This article has been updated


Listeria monocytogenes (Lm) is a major human foodborne pathogen. Numerous Lm outbreaks have been reported worldwide and associated with a high case fatality rate, reinforcing the need for strongly coordinated surveillance and outbreak control. We developed a universally applicable genome-wide strain genotyping approach and investigated the population diversity of Lm using 1,696 isolates from diverse sources and geographical locations. We define, with unprecedented precision, the population structure of Lm, demonstrate the occurrence of international circulation of strains and reveal the extent of heterogeneity in virulence and stress resistance genomic features among clinical and food isolates. Using historical isolates, we show that the evolutionary rate of Lm from lineage I and lineage II is low (2.5 × 10−7 substitutions per site per year, as inferred from the core genome) and that major sublineages (corresponding to so-called ‘epidemic clones’) are estimated to be at least 50–150 years old. This work demonstrates the urgent need to monitor Lm strains at the global level and provides the unified approach needed for global harmonization of Lm genome-based typing and population biology.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Change history

  • 14 July 2017

    In the PDF version of this article previously published, the year of publication provided in the footer of each page and in the 'How to cite' section was erroneously given as 2017, it should have been 2016. This error has now been corrected. The HTML version of the article was not affected.


  1. 1.

    et al. Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 477, 462–465 (2011).

  2. 2.

    et al. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proc. Natl Acad. Sci. USA 109, 3065–3070 (2012).

  3. 3.

    , & Lessons from Ebola: improving infectious disease surveillance to inform outbreak management. Sci. Transl. Med. 7, 307rv5 (2015).

  4. 4.

    et al. Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin. Microbiol. Infect. 13, 1–46 (2007).

  5. 5.

    , , , & Others. A global initiative on sharing avian flu data. Nature 442, 981–981 (2006).

  6. 6.

    et al. Pulsenet USA: a five-year update. Foodborne Pathog. Dis. 3, 9–19 (2006).

  7. 7.

    et al. Geographic distribution of Staphylococcus aureus causing invasive infections in Europe: a molecular-epidemiological analysis. PLoS Med. 7, e1000215 (2010).

  8. 8.

    ECDP and Control Surveillance of Seven Priority Food- and Waterborne Diseases in the EU/EEA (ECDC, 2015).

  9. 9.

    et al. An outbreak of gastroenteritis and fever due to Listeria monocytogenes in milk. N. Engl. J. Med. 336, 100–106 (1997).

  10. 10.

    et al. A new perspective on Listeria monocytogenes evolution. PLoS Pathog. 4, e1000146 (2008).

  11. 11.

    et al. Worldwide distribution of major clones of Listeria monocytogenes. Emerg. Infect. Dis. 17, 1110–1112 (2011).

  12. 12.

    , , , & The ubiquitous nature of Listeria monocytogenes clones: a large-scale multilocus sequence typing study. Environ. Microbiol. 16, 405–416 (2014).

  13. 13.

    et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science 327, 469–474 (2010).

  14. 14.

    et al. MLST revisited: the gene-by-gene approach to bacterial genomics. Nat. Rev. Microbiol. 11, 728–736 (2013).

  15. 15.

    et al. Short-term genome evolution of Listeria monocytogenes in a non-controlled environment. BMC Genomics 9, 539 (2008).

  16. 16.

    et al. Evolutionary relationships of outbreak-associated Listeria monocytogenes strains of serotypes 1/2a and 1/2b determined by whole genome sequencing. Appl. Environ. Microbiol. 82, 928–938 (2015).

  17. 17.

    et al. Whole genome sequencing as a tool to investigate a cluster of seven cases of listeriosis in Austria and Germany, 2011–2013. Clin. Microbiol. Infect. 20, 431–436 (2014).

  18. 18.

    et al. Prospective whole genome sequencing enhances national surveillance of Listeria monocytogenes. J. Clin. Microbiol. 54, 333–342 (2016).

  19. 19.

    et al. Defining and evaluating a core genome MLST scheme for whole genome sequence-based typing of Listeria monocytogenes. J. Clin. Microbiol. 53, 2869–2876 (2015).

  20. 20.

    , , & Whole genome sequencing allows for improved identification of persistent Listeria monocytogenes in food associated environments. Appl. Environ. Microbiol. 81, 6024–6037 (2015).

  21. 21.

    et al. Update: multinational listeriosis outbreak due to ‘quargel’, a sour milk curd cheese, caused by two different L. monocytogenes serotype 1/2a strains, 2009–2010. Euro Surveill 15, 19543 (2010).

  22. 22.

    , & Choice of reference sequence and assembler for alignment of Listeria monocytogenes short-read sequence data greatly influences rates of error in SNP analyses. PLoS ONE 9, e104579 (2014).

  23. 23.

    & BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11, 595 (2010).

  24. 24.

    , & The Listeria monocytogenes core-genome sequence typer (LmCGST): a bioinformatic pipeline for molecular characterization with next-generation sequence data. BMC Microbiol. 15, 29 (2015).

  25. 25.

    et al. Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity. Nat. Genet. 48, 308–313 (2016).

  26. 26.

    et al. ‘Epidemic clones’ of Listeria monocytogenes are widespread and ancient clonal groups. J. Clin. Microbiol. 51, 3770–3779 (2013).

  27. 27.

    et al. Clonogrouping, a rapid multiplex PCR method for identification of major clones of Listeria monocytogenes. J. Clin. Microbiol. 53, 3355–3358 (2015).

  28. 28.

    , , & Listeria monocytogenes persistence in food-associated environments: epidemiology, strain characteristics, and implications for public health. J. Food Prot. 77, 150–170 (2014).

  29. 29.

    et al. Genetic characterization of clones of the bacterium Listeria monocytogenes causing epidemic disease. Proc. Natl Acad. Sci. USA 86, 3818–3822 (1989).

  30. 30.

    et al. Ribotypes and virulence gene polymorphisms suggest three distinct Listeria monocytogenes lineages with differences in pathogenic potential. Infect. Immun. 65, 2707–2716 (1997).

  31. 31.

    et al. Characterization of the novel Listeria monocytogenes PCR serogrouping profile IVb-v1. Int. J. Food Microbiol. 147, 74–77 (2011).

  32. 32.

    et al. Listeriolysin S, a novel peptide haemolysin associated with a subset of lineage I Listeria monocytogenes. PLoS Pathog. 4, e1000144 (2008).

  33. 33.

    et al. A molecular marker for evaluating the pathogenic potential of foodborne Listeria monocytogenes. J. Infect. Dis. 189, 2094–2100 (2004).

  34. 34.

    et al. Comk prophage junction fragments as markers for