High-tech sleuthing helped SA scientists find the DNA ‘fingerprint’ of deadly listeria – and save lives

Business Insider SA
A transmission electron micrograph (TEM) of a Listeria bacterium in a tissue sample. Listeria monocytogenes is the infectious agent responsible for the food borne illness listeriosis. Photo: Getty Images

  • SA scientists' DNA sleuthing has probably prevented listeria from killing more people.
  • Researchers at the National Institute for Communicable Diseases tested the genome sequences of thousands of bacteria cultures.
  • A brand-new genome sequencing facility allowed them to do the tests in South Africa.

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.

See also: Tons of recalled meat are headed for public landfill sites – and that could spell an entirely new disaster

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."

See also: How the deadly strain of listeriosis was traced to Tiger Brands’ Enterprise polony factory

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.

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