The role of microorganisms in childhood diarrhoea has been greatly underestimated, with pathogens including bacteria, viruses and parasites responsible for almost twice as many cases as previously thought, research shows.

A study published in the Lancet journal, which involved the analysis of stool samples from more than 10,000 children in countries across Africa and south Asia, found that nearly 78% of cases of diarrhoea were caused by six bugs, an insight that could help tackle the problem, scientists believe.

Eric Houpt of the University of Virginia, who co-authored the study, said: “It really comes down to just a handful of pathogens that are most important. So it is not a hopelessly long list of infections that we can’t do anything about.”

Diarrhoea is the second most common cause of death in children under five, after pneumonia, and has been linked to stunted growth. It is believed to be caused by infections that spread between people from contaminated food and water, but it has been difficult to pinpoint the cause of each case.

“Diarrhoea in children under five remains an enormous public health problem, with half a million deaths each year or more, mostly in Africa and south Asia,” Houpt said.

The research will galvanise scientists to develop new ways to tackle the pathogens responsible for diarrhoea, he said. “My feeling is that vaccine developments and proper use of antibiotics can lead to a large decrease in childhood diarrhoea over the next 10 to 20 years, if we target these six pathogens, while hopefully economic development trickles along,” Houpt said.

Writing in the Lancet, an international team of researchers describe how they reanalysed stool samples collected as part of an earlier multi-year project called the Global Enteric Multicenter Study, which looked at cases of moderate to severe diarrhoea in children under five in seven countries across Africa and south Asia.

The initial results, published three years ago, suggested that 51.5% of cases were down to pathogens, with the findings based on a suite of analytical methods, including culturing bacteria. But researchers decided to reanalyse the samples in the light of the recent development of highly sensitive genetic analysis techniques.

The latest study analysed samples from 10,608 children, half of whom had diarrhoea and half were unaffected “controls”, in an attempt to unpick the proportion of cases caused by bacteria, viruses and other pathogens, focusing on 32 known to be linked to diarrhoea.

“These [techniques] get down to lower amounts. We can tell not only what is there for the 32, but how much is there, so they give a quantitative result as well,” Houpt said.

The results show that the influence of pathogens has been underestimated, with 89.3% of childhood diarrhoea cases caused by pathogens. Six pathogens, including rotavirus and Cryptosporidium parasites, were responsible for almost 78% of cases.

Nearly 40% of diarrhoeal cases showed evidence of two or more pathogens, suggesting that multiple infections are at play, while even among the apparently healthy children, many were found to have low levels of infection. “What happens is if certain infections multiply and replicate in a child’s [gastrointestinal] tract, and you get to a certain threshold, then the child gets diarrhoea,” Houpt said.

“By looking at not just which infections are present, but the quantities that are present, we are able with very high resolution to understand and document the cause of diarrhoea.”

Of the six key pathogens identified, only one, rotavirus, currently has a vaccine available, although vaccines for two of the other pathogens, bacteria known as Shigella and ETEC (a type of E coli), are in the pipeline.

Prof Val Curtis, the director of the environmental health group at the London School of Hygiene and Tropical Medicine, welcomed the findings, saying the research has demystified the causes of the condition. “It is exciting because we are no longer in the dark ages about diarrhoea,” she said. “We are moving into a new era where we can actually use molecular methods to detect with much more sensitivity the pathogens in stools.

“Diarrhoeal disease is not sexy. It sounds unpleasant. It has never been the area that people have really, really wanted to put their effort into. ‘We need to talk about shit’ is my campaign slogan.”