Whole genome sequence-based serogrouping of Listeria monocytogenes isolates

Abstract

Whole genome sequencing (WGS) is currently becoming the method of choice for characterization of Listeria monocytogenes isolates in national reference laboratories (NRLs). WGS is superior with regards to accuracy, resolution and analysis speed in comparison to several other methods including serotyping, PCR, pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), multilocus variable number tandem repeat analysis (MLVA), and multivirulence-locus sequence typing (MVLST), which have been used thus far for the characterization of bacterial isolates (and are still important tools in reference laboratories today) to control and prevent listeriosis, one of the major sources of foodborne diseases for humans. Backward compatibility of WGS to former methods can be maintained by extraction of the respective information from WGS data. Serotyping was the first subtyping method for L. monocytogenes capable of differentiating 12 serovars and national reference laboratories still perform serotyping and PCR-based serogrouping as a first level classification method for Listeria monocytogenes surveillance. Whole genome sequence based core genome MLST analysis of a L. monocytogenes collection comprising 172 isolates spanning all 12 serotypes was performed for serogroup determination. These isolates clustered according to their serotypes and it was possible to group them either into the IIa, IIc, IVb or IIb clusters, respectively, which were generated by minimum spanning tree (MST) and neighbor joining (NJ) tree data analysis, demonstrating the power of the new approach.

Genomic Diversity of Common Sequence Types of Listeria monocytogenes Isolated from Ready-to-Eat Products of Animal Origin in South Africa

“…Recently, molecular-based subtyping comparisons to match human isolates to food or environmental isolates have become critical for tracking and source identification of the cause of outbreak [7]. Traditionally, pulsed-field gel electrophoresis (PFGE) has been used as the "gold standard" for subtyping of L. monocytogenes isolates involved in outbreaks and sporadic cases; however, Whole Genome Sequencing (WGS) has emerged as a powerful tool for subtyping and investigation of L. monocytogenes outbreak cases [8].…”

An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes

“…The core genome consists of all genes present in all genomes of L. monocytogenes while the pan-genome consists of all the genes present in any strain of the species (supra-genome). Different cg or wgMLST schemes have been developed: in Germany (Ruppitsch et al, 2015 ), Austria (Hyden et al, 2016 ), and USA (Chen et al, 2016b ), as well as by a consortium comprising the CDC (USA), the Pasteur Institute (France), the SSI (Denmark), PHAC Canada and PHE (UK) (Moura et al, 2016 ). The SNP approach is based on mapping raw sequence reads against a reference genome to call variations in both genes and intergenic regions.…”

Looking Backward To Move Forward: the Utility of Sequencing Historical Bacterial Genomes

“…Other genomic investigations using isolates from this collection are also advancing insights into listeriosis, including the generation of a draft genome of a 94-year-old isolate, which may provide historical context for future studies (37), and the use of the isolates in increasing the genetic diversity available to characterize the population structure of L. monocytogenes (38).…”