Abigail, is nearby, lying in a wooden cot with a UV light overhead keeping her at the right temperature. Her head wrapped in a bandage, Abigail has a plastic feeding tube going into her nose.

Matchaya, 38, inserts a syringe of breast milk into the tube, and it travels slowly down the translucent pipe. The sounds of infants crying, machines beeping and nurses pushing trolleys fill the ward.

Abigail Matchaya weighed just 3 pounds at birth, having been born prematurely, and soon developed sepsis.

Abigail was born prematurely at seven months and weighed just 1.8 kilograms (3 pounds) at birth, little more than a bag of flour. She needed an injection of aminophylline, which dilates the lung's cells, to help her breathe, and the day after her birth, nurses found her passed out with blood in her stool.

Babies, especially those born prematurely, are especially vulnerable to infection, as their immune systems haven't developed properly. Doctors suspected that Abigail had sepsis, a serious and potentially fatal condition in which bacteria get into the bloodstream. In response, the body's immune system goes into overdrive, and organs begin to shut down.

Abigail was given two antibiotics, penicillin and gentamicin, a combination meant to kill a wide range of bacteria. The drugs didn't seem to work, and she was soon given ceftriaxone and metronidazole, but there was still no improvement.

Her medical notes state that she then became floppy and passed out once more.

Lab results revealed that she was infected with a drug-resistant form of Klebsiella. The bacteria were resistant to most of the drugs Abigail had been given, meaning the medications were not working to kill her infection.

For four days, she had been given ineffective drugs.

For every hour that a baby in septic shock is given ineffective drugs, the chance of survival decreases by 7.6%, one study found . Dr. Kondwani Kawaza, a neonatologist at the Chatinkha nursery, said that even if the baby doesn't die, sepsis can cause disabling complications such as brain damage, meningitis and impairment to vital organs like the kidneys and the liver.

Doctors at the hospital also face another problem: The antibiotics they needed to treat Abigail's superbug are expensive and not part of Malawi's standard drug regimen, meaning they're not always available in the hospital.

On this occasion, Abigail was lucky: The pharmacy had one of the drugs they needed, amikacin, which can be given for only short periods, as it can trigger deafness as well as kidney and nerve damage.

Abigail was promptly given amikacin, after which her family faced a waiting game.

"The first thing I do when I wake up daily is to pray for my baby to get well. Then I check on her with the hope that she will be OK," said Matchaya, a soft-voiced housewife, through an interpreter. She lives with her husband, a teacher, and three sons in Nancholi, on the outskirts of Blantyre.

Lilian Matchaya holds her daughter, Abigail, praying for her to get better.

According to Kawaza, 20% to 40% of infections his team diagnoses are now resistant to antibiotics. The proportion was a lot lower five years ago, he said.

"Four patients grew Klebsiella in this ward alone in a single week, where in the past, we would say it would be for the whole month," he said. "It's becoming a bigger and bigger problem."

A nation in crisis

Malawi is one of the poorest countries in the world, ranking 170th out of 188 on the United Nations' human development index. More than 70% of its 18 million people survive on less than $1.90 a day, the international benchmark of poverty.

Most Malawians do not own televisions, cars or phones or have internet. In rural areas, people grow their own food.

And now, the country is facing an epidemic of infections causing sepsis, one of the leading causes of death among newborns. It killed nearly 20% of them in 2016; by comparison, in the UK, sepsis is responsible for less than 2% of infant deaths.

A combination of factors, all related to poverty, mean the percentage of babies dying of sepsis has barely fallen since 2000 despite improvements in the health care system.

Mothers and babies at Queen Elizabeth Central Hospital in Blantyre wait for treatment.

To make things worse, these figures are thought to be vast underestimates, as most health care facilities do not have the tests to diagnose sepsis.

Across Malawi, it is common to find mothers who have lost a child.

Malnutrition and a high burden of diseases such as HIV and malaria mean mothers and babies' immune systems are even weaker, so they catch infections a healthy body might easily quash.

This is all further fueled by the fact that the majority of Malawians don't have running water, so keeping clean is difficult, and soap is expensive. Many lack education on the importance of washing their hands, how to hygienically prepare food or how to change their baby's diaper, and not many can afford to go to a doctor when they become ill.

More than half of the country's health care facilities are also failing to meet World Health Organization standards on water and sanitation facilities, according to UNICEF. Even Queen Elizabeth hospital, Malawi's biggest, does not have running water in every room.

Many hospitals report "stockouts," periods when supplies like soap, chlorine, bleach and sterile gloves run out.

This culmination of poor hygiene means there is a constant cycle of infection and, in turn, a constant need for antibiotics, whose overuse has now fueled resistance.

For example, a three-month spike in sepsis rates from October occurred at the same time as a shortage of chlorhexidine, an antiseptic put on a baby's umbilical cord to prevent infection, said Wezi Kalumbu, an adviser on child health for the Organized Network of Services for Everyone's Health, a USAID-funded program to improve health care in 16 districts of Malawi.

