DNA sleuth work curbed the death toll from a listeria outbreak in South Africa that has left at least 180 people dead and hundreds more ill.
Researchers at the National Institute for Communicable Diseases (NICD) tested the genome sequences of between 1,500 and 2,000 bacteria cultures, grown from contaminated food and human blood or spinal-fluid samples.
Each test cost between R3,000 and R5,000.
The NICD led the scientific charge to trace the source of contaminated food, testing as many food and human samples as possible, says Kerrigan McCarthy, head of the outbreak response unit at the NICD.
The government on Sunday announced that an Enterprise-owned meat-processing facility in Polokwane was the source of the outbreak. By DNA "fingerprinting" and sequencing the genome of the Listeria monocytogenes retrieved from patients, researchers found that a single strain – ST6 – was responsible for 95% of the cases, McCarthy says.
To trace the outsource of the outbreak, they had to show that the strain in patient and food samples was different to other listeria strains. All listeria bacteria strains have about three million base pairs, the building blocks of DNA. If the base pairs of two listeria specimens match exactly, then they are descended from the same parent.
For those sampled at the NICD, "fewer than 20 base pairs were different from each other".
"That is out of three million base pairs. The samples are on the same spot of the phylogenetic tree [an evolutionary map of how organisms are related to each other]. It is irrefutable," McCarthy says.
"The achievement of the NICD is not so much that we were able to pinpoint the source, but that we had the tech to do it."
If the outbreak had occurred three years ago, more people would have died. The NICD recently established a core genome sequencing facility, which meant that researchers could sequence the L. monocytogenes genome locally.
"We would not have had the capacity, and we would have had to outsource [the sequencing] internationally, and it would have taken longer," she says.
Receive a single WhatsApp message every morning with all our latest news. Sign up here.