South Africa has been hit with the world’s worst outbreak of listeria, a bacteria that seen more than 180 people die and hundreds fall ill. Scientists have managed to trace the source of contamination by reading the millions of letters encoded in listeria’s DNA.

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

This is how SA scientists did it:

1. When patients are ill and doctors do not know what it wrong with them, they send blood and spinal fluid samples to a laboratory. In South Africa, that’s the National Health Laboratory Service or a private laboratory.

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2. The technicians add the sample to a nutrient-enriched broth, so that the bacteria can incubate and grow.

3. The lab performs a diagnostic test on the bacteria, and if it is listeria, they package it up in agar (which is a jelly-like culture medium), and send it to the National Institute for Communicable Diseases (NICD). (The NICD does this in a biochemical diagnostic machine produced by a company called VITEK.)

Listeria monocytogenes in agar. Photo: James Folsom

4. Even though they are tiny (a thousand bacteria can fit on the tip of a pin), bacteria have a number of cellular components (such as cell walls, etc), and scientists have to extract the bacterium’s DNA from everything else in the bacterium.

5. But this extraction process only yields miniscule amounts of DNA. But high-throughput DNA sequencers amplify or elongate the fragments of DNA so that there is enough for the sequencer to sequence.

6. DNA comprises molecules of nucleic acid, called base pairs. There are four different types -- Adenine (A), Guanine (G), Cytosine (C) , and Thymine (T) -- that are usually known by their first letters. These building-block molecules, arranged in different ways, create uniquely identifiable DNA. Listeria has 3 million base pairs. Humans, on the other hand, have about 3 billion.

7. The DNA sequencer identifies the code of the DNA, its series of A, G, C, and T, and researchers feed this code into international genomic databases containing the DNA sequences of other organisms.

A, T, C, and G are the basic nucleic acid codes in DNA. Image: Oxford Nanopore

8. Bacteria reproduce by fission: the single-celled organism splits into two other single-celled organisms each bearing the exact same DNA. What this meant for the researchers trying to trace the source of the listeria outbreak was that if the bacteria that was cultured and sequenced had similar DNA, they were from the same original bacterial strain.

9. In the NICD’s listeria samples, “less than 20 base pairs different” out of about 3-million, says Kerrigan McCarthy, head of the outbreak response unit at the NICD. “It’s irrefutable.”

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