Outbreak ofListeria monocytogenesin 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 monocytogene s 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. monocytogene s 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.

Retrospective Study of Listeria monocytogenes Isolated in the Territory of Inner Eurasia from 1947 to 1999

“…The predominant clonal complexes in China are CC9 and CC8 in food and ST87 in clinics [53,54]. In the last decade, CC6 noticeably increased in significance as a causative agent of human listeriosis in Africa, Europe, and North America [31,33,[55][56][57]. In Russia, current human listeriosis is associated with the CC1, CC2, and CC20 strains [38].…”

An outbreak of multiple genotypes of Listeria monocytogenes in New Zealand linked to contaminated ready-to-eat meats—a retrospective analysis using whole-genome sequencing

“…The results observed in this study are similar to those reported for the largest outbreak of listeriosis to date (total of 1060 cases) that was attributed to a processed RTE meat in South Africa. That investigation also used the same cgMLST scheme (Moura et al ) and reported that clinical isolates were highly related to nonclinical isolates with <10 SNP and four allele differences suggesting a high probability of epidemiological relatedness (Smith et al ).…”

“…Internationally recognized thresholds for cgMLST allele or SNP analysis differences between genetically related isolates are still being established. Publications describing the use of WGS within listeriosis outbreaks globally have reported ≤12 alleles by whole‐genome MLST or ranges of 0–50 SNPs as criteria to distinguish outbreak‐related isolates from unrelated isolates (Ruppitsch et al ; Jackson et al ; Moura et al ; Chen et al ; Moura et al ; Smith et al ). However, there is some variation between studies regarding the classification of strains as closely linked (Jackson et al ; Besser et al ).…”

The Antimicrobial Effect of Radiant Catalytic Ionization on the Bacterial Attachment and Biofilm Formation by Selected Foodborne Pathogens under Refrigeration Conditions

“…The study materials consisted of 3 Campylobacter jejuni strains (one reference strain ATCC 33560 and two isolated from poultry meat), 3 Listeria monocytogenes strains (one reference strain ATCC 19111 and two isolated from poultry meat), and 3 Salmonella Enteritidis strains (one reference strain ATCC 13076 and two isolated from poultry meat).…”