How safe is our groundwater?

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Clarissa van der Loo

University of Johannesburg – PhD



A girl walks through the dew-covered grass just before the sun rises. Other children and women join her. Before they get ready for school or work, they need to fetch water. They are some of the 5.8 million people in South Africa without access to water within 200 metres of their home. Because of lack of municipal water to these usually semi-rural areas, fetching water for the household often trumps going to work, or even school.

In areas where there is no access to piped water, many South Africans rely on groundwater, accessed through boreholes that tap into underground aquifers. A few hundred years ago – before the advent of mining, commercial agriculture, and a burgeoning population – this groundwater was pristine. The soil and rocks acted as a filter, absorbing all of the impurities out of the water before it reached the underground reservoirs.

This may no longer be the case. And it is threatening millions of people’s health and well-being.

The aquifers under our feet now contain a veritable cocktail of chemicals and pollutants, from mine drainage, abattoir scraps, and hospital waste, through to human and animal faeces. While there have been a number of studies looking at the condition of the groundwater globally, they mainly focus on the chemicals present. Some studies do focus on the microbiological quality of the water, meaning that they’re looking for bacteria, viruses or fungi; but this is an academic exercise, rather than an effort to see whether the water is fit for daily human use – as is the case in our study. This project at the University of Johannesburg, along with our collaborators at the National Institute of Occupational Health and the University of Venda, focuses on the groundwater consumed by residents from seven rural informal settlements in Gauteng and Mpumalanga. Our aim is to determine which microbes are present. Knowing this is important because people use this water every single day, with no alternative.

There are many types of microorganisms, but my focus is on amoebae and bacteria. Bacteria are everywhere, inside and outside our bodies. These organisms are so small that hundreds of thousands can fit into the fullstop at the end of this sentence. Bacteria play many roles in our bodies, but the main function of good bacteria – those which promote our health and wellbeing – is to protect us from harmful bacteria. If left unchecked, or if our immune systems aren’t strong enough, these harmful bacteria cause infections and disease.

Amoebae are not as well known. These tiny single-celled organisms are larger than bacteria, but still small – about the size of a grain of pollen. They look innocent in most cases, hardly visible creatures that resemble the shape of a fried egg. When grown in petri dishes, amoebae slowly patrol the dish, searching for bacteria to become their next meal.

Scientists assumed for many years that bacteria were simply food for amoebae. Now we know that some bacteria have adapted to withstand the amoebal attack, and live inside their would-be assailant. Inside amoeba, these bacteria have a protected habitat. They are safe from outside factors, such as disinfection by chemicals or drastic environmental changes, and have a cosy place in which to multiply and grow stronger. Once the bacteria are ready, they kill the amoeba rather dramatically: the amoeba’s cell wall is ripped open so all its insides – including the bacteria – explode into the water.

There is another threat to humans and animals: amoebae can cause disease and in most cases, their infections are fatal, regardless of your immune status. People with HIV or other diseases, such as cancer or diabetes, are more prone to infections like tuberculosis or the seasonal flu, because their body’s defence mechanisms are not at their peak. People with healthy immune systems are able to ward off microorganism assault. But with amoebae, the rules change. Amoebae don’t discriminate – they infect humans and animals, whether they have weak or strong immune systems. Recent news reports of “brain-eating amoebae” implicated in infections and deaths of young people in America have caused uproar and have struck fear into water-loving adventurists. More than 97% of people infected with this particular amoeba will die.

In our study, we found numerous species of amoebae and bacteria in the settlements’ groundwater. Some of them are not harmless and may cause serious illness, such as a vision-threatening eye infection (Acanthamoeba castellanii), bloody diarrhoea and liver abscesses (Entamoeba histolytica), and brain infection (Naegleria fowleri). Patients have on average five days between the first symptoms of infection and death.

The bacteria we found gave us more questions than answers. Many were (as expected) environmental organisms, which are usually recovered from soil, water, and plants (such as Mycobacterium chlorophenolicum). But we also found some organisms that aren’t meant to be in the environment (Klebsiella oxytoca), and quite a few bacteria had previously only been recovered from human samples (mainly in hospital settings), not from groundwater. One of the predominant bacteria we found, Stenotrophomonas maltophilia, was recently named as an “emerging pathogen” by the international scientific community. That means it was identified as a disease-causing agent that has either been causing more infections over the last two decades, or is expected to cause more infections in future. It’s particularly worrying because it easily infects immunocompromised patients, and is often resistant to the multiple drugs used to treat the infection it causes. That means it could cause serious infections in any person with decreased immunity.

For now, our study team can only speculate as to what illnesses these organisms may cause in people who use the water daily. Our study was done purely to see what types of organisms we can find in our groundwater, because this type of study, focussing on water for human consumption, has not been done in South Africa before. We will, however, try to study the population further to see whether the amoebae- and bacteria-infected water causes any harm and whether we can implement methods to purify the water in areas that do not yet have access to clean municipal water.

Our other studies at the University of Johannesburg are currently looking at the amoebae and bacteria in hospital water, to see whether the infections seen in hospitals themselves are caused by the same organisms. Our initial study was only the first step in a very large dream to determine what is in our water, how can we improve it, and ultimately, how we can save lives.



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