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

Clementine Henri, Pimlapas Leekitcharoenphon, Heather A. Carleton, Nicolas Radomski, Rolf Sommer Kaas, Jean-Francois Mariet, Arnaud Felten, Frank Møller Aarestrup, Peter Gerner Smidt, Sophie Roussel, Laurent Guillier, Michel-Yves Mistou, Rene S. Hendriksen

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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.
Original languageEnglish
Article number2351
JournalFrontiers in Microbiology
Volume8
Number of pages13
ISSN1664-302X
DOIs
Publication statusPublished - 2017

Keywords

  • Listeria monocytogenes
  • WGS
  • cgMLST
  • wgMLST
  • SNPs
  • PFGE
  • conventional MLST
  • surveillance

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