Two superbugs cause more than half of the infections killing newborns in Soweto. The germs are fast outsmarting treatment

Over the past 10 years, researchers from Wits University’s vaccines and infectious diseases analytics unit analysed small tissue samples of 1,586 children under five who died at public health facilities in Soweto.

With people living in both informal settlements and structured houses, the cases presented here are a window into what is likely to be seen in other urban townships in South Africa, says the team.

The study found that many babies die from preventable infections. This is not new knowledge, but it’s the detail in the data that is so valuable, says Ziyaad Dangor, who heads up the South African leg of the nine-country Child Health and Mortality Prevention Surveillance (Champs) study.

Results show that of the infections that led to deaths, more than half of those in newborns (babies up to one month of age) and about a third in infants (babies between one and 12 months) were caused by two types of bacteria — Acinetobacter baumannii and Klebsiella pneumoniae — both of which are fast becoming resistant to antibiotics, says Dangor.

Antibiotics can kill bacteria, but when they figure out how to sidestep the medicine, this no longer happens. When bacteria become resistant to drugs by changing themselves, they are no longer effective. This can be because people don’t finish their antibiotic courses or too many people are using them.

Child health, including preventing children from dying, was a big talking point at the 80th UN General Assembly in September.

And rightly so.

With five years to go to the cut-off for meeting the UN’s sustainable development goals, a global report published in March shows that babies dying within the first month of life made up almost half of the roughly 4.8-million deaths in children under five in 2023.

Although the number of children dying before their fifth birthday has halved in just over 20 years — dropping from 77 to 37 per 1,000 live births between 2000 and 2023 — progress has slowed in the past decade. Some 65 countries won’t make the UN’s target of getting this rate to below 25 in 1,000 by 2030.

South Africa is one of them.

In 2023 — the last year for which data is included in the report — the country’s under-five mortality rate sat at just under 35 per 1,000 births — almost 1.5 times higher than the ideal. This works out to almost 112 children dying in South Africa every day in 2023, based on UN data. (The rate differs from Stats SA’s data — around 30 per 1,000 births. However, Stats SA also notes that the estimates it shows “are based on the selected model life table and may differ from similar indices published elsewhere”.)

Many of the under-five deaths are babies who die before they’re a month old (newborn death) or before they’re one year old (infant death).

At the current rate of 13.4 newborn deaths per 1,000 births, South Africa is close to the UN’s target of no more than 12 per 1,000. However, it’s the highest it has been in almost 10 years.

The number of babies in a population who die young is a mirror of how healthy a country is. Many of the problems that lead to children’s deaths — such as infections, lack of access to medicine or health care and not having clean water, good housing or nutritious food — also affect the health of the rest of the population.

By this measure, things could go awry if the government doesn’t think wisely about how best to spend its health budget, which will likely become tighter as money is shifted to plug holes left by international funding cuts.

This is why understanding the causes of child deaths is all the more important, says Dangor. “If you don’t know what you’re fighting against, it’s very difficult to treat.”

Here are four takeaways — in graphs — from the South African data so far.

1. On-time screening = fewer stillbirths

Of the 460 stillbirths investigated in the Champs study, nine out of 10 were due to mostly preventable issues during pregnancy, such as the baby not getting enough oxygen while in the womb or an infection passed on from the mother to the foetus.

During pregnancy check-ups, health workers test for conditions such as high blood pressure, which can reduce oxygen supply to the growing baby, or common bacterial infections such as those from Group B Streptococcus (often lying dormant in the genital tract).

Group B Streptococcus is a common type of bacteria, and though it’s usually harmless in healthy adults, it can cause group B strep disease in newborns, with symptoms such as fever, low body temperature and seizures.

Nurses also check pregnant women for the germ that causes syphilis (a sexually transmitted disease). A pregnant woman with syphilis can pass it to her baby before birth. Having syphilis can also increase the chance of miscarriage, giving birth too early or stillbirth.

If found early, these issues can be treated with medication and good health checks.

But the finding that so many stillbirths were preventable suggests there are holes in the safety net of antenatal care, says Dangor. It could be that the mother didn’t book for a pregnancy check-up, had a screening test only late in her pregnancy, or may have tested negative for something like syphilis once and then not tested again later during her pregnancy as she should have been.

South Africa’s national guidelines follow the World Health Organisation’s recommendation of eight pregnancy check-ups that can start within 14 weeks of conception. Despite data from the 2023/24 District Health Barometer showing that close to 70% of pregnant women go to a clinic for at least one antenatal check-up, and usually before 20 weeks, many don’t go for follow-ups because it’s difficult, costly or time-consuming.

2. Preventing early births = preventing untimely deaths

In newborns, issues linked to being born too early were the underlying cause of more than half of deaths and the immediate cause of death in about a third of this group.

When someone dies, the condition that killed them (the immediate cause of death) may have been brought on by an existing health problem (the underlying cause of death).

In the case of children dying within the first year of life, prematurity is a big contributor. A full-term pregnancy is 40 weeks. A baby born before 37 weeks — in other words, prematurely — is “not quite ready to be in the world because their organs aren’t fully grown yet”, explains Dangor.

For example, a premature baby’s lungs aren’t strong enough, so they have to be admitted to hospital to be given oxygen. Not only are their bodies weaker than they should be, says Dangor, but being in hospital also means they have a greater chance of exposure to germs that they can’t fight or that are difficult to treat. These are common in health facilities and can easily lead to sepsis.

Sepsis occurs when the body’s immune system has an extreme response to an infection that causes damage to tissues and organs. If it is not treated early, sepsis can lead to shock and organs shutting down.

3. Superbugs = bad for babies

More than half of the infections that led to deaths in newborns and about a third of deaths in infants were caused by just two types of bacteria — Acinetobacter baumannii and Klebsiella pneumoniae — both of which are fast becoming resistant to antibiotics.

“Before the Champs study, we knew, for example, that Klebsiella pneumoniae caused infections, but not to the extent that we saw. So, either it’s become a much more common problem or it has been underrecognised.”

The same goes for A. baumannii, a stubborn germ common in hospitals which can cause pneumonia, and for which there is only one type of antibiotic available in the public sector. This is also difficult to access and often doesn’t work well.

Says Dangor: “As a clinician on the ground it makes you feel helpless.”

4. Prevention = better than cure

That’s the beauty of having detailed data.

Knowing where the problems are means solutions can be built around them. With few treatment options available for in-hospital infections, it’s “best to limit exposure” by fixing things in the health system before a woman has to give birth, says Dangor.

There are many ways to do this, says Dangor, with some things more powerful than others. The data shows three things — better health checks during pregnancy, preventing in-hospital infections and helping new moms understand when to ask for medical advice — can go a long way to preventing early child deaths.

The findings don’t put a number on how many deaths would be prevented but rather show where efforts could be best spent to keep children safe depending on their age group. And this, says Dangor, is a win, especially at a time when international funding cuts to the HIV programme are putting extra pressure on the health system.

Says Dangor: “Anything that’s going to cause reprioritisation of the available budget is going to put pressure on the health system throughout.” And that can have a ripple effect on child health in South Africa — and the country’s future.