'Embarrassing' conditions

Down a sandy, potholed track near the border of Mozambique lies the Nayuchi health centre, in Machinga district. Tamandua Chirwa, 26, runs the rural hospital and remembers how delighted she was the day running water was installed in March 2017.

Before that, it was difficult to recruit staff, as there was no toilet. Buckets of water had to be carried from a borehole in the nearby village to wash hands or clean the hospital.

Nyambi health center does not have running water; instead, buckets of water must be carried from a nearby borehole to wash hands or clean the hospital.

Pregnant women would avoid coming to the center because conditions were unhygienic and they believed it was safer to give birth at home -- even though nine out of 10 people in Malawi do not have electricity, and one in three doesn't have clean water.

After WaterAid, a nonprofit organization working to improve water and sanitation, installed a borehole and solar-powered water supply system, the rooms could be cleaned properly. "It was very encouraging when we had water," Chirwa said. "We had more women delivering at the hospital. They knew, after delivery, we will have safe water to clean ourselves up."

The Nyambi health care center is 60 miles away in the same district, but has no running water. Green vats that once held rainwater from the roof now lie broken on the floor. There are six toilets, but all but one is broken, and it must be shared by roughly 300 people -- including pregnant women, families and staff.

Here, women are asked to bring candles or flashlights in case there is no power. They are also told to bring razor blades to cut their children's umbilical cords as well as a plastic sheet, called a macintosh in Malawi, on which to give birth. Such requests are common in health centers and hospitals across the country.

Women are asked to bring a plastic sheet on which to give birth and a razor blade to cut their baby's umbilical cord.

Blackouts are also a regular occurrence at Nyambi, so staffers cannot always sterilize equipment like forceps to use during labour. There is also no incinerator for placentas.

Sphiwe Kachimangha, infection prevention control lead for Machinga district, called the conditions "embarrassing." "We are in financial crisis, so it is difficult to tackle all the problems at once."

In 2013, the "cashgate" scandal was uncovered, revealing that an estimated $250 million (£150 million) worth of public money was stolen through fraudulent payments. The crisis led to the freezing of $150 million worth of international aid, which plunged the government budget into deficit.

In the cobweb-ridden waiting room in Nyambi, which has a broken sink full of dried corn and a rusty wheelchair in a corner, are young mothers-to-be Ruth White, 23, and Jenifa Lyson, 24, who are staying nearby in case their waters break. "This place is very untidy, and it stinks a lot," Lyson said through an interpreter.

They sleep on the same black plastic sheet on which they plan to give birth, risking future infection or passing an infection on to their babies.

Midwives or nurses from both health centers and Queen Elizabeth hospital also voiced concerns about cultural practices around cutting the umbilical cord. Sometimes, animal dung or the juice of pumpkin flowers is rubbed on the wound, which could cause infections that lead to sepsis. However, many said these practices are dying out due to education campaigns.

The luxury of being clean

Simple measures like washing hands could prevent many infections, but for people in poverty, soap is a luxury.

Buying enough soap to wash hands and clean plates and clothes costs about 3,000 kwacha (£3.30 or US $4.27) a month, said Bertha Gesinao, 19, through an interpreter. She lives in the village of Khambo in Chikwawa, a poor district an hour and a half outside Blantyre. The London School of Hygiene and Tropical Medicine in the UK is running a project there to help improve sanitation practices.

Gesinao, who sorts cotton, and her husband, who works on a sugar cane plantation, earn 9,200 kwacha (£9.60 or US $12.42) between them a month. "I can't spend all my earnings on buying soap, as I'm also relying on the same to buy food and other basic needs," she said.

A patchwork of nongovernmental organizations like WaterAid are building boreholes to give rural communities access to water, but it is also not in all of these organizations' remits to check and monitor that the water remains safe.

Save Kumwenda, senior lecturer in environmental health at the University of Malawi's Polytechnic, explained that surveys in the Chikwawa district and another southern district, Mulanje, found that approximately 20% of the boreholes there were contaminated with fecal matter. Some were built on sandy soil that allowed bacteria to get into the water; others were built too close to nearby toilets. People also throw household waste down the borehole or bring their animals to drink there, leading to contamination, he said.

Even in Blantyre, there are areas such as Ndirande, one of the largest slums in southern Africa, where people drink unsafe water out of shallow wells. "We are sitting on a ticking bomb," he said of the threat of unclean water.

There are shortages of soap in the maternity ward at Queen Elizabeth hospital, where many mothers and babies receive care.

Resistance as high as 90%

An unhygienic environment will lead to infection and more antibiotic use, which leads to antimicrobial resistance, said Nicholas Feasey, an infectious disease researcher and microbiologist at the Malawi Liverpool Wellcome Centre, the research institution next to Queen Elizabeth hospital.

Feasey and his team have tracked the rise of antibiotic resistance at the hospital as part of a major study, the only one of its scale across sub-Saharan Africa, where data on resistance are scarce.

