Clues litter the trail in the hunt for SA's killer bug

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Clues litter the trail in the hunt for SA's killer bug

It's ‘CSI for bacteria’ as scientists at the National Institute of Communicable Diseases search for the source of listeria outbreak

Journalist

A rash of purple dots is eating up Gauteng and they stare back at bioinformaticist Mushal Allam every morning as he and his team settle in for another day of fighting one of the worst epidemics South Africa has ever seen.
The DNA of listeria samples is sequenced at Allam’s lab at the National Institute of Communicable Diseases (NICD) and the purple dots on his screen represent each listeria sample that is identified as strain ST6.
ST6, the abbreviation for the innocuously named “sequence type 6”, is currently causing the world’s largest documented outbreak of listeria here in South Africa.
Allam explains the ST6  strain is “virulent”, and particularly good at making humans sick. What no one knows yet, is why.
Even more urgently, scientists don’t know which food is causing the outbreak.
In the meantime, the bacteria, which is carried in food, kills one in three babies it infects. Pregnant women are at high risk of developing listeria but, scarily, many have no symptoms at all, so they don't even know they will still pass it on during pregnancy or labour. 
Most babies who get infected will spend the first six days of their life sick.The hunt for the source is difficult. Listeria is ubiquitous. It lives in soil and can survive for months on inanimate surfaces.
Listeria can also infect an impossibly wide range of foods.  Dr Juno Thomas, head of the Centre for Enteric Diseases at NICD, said people, especially pregnant women at high risk, have been “angry” with the national Health Department for not telling them what to eat to avoid the disease.
But, the answer, at this point, would be food.
Globally, there have been listeriosis outbreaks caused by cantaloupe (spanspek), ice cream, sausages, corned beef, tongue, ham and other processed meats. Also to blame have been soft cheese, corn, mussels, salmon, chicken, eggs, pasteurised and unpasteurised milk, chocolate drinking milk, spinach, lettuce, butter and prepared fruit salad.Thomas and her team are working long hours to find the culprit behind the current outbreak. 
Allam didn’t go home to Sudan for a holiday with his wife and baby because he was hunting for the source of listeria in December.
Allam, who has a PhD in bioinformatics, works in the DNA laboratory and uses his computer to interpret data the bacteria's genetic code is offering to the machines.
Because Allam can show most infections are a genetic clone of the other, the hypothesis is that there could be a single infection point, perhaps a single farm, or abattoir, or individual food processing plant.He can also see that cases are spread across the country in middle-class and lower socio-economic groups. This means the source is a food product eaten countrywide, and one that is affordable.
But these clues aren’t making the hunt any easier.
Thomas explains the bacteria can outsmart humans and survive cleaning.
Bacteria sense when they are nearby the exact same bacteria and “speak” to each other using molecules. They then excrete a sugary substance called a biofilm (plaque on teeth is an example) to cover them, allowing them to live on inanimate surfaces for months.With biofilm bacteria can survive even if factories are using detergents.
A dairy abroad once had a listeria outbreak for 10 years and eventually staff dismantled the entire plant and steam-cleaned every bit of equipment, says Thomas.
The search is not being helped by unco-operative elements in the food industry.
The national Health Department asked food industry bodies the SA Meat Producers Association and the Red Meat Industry Forum in December to tell their members – who make processed food – to provide samples of tested food or lab results looking for listeria monocytogenes in processed meat.This is because historically, processed meat is often to blame for listeria outbreaks.
Neither the forum nor the association or their members have complied with the request. The Health Department is unimpressed.
Health Department spokesman Popo Maja said: “The lack of information from South African Meat Processors Association (Sampa) members is a cause for concern in light of the high probability of listeria in processed meat products such as polony, ham [and] viennas.”
Sampa spokesperson Nadine Naylor said testing for microbes in food was not the voluntary association's mandate and it was doing all it could to help.
“We are co-operating with DoH as best we can at this stage,” she said.
“We do not test for microbes, as this is the responsibility of the manufacturer and retailer given that any infection could be at various points along the value chain.
“We also do not have the infrastructure to facilitate the gathering of test results, hence the reason we supplied the department with the database and contact details of all processed food manufacturers so they were able to get in touch with those who are not supplying the information.”
Besides testing for listeria, the National Institute for Communicable Disease is recording what food people who are sick have eaten to work out which is the culprit.
This is where Nevashan Govender, emergency operations centre manager at the NICD, comes in.
“I don’t sleep much,” he says.
Govender’s teams interview patients using a standardised survey to determine their food diary for the past 21 days.
Working out the food or foods to blame is still tough.
For example, if margarine in a sandwich was making a person sick, but if the sandwich had been bought by the patient, it would be impossible to know what brand of margarine was used.
In the case of toffee apples, which once caused an outbreak in the United States, people may not report eating a toffee apple because it is not commonly thought of as a meal.
NICD scientist Dr Anthony Smith calls the lab’s work “CSI for bacteria”, but, unlike in the TV shows, finding an answer is slow. It takes five days to get a listeria sample’s DNA identified from the time the sample arrives at the lab.
Finding the source of a listeria outbreak in smoked pork products in Germany once took four years to crack.
Could it take that long to find South Africa's source? Thomas put in her head in her hands, sighs and says she hopes not. They hope to find it in weeks.
As Govender describes it, his colleagues are “a small team doing a hell of a lot of work”.

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