Why is tracing the source of cyclosporiasis outbreaks so difficult?

Compared with bacterial food spoilers such as Salmonella, Escherichia coli, or Campylobacter, which each cause many more cases annually, Cyclospora, a protozoan parasite, hasn’t been “on the radar” as much, says Kellogg Schwab, a public health scientist at Johns Hopkins University. PulseNet, a national network that uses DNA data from pathogens to connect cases across states, only tracks bacteria-related foodborne illnesses.

And unlike bacteria, Cyclospora only reproduces in humans’ small intestine; it can’t be grown in the lab. That gives researchers considerably less material to analyze. “All we can work with is the parasites that are in the person’s stool,” says Joel Barratt, an associate professor at Emory University’s School of Medicine who led the Cyclospora laboratory team of CDC’s Division of Parasitic Diseases and Malaria until his resignation last year. What’s more, whole-genome sequencing, which makes it easy to compare organisms, would be too expensive for Cyclospora because its genome is “massive,” Barratt says: some 44 million base pairs, about 10 times larger than those of Salmonella or E. coli. Instead, CDC relies on tests that target eight specific genetic markers.

And finally, bacteria reproduce asexually in the human gut, creating nearly perfect clones that make it easy to identify genetic clusters. Cyclospora reproduces sexually, a process in which two parasites scramble their genes. That means even samples from the same source “are not going to be genetically identical,” Barratt says.