They analyzed bacteria causing bloodstream infections in adults and children from 1998 to 2016. The good news, he said, is that such infections fell from 2005 on, overlapping with improvements in HIV and malaria care in Malawi and a fertilizer subsidy that helped people grow more food, reducing malnutrition.

Mothers on the postnatal ward at Queen Elizabeth hospital.

But the bad news is that more than half of infections are now resistant to the first-line antibiotics available in Malawi: penicillin, ampicillin and chloramphenicol. Resistance to co-trimoxazole -- a combination also known as Bactrim -- which is taken daily by people with HIV to prevent infections has also risen.

The study revealed soaring resistance to the two classes of antibiotics regularly stocked in Malawian hospitals, penicillins and cephalosporins, among bacteria that commonly cause sepsis.

In Klebsiella, the bacteria that infected baby Abigail, resistance rose from 12% in 2003 to more than 90% in 2016. In E. coli, resistance rose from 1% to 30% in the same time period.

"So the good news story about bloodstream infections falling is tempered by the rise of locally untreatable bacteria," Feasey said. "In other [countries] where there is a broad range of antibiotics available, these infections are difficult to treat but far from impossible, but here, they are they are effectively untreatable."

Black market antibiotics

Limbe market, on the outskirts of Blantyre, is a bustling place. You can barely move for the crowds of people amid stalls selling colorful clothes, dried fish, chicken feet, puffed crisps and sacks of maize.

At the top is a forked road locals call The One That God Bent, which is home to a row of pharmacies and drug stores where antibiotics are easy to access.

Drug stores near Limbe market sell antibitoics despite this being illegal without a prescription.

It is illegal to sell antibiotics without a prescription in Malawi, but reporters from the Bureau of Investigative Journalism visited four pharmacies and one drugstore and were able to purchase a range of drugs, including injectable ceftriaxone, the last-line drug available in most Malawian hospitals. Only painkillers were for sale at Limbe and Blantyre's open-air markets, though market sellers said Bactrim was available a year ago.

Ibrahim Chikowe, a medicinal chemist at the University of Malawi, said the problem with easy access to antibiotics is that people tend to take the medications only until they start feeling well. This leads to resistance among the bacteria, which then spread from one person to another. "Soon, you may find the population might not be cured by a particular antibiotic or class of antibiotic, and this might lead to disaster," he said.

In cities, antibiotics can be bought from shops. In smaller towns there are drugstores on the roads leading up to hospitals. In rural areas, salesmen pass through villages selling medicines, including antibiotics, out of plastic bags.

It is illegal to sell antibiotics without a prescription in Malawi, but pharmacies in Blantyre sold reporters a range of drugs.

Nearly 65 miles south of Blantyre is such a place, the village of Khambo, in the Chikwawa district. It is a rural part of the country: Goats graze on the sides of the road, and herds of cattle block traffic. Khambo is accessible only by foot or bicycle, as there is no road to the handful of houses found in the middle of the fields.

The nearest health center the villagers can use is a 15-kilometer walk, so village women say that when the drug salesmen pass through, they buy as many tablets as they can afford.

Elizabeth Love, 32, who lives in a straw-roofed house with a dirt floor, said her 18-month-old daughter, Rebecca, had diarrhea. She bought two Bactrim tablets from a passing salesman in June. They had expired in 2016.

More resistance to come

The Queen Elizabeth hospital is lucky enough to be one of a handful in Malawi that has access to blood culture facilities. But by the time blood culture tests confirm that an infant has a superbug infection, typically two to four days later, it is often too late.

"Whenever we are sure it's Klebsiella, we are already 24 to 48 hours late," said Kawaza, the neonatologist. "If they don't die today, they will die tomorrow. If they don't die tomorrow, they will die in two weeks time. If they survive, they will be weak for weeks to come."

There are hospital-wide discussions about whether amikacin and another expensive antibiotic, meropenem, can be made more widely available. But many doctors are concerned that widespread use would drive resistance against these new drugs, meaning even fewer antibiotic options would be left.

The amikacin given to baby Abigail seemed to work to kill her infection, and within a few days, she was able to move from the small room in which she was isolated to the nursery's main ward. However, the infection had taken its toll on her body, and she died one month after contracting drug-resistant Klebsiella.

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If resistance continues to rise, more babies will follow, Kawaza said. "Some people think that antibiotic resistance is a hypothetical threat, a nonexistent threat, something that only academics talk about," he said. "But for us, we do see it every day. We do see babies change suddenly from a robustly active baby to a profoundly sick baby."

Feasey, the microbiologist, believes that antimicrobial resistance is just one part of a bigger problem. "It is one of many things: poverty of the individual and poverty of systems," he said.

"At any time you walk through the hospital, though, there's a high chance that a funeral procession will go by, and there is just a deep sense of frustration at the waste of human life because of the overwhelming interaction of lots of different factors, which are mediated by poverty."