Probing Poop for Pathogen DNA: Diarrhea Genomics, a First-World Advance Contrasts with USAID Cuts in Africa

When I saw a news release describing a test in development to sequence pathogen genomes in diarrhea, my geneticist side was, at first, impressed – why not track DNA to identify a specific virus, bacterium, parasite, or fungus? A research team from the University of Liverpool published their findings in Genome Medicine.

Each year in the UK, 18 million people suffer from diarrhea. Presumably, a genomic tool to illuminate the cause could help choose the most appropriate treatment.

But tailored treatment for diarrhea would be a luxury for much of the world, where diarrhea kills quickly, and treatment is the ages-old rehydration therapy and zinc to replace lost electrolytes. That need is particularly fierce in Africa, suffering from the dismantling of the US Agency for International Development (USAID).

So before describing the nifty new genetics, I’ll consider diarrheal disease in the so-called shi_hole countries. Our adopted son Eman lives in one of them, Liberia. We’ve supported him since Obama ran for president – Eman is now a surgeon, saving women from the horrors of genital mutilation. He’s no stranger to the terror of diarrhea. He once had it from simultaneous cholera, amebiasis, and malaria.

Diarrhea Kills

Eman reports:

“I’ve suffered from diarrhea so many times, but on three occasions it almost killed me. I remember spending weeks in the hospital, lying there so weak, and not even able to lift my head. I was dehydrated and on one occasion disoriented, I was told.

My lips were dried and cracked, feeling thirsty but unable to drink, my skin dry and burning, my body felt like it was fading away. I honestly thought I wouldn’t make it. Every time I took in food it would come out the other way.

I got hooked up on IV fluids, rehydration salts and zinc, and survived by an inch. This is the reality for so many kids in Africa right now, kids who won’t survive because of cuts in international aid for oral rehydration salts, zinc, and access to clean water.”

Stats back up Eman’s view.

According to the WHO, nearly 1.7 billion cases of childhood diarrheal disease occur globally every year.

It’s the third leading cause of death in children 1 to 59 months of age. Death can come quickly from sudden loss of fluids and electrolytes (sodium, chloride, potassium and bicarbonate), or more slowly from persistent malnutrition.

In most of the world, oral rehydration replaces water and electrolytes, plus a week or two of zinc tablets. But the recent cuts to USAID have already robbed many children from easily-available treatments for diarrhea. The news coverage is extensive. See Children at Risk: The Growing Impact of USAID Cuts on Pediatric Malnutrition and Death Rates, in Maternal and Child Nutrition, The Devastating Impacts of the USAID pullout on Africa, from the University of Michigan, Children Seeking Cholera Care Die After U.S. Cuts Aid, Charity Says, in the New York Times, and Africa Battles to Halt Cholera Cases as Funding Cuts Hurt in Bloomberg News.

Enter Genomics

The rationale for developing DNA and RNA-based tests to identify pathogens that cause diarrhea is that traditional diagnostics based on microbiology – growing microorganisms in lab glassware – often fail to identify a specific cause, especially for emerging pathogens. More precise diagnostics could make possible treatments more targeted than simple rehydration.

The researchers analyzed 1,000 stool samples from people with diarrheal disease using DNA-based (metagenomics) and RNA-based ( metatranscriptomics) techniques. Analyzing DNA and RNA reveals the workings of pathogens that can’t grow in culture, and of viruses that use RNA as their genetic material.

And the strategy works. “This is the UK’s largest study to compare traditional diagnostics with these next-generation tools. We not only found infections missed by standard tests, but we could see what the bugs were doing inside the gut—something standard diagnostics just can’t show,” said co-lead author Edward Cunningham-Oakes.

The investigation focused on Salmonella, a major pathogen in the UK. The findings provide new insights into how the bacteria survive and adapt after leaving the human gut and infecting others. (In Africa, the most common cause of diarrhea is rotavirus.)

Calculating ratios of RNA to DNA enabled the researchers to distinguish active infections from the harmless residents of the human gut microbiome. The RNA molecules also revealed which proteins pathogens produce as an infection runs its course, as well as in subclinical infections.

A surprise finding was that RNA stays more stable in stool than previously thought. “RNA, once thought too fragile to use in stool testing, can actually give us powerful insights into how infections work. That opens up new possibilities for diagnosing and treating these illnesses more effectively,” said Cunningham-Oakes.

Alistair Darby, Co-Director of the University’s Centre for Genomic Research, put the work into perspective. “This study shows how genetic tools can revolutionize how we identify and understand intestinal infections. By understanding not just what’s there, but what it’s doing, we can improve public health responses, particularly around foodborne outbreaks.”

Darby added in a news release that healthcare professionals are open to the idea of genomics-based diagnosis. “This is about more than diagnosing infections—it’s about building a platform for innovation in healthcare. By making our data open-access, we hope to help other researchers, NHS labs, and public health agencies build on our work.”

All that is well and good, but my thoughts keep going back to Africa.

I know I’m taking a bit of a leap. The research is being done in the UK, not the US, and obviously began long before the devastating aid cuts in Africa and elsewhere. But I can’t help but wonder whether more lives would be saved if funds could somehow be diverted to the more obvious and numerous cases, in neither the UK nor the US, that are quickly fatal.

In the US these days, it is difficult to read of any research advance outside the lens of the current war on science and health care.