Malaria has proved one of the hardest diseases on the planet to treat. The World Health Organization estimates there are nearly 200 million cases each year, and the parasitic infection is blamed for some 700,000 deaths annually.

One reason malaria may be so difficult to treat is that different types of malaria parasites can be streaming through the victim's body at the same time. Researchers at the Texas Biomedical Research Institute in San Antonio are now applying a form of DNA analysis called single-cell genome sequencing to better understand the various parasites in a single case.

For instance, the researchers found that people who'd come down with malaria along the Thai-Myanmar border had both Plasmodium vivax and Plasmodium falciparum parasites in their blood. This is problematic, because the standard drugs to treat each of these types are completely different. In addition, the San Antonio academics found that some of the parasites multiplying in the blood cells are resistant to antimalarial drugs, while others show no resistance.

Older DNA sequencing methods didn't allow researchers to analyze single parasites, according to Dr. Ian Cheeseman, who led the study.

"There were so many different strains of parasites within [a malaria infection] that we couldn't tell which was responsible for drug resistance or disease severity," Cheeseman tells Shots. "We really needed a method where we could work out the individual genome sequence of each parasite."

With single-cell genome sequencing Cheeseman and his colleagues found that some of the parasites were very closely related, but others were completely different strains. This raises the question of which strain is driving the illness inside the sick person, whether that could help tailor treatment.

According to Cheeseman's co-author, Shalini Nair, up to 70 percent of malaria cases in sub-Saharan Africa are "multiple genotype infections," meaning they're caused by multiple strains of the parasite.

"And we currently don't know how many genotypes are present and whether parasites come from a single mosquito bite or multiple mosquito bites," says Nair.

Single-cell genomics could help researchers figure this out. But the sophisticaed equipment used to do this won't be coming any time soon to a malaria field clinic in, say, Malawi.

"This isn't going to be used on a routine diagnostic basis for a long, long time ... possibly ever," Cheeseman says. But learning about the basic biology of parasites, he believes, will enable researchers to find better treatments or more effective ways to use treatments that already exist.

