Outbreak of Listeria monocytogenes in South Africa, 2017-2018: Laboratory Activities and Experiences Associated with Whole-Genome Sequencing Analysis of Isolates

Abstract

In South Africa, a progressive increase in listeriosis cases was noted from mid-June 2017, heralding what was to become the world's largest listeriosis outbreak. A total of 1060 cases were reported for the period January 1, 2017 to July 17, 2018. We describe laboratory activities, experiences, and results of whole-genome sequencing (WGS) analysis of Listeria monocytogenes isolates associated with this outbreak. Bacteria were identified using the VITEK-2 COMPACT 15 microbial identification system. WGS was performed using Illumina MiSeq technology. WGS data were analyzed using CLC Genomics Workbench Software and free-to-use on-line analysis tools/pipelines. Multilocus sequence typing (MLST) showed that 91% of clinical isolates were sequence type 6 (ST6), determining that the outbreak was largely associated with L. monocytogenes ST6. Epidemiological and laboratory findings led to investigation of a large ready-to-eat processed meat production facility in South Africa, named Enterprise Foods. L. monocytogenes ST6 was found in environmental sampling swabs of the production facility and in ready-to-eat processed meat products (including polony, a product similar to bologna sausage) manufactured at the facility. ST6 isolates, sourced at the Enterprise Foods production facility and from Enterprise food products, were shown by single nucleotide polymorphism (SNP) analysis to be highly related to clinical isolates; these nonclinical ST6 isolates showed <10 SNP differences when compared to clinical ST6 isolates. Core-genome MLST showed that clinical ST6 isolates and Enterprise-related ST6 isolates had no more than 4 allele differences between each other, suggestive of a high probability of epidemiological relatedness. WGS data interpreted together with epidemiological data concluded that the source of the listeriosis outbreak was ready-to-eat processed meat products manufactured by Enterprise Foods. Listeriosis has now been added to the South African list of mandatory notifiable medical conditions. Surveillance systems have been strengthened to facilitate prevention and early detection of listeriosis outbreaks.

Keywords: Listeria monocytogenes; ST6; South Africa; listeriosis; outbreak; sequence type 6; whole-genome sequencing.

FIG. 1.

Epidemiological curve of laboratory-confirmed listeriosis showing number of cases by week (listed according to date of sample collection), South Africa, January 1, 2017 to July 17, 2018 (n = 1060).

FIG. 2.

Maximum likelihood tree (circular tree) drawn using SNP alignments from WGS data of clinical Listeria monocytogenes isolates. The ST6 outbreak cluster representing 91% of the clinical isolates is highlighted with shading. SNP, single nucleotide polymorphism; ST6, sequence type 6; WGS, whole-genome sequencing.

FIG. 3.

Minimum spanning tree drawn using cgMLST data from 374 Listeria monocytogenes ST6 isolates from several sources including clinical (human), food, and production facility. The circular nodes represent isolate(s) having the identical cgMLST profile; the larger the node, the more isolates are reflected. The number values between adjacent nodes indicate the number of allele differences between nodes. Gray shading encompasses all nodes (isolates) that have no more than four allele differences when compared to their adjacent neighboring nodes (isolates). The source of isolates is reflected in the coloring of the nodes. cgMLST, core-genome multilocus sequence typing.