Real-Time Whole-Genome Sequencing for Surveillance ofListeria monocytogenes, France

Abstract

During 2015–2016, we evaluated the performance of whole-genome sequencing (WGS) as a routine typing tool. Its added value for microbiological and epidemiologic surveillance of listeriosis was compared with that for pulsed-field gel electrophoresis (PFGE), the current standard method. A total of 2,743 Listeria monocytogenes isolates collected as part of routine surveillance were characterized in parallel by PFGE and core genome multilocus sequence typing (cgMLST) extracted from WGS. We investigated PFGE and cgMLST clusters containing human isolates. Discrimination of isolates was significantly higher by cgMLST than by PFGE (p<0.001). cgMLST discriminated unrelated isolates that shared identical PFGE profiles and phylogenetically closely related isolates with distinct PFGE profiles. This procedure also refined epidemiologic investigations to include only phylogenetically closely related isolates, improved source identification, and facilitated epidemiologic investigations, enabling identification of more outbreaks at earlier stages. WGS-based typing should replace PFGE as the primary typing method for L. monocytogenes.

Next-generation sequencing technologies and their application to the study and control of bacterial infections

“…The number of outbreaks detected increased 36% after implementation of real-time WGS based surveillance, and likewise the number of solved outbreaks increased more than three-fold (figure 1) while the incidence of disease remained constant at approximately 0.2 cases per 100,000 (17). Similar improvements in surveillance of listeriosis were found in France after WGS implementation (18). …”

Whole‐genome sequencing reveals Listeria monocytogenes diversity and allows identification of long‐term persistent strains in Brazil

“…Existing national epidemiological surveillance programs actively detect and investigate clusters of cases, identify the origin of food contamination and implement control measures. Whole-genome sequencing (WGS) has recently emerged as a powerful tool for national and international outbreak investigations (Schmid et al, 2014;Ruppitsch et al, 2015;Moura et al, 2017;Nielsen et al, 2017;Van Walle et al, 2018). WGS allows an unprecedented subtyping resolution by analysis of the core genome, as well as the accessory genome.…”

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

“…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 ).…”

“…Single‐nucleotide polymorphism (SNP) analysis assesses a WGS base by base, while a multilocus sequence typing (MLST) approach involves a gene by gene analysis that can include core genes (cgMLST) or both core and accessory genes (whole‐genome MLST) (Besser et al ). The application of cgMLST analysis for L. monocytogenes has been demonstrated as a highly reproducible method with the ability to standardize nomenclature of alleles and types (Ruppitsch et al ; Moura et al ; Moura et al ; Nadon et al ; Pietzka et al ). Depending on the discriminatory ability of cgMLST, additional typing procedures such as SNP analysis can also be applied.…”