Statement regarding the source of the Listeriosis outbreak
2 April 2018
The National Institute for Communicable Diseases (NICD) is concerned about recent developments and statements supposedly released as facts into the public domain about the listeriosis outbreak.
We are particularly worried about the confusion that emanated from statements made at the meeting called by the Parliamentary Portfolio Committee on Agriculture on 28 March 2018.
Of major concern are the claims that the primary source of the outbreak is still unknown, and that the Minister of Health has backed down on his previous announcement that the source had been identified, both of which we refute. The statements the Minister of Health has made have emanated from epidemiologic and scientific investigations conducted by the NICD.
The implication that the NICD has misled the Minister of Health and the public is rejected. Furthermore, we condemn the statement made that the government prematurely scapegoated ‘Enterprise and Rainbow’ without sufficient evidence. We contend that this evidence has been amply provided by the NICD.
We do not regard these claims as a small matter, because the NICD is not just a routine diagnostic laboratory with an impact localised to South Africa. The NICD’s work goes far beyond the borders of our country and has an international impact. In outbreaks of this nature, the NICD is obligated by the International Health Regulations to report findings through the National Department of Health to the World Health Organization, and cannot afford to, and does not mislead.
To serve its purpose, the NICD has specialised laboratories and public health and epidemiologic expertise. This expertise leads it to serve as a reference centre, not only for the public and private sectors in South Africa, but across Africa. It shares information and works together with the World Health Organization (WHO) and eminent international institutions (including the Centers for Disease Control and Prevention (CDC) and the National Institutes of Health (NIH) of the USA, the European Centre for Disease Control (ECDC) and Public Health England. The NICD is the co-ordinator of the prestigious PulseNet Africa network, within PulseNet International. PulseNet is a global network of laboratories dedicated to tracking foodborne infections (including listeriosis) world-wide, all of whose laboratories, including the NICD, utilise internationally-recognised standardised genotyping methods and share information in real-time.
Therefore, the work of the NICD is scientifically sound and evidence-based. For those who still have lingering doubts, this is how we arrived at the conclusions announced by the Minister of Health on 04 March 2018.
The search for the cause of the outbreak began with the isolates of Listeria monocytogenes bacteria from case-patients referred from National Health Laboratory Service (NHLS) and private sector clinical laboratories to the NICD, where they underwent confirmatory testing and whole genome sequencing (WGS). WGS is the most sensitive and specific molecular tool available to assess genetic relatedness of bacterial isolates. Of the 439 clinical isolates from case-patients sequenced to date, 92% belong to sequence type 6 (ST6) and are highly genetically related. This confirms that this single strain is causing the outbreak and is responsible for disease in the vast majority of patients with listeriosis.
At the same time, an intensive process of trying to identify the source of the outbreak was undertaken by the Departments of Health (DoH), Agriculture, Forestry and Fisheries (DAFF) and Trade and Industry (DTI), municipalities and the NICD. Epidemiological investigations included interviewing patients. As 86% of patients interviewed reported eating polony in the month before falling ill with listeriosis, ready-to-eat processed meat products became the focus of investigations. The key breakthrough came when a group of nine children attending the same crèche in Soweto developed febrile gastroenteritis in January 2018. The L. monocytogenes ST6 outbreak strain was identified in one child and in three samples of two brands of polony from the refrigerator at the crèche. This prompted further investigation of the production facilities manufacturing these polony products.
Enterprise Foods’ Polokwane production facility was visited on 2 February 2018 by a team, which included two WHO food safety experts. Extensive sampling was done. Polony production involves a number of steps: raw ingredients are mixed into an emulsion, the polony emulsion is poured into casings (the plastic wrapping) and clipped at either end of the casing, the polony is cooked in its casing, then finally it is cooled. Any Listeria that is present in the raw ingredients or emulsion should be killed during the cooking process. However, any L. monocytogenes found beyond the cooking stage poses the danger of contaminating the polony and causing disease, because polony is not usually cooked again before it is eaten. Of great concern was that the L. monocytogenes ST6 outbreak strain was found in the post-cooking processing environment, and also on the final polony products.
The whole genome sequencing (WGS) technology that identified the ST6 outbreak strain is the gold standard method for characterising which specific L. monocytogenes strain is causing an outbreak. This highly specialised test is performed at the NICD. WGS essentially shows the genetic fingerprint of the bacteria, by sequencing the chemical building blocks (nucleotides or base pairs) that make up its genome (the complete set of its DNA, including all of its genes). The L. monocytogenes genome has approximately 3 million base pairs. The outbreak strain isolates from patients and from the Enterprise Foods’ Polokwane production facility (notably, the post-cooking area and the final product clips and casing) differ by only ≤7 single base pairs out of 3 million. This extremely high level of genetic relatedness (99.99% similarity) means there can be no doubt that these L. monocytogenes ST6 strains are all linked, and that there is certainty that products manufactured at Enterprise Polokwane are the source of the outbreak. This is much like paternity confirmation by DNA testing.
From the evidence above, it is extremely misleading for anyone to claim that the primary cause of this listeriosis outbreak is unknown.
Since the first press conference held by the Minister of Health on 05 December 2017, it has been reiterated many times that L. monocytogenes is widely found in nature and can be found in water, soil, vegetation, and the faeces of some animals. Food can be contaminated from any of these sources throughout the food chain (farm, processing, packaging, retail and home food preparation). However, normal food production safety measures and water treatment procedures should deal with the risk of contamination. In addition, the WHO’s five keys to safer food should be practiced by all. These are:
Wash hands and surfaces before, and regularly during food preparation.
Separate raw and cooked food, and don’t mix utensils and surfaces when preparing food.
Cook food thoroughly – all bacteria are killed above 70°C.
Keep food at safe temperatures – either simmering hot, or in the fridge. Use safe water and safe ingredients to prepare food.
We can report today that additional results from samples of products produced at the Enterprise Polokwane production facility and sold at the Enterprise Germiston factory shop are available. Seven samples of ready-to-eat processed meat products taken on 15 February 2018 tested positive for L. monocytogenes ST6 (outbreak strain). This means that the outbreak strain has been found inside the ready-to-eat processed meat products manufactured at Enterprise Foods’ Polokwane production facility, dispelling claims made to the contrary.
Issued by Juno Thomas, Head: Centre for Enteric Diseases (NICD), 3 April 2018