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

Clémentine Henri,René S Hendriksen,Nicolas Radomski,Arnaud Felten,Michel-Yves Mistou,Sophie Roussel,Frank M Aarestrup,Jean-François Mariet,Rolf S Kaas,Pimlapas Leekitcharoenphon,Laurent Guillier,Heather A Carleton,Peter Gerner Smidt

doi:10.3389/fmicb.2017.02351

Abstract

Background/objectives: Whole genome sequencing (WGS) has proven to be a powerful subtyping tool for foodborne pathogenic bacteria like L. monocytogenes. The interests of genome-scale analysis for national surveillance, outbreak detection or source tracking has been largely documented. The genomic data however can be exploited with many different bioinformatics methods like single nucleotide polymorphism (SNP), core-genome multi locus sequence typing (cgMLST), whole-genome multi locus sequence typing (wgMLST) or multi locus predicted protein sequence typing (MLPPST) on either core-genome (cgMLPPST) or pan-genome (wgMLPPST). Currently, there are little comparisons studies of these different analytical approaches. Our objective was to assess and compare different genomic methods that can be implemented in order to cluster isolates of L. monocytogenes.Methods: The clustering methods were evaluated on a collection of 207 L. monocytogenes genomes of food origin representative of the genetic diversity of the Anses collection. The trees were then compared using robust statistical analyses.Results: The backward comparability between conventional typing methods and genomic methods revealed a near-perfect concordance. The importance of selecting a proper reference when calling SNPs was highlighted, although distances between strains remained identical. The analysis also revealed that the topology of the phylogenetic trees between wgMLST and cgMLST were remarkably similar. The comparison between SNP and cgMLST or SNP and wgMLST approaches showed that the topologies of phylogenic trees were statistically similar with an almost equivalent clustering.Conclusion: Our study revealed high concordance between wgMLST, cgMLST, and SNP approaches which are all suitable for typing of L. monocytogenes. The comparable clustering is an important observation considering that the two approaches have been variously implemented among reference laboratories.

Highlights

Listeria monocytogenes (L. monocytogenes) is one out of 17 species belonging to the genus Listeria, a Gram-positive rod-shaped bacterium (Weller et al, 2015)
The inferred cgMLST and wgMLST phylogenies were in perfect accordance with the lineage classification whereas for the molecular serotyping, the concordance was slightly lower with a concordance of 96.6% for cgMLST and 97.6% for wgMLST (Table 1 and Supplementary Table 2)
The gene by gene approaches displayed a high concordance with conventional multilocus sequence typing (MLST) i.e., 99.5% concordance with the cgMLST approach and 97.1% with the wgMLST (Table 1 and Supplementary Table 2)

Summary

Introduction

Listeria monocytogenes (L. monocytogenes) is one out of 17 species belonging to the genus Listeria, a Gram-positive rod-shaped bacterium (Weller et al, 2015). L. monocytogenes has the ability to grow at low temperatures, form bio-films and persist in food processing plants (Carpentier and Cerf, 2011). It represents a significant challenge for the foodproducing industry (Ferreira et al, 2014). L. monocytogenes is one of the foodborne pathogens that cause the highest rate of mortality, yet its incidence is low (EFSA, 2014). In 2015, over than 2200 cases were reported in Europe. This highlights L. monocytogenes as a serious re-emerging public health concern and it is intensively monitored in developed countries (de Noordhout et al, 2014; EFSA, 2014)

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Discussion

Conclusion