Researchers have described how a laboratory handled increased demand during the 2017-2018 listeriosis outbreak in South Africa.

Whole genome sequencing (WGS) and epidemiological data were used to determine the source of the outbreak as ready-to-eat processed meat manufactured by Enterprise Foods.

A total of 1,060 cases were reported from January 2017 to July 2018 and 216 people died.

The largest ever reported outbreak of listeriosis included an alert in mid-June 2017, a peak in mid-November 2017, and identification of the outbreak source in mid-February 2018.

“This eight-month timeline was rather remarkable, considering the large number of cases involved and the limited capacity and resources available for foodborne disease outbreak investigations in South Africa,” according to researchers.

The study published in the Foodborne Pathogens and Disease journal described laboratory activities, experiences and results of WGS analysis of Listeria monocytogenes isolates at the Centre for Enteric Diseases (CED). It is a prelude ahead of more detailed articles.

Last month, Tiger Brands, which owns Enterprise Foods, revealed it planned to fight a class action lawsuit relating to the company’s part in the outbreak.

In the study, multilocus sequence typing (MLST) showed that 91 percent of clinical isolates were sequence type 6 (ST6). The rest belonged to 14 different STs (ST1, ST101, ST155, ST2, ST204, ST219, ST224, ST3, ST5, ST54, ST7, ST8, ST87, and ST876).

Listeria monocytogenes ST6 was found in environmental sampling swabs of an Enterprise Foods production facility and in RTE processed meat products including polony, a product similar to bologna sausage manufactured at the site in Polokwane.

ST6 isolates from the Enterprise Foods production facility, including post cooking areas, and from food were shown by single nucleotide polymorphism (SNP) analysis to be highly related to clinical isolates.

Core-genome MLST showed clinical ST6 isolates and Enterprise-related ST6 isolates had no more than 4 allele differences between each other, suggesting a high probability of epidemiological relatedness. The 372 ST6 isolates included 326 clinical isolates, 22 Enterprise food isolates, and 24 environmental isolates recovered from the Polokwane production facility.

Increase in isolates sent to lab
Molecular epidemiology of the outbreak was investigated using WGS analysis of Listeria monocytogenes isolates.

“This was a massive undertaking for a relatively small reference public health laboratory in South Africa, the Centre for Enteric Diseases, a laboratory that was still in its WGS ‘infancy’ and still in the process of taking “small steps” toward the implementation of WGS for analysis of enteric pathogens,” according to researchers.

The CED is a member of PulseNet International, a global molecular subtyping network for foodborne disease surveillance. It started WGS activities in September 2015.

For 2013 to 2016, a range of 55 to 113 laboratory-confirmed cases of listeriosis occurred annually in South Africa. At the peak of the polony outbreak in mid-November 2017 there were 41 cases were reported in one week. Final outcome was known for 806 out of 1,060 patients, with a 27 percent fatality rate.

At the onset of the outbreak, the team decided to investigate all bacterial isolates using WGS but admitted they did not anticipate the mammoth task that awaited them.

“The weekly number of Listeria monocytogenes isolates received at our laboratory multiplied rapidly, increasing 40-fold at the height of the outbreak. The laboratory staff (two technicians, two technologists, and two scientists) were rapidly overwhelmed with the increased workload. From isolate reception at CED to WGS data availability, the timeline ranged from seven to 10 working days,” according to the report.

As a result of the outbreak, listeriosis has been added to the South African list of mandatory notifiable medical conditions and surveillance systems have been strengthened to help prevention and early detection of listeriosis outbreaks.

Government oversight
A different review, published in the journal Food Control, found the inability of the South African government to effectively regulate the sector is a contributing factor to increased food safety risks.

The study provides an overview of the current state of food safety policies and regulations, challenges and practices in the sector after the listeriosis crisis of 2017 and 2018.

Researchers found enforcement of different regulatory processes is often poorly coordinated.

“Responding to this regulatory environment, food safety activities of the food retail industry include a self-regulatory system reliant on internal and third-party food audits, worker training, external testing, and consumer education,” they wrote.

“Given this fragmented framework and the lack of interaction, it is clear that the governance of the South African food safety system is not ‘fit for purpose’ in that there is a gap in the effectiveness of government regulation and the self-regulation of the formal sector, and a growing risk from an inability to regulate the large informal sector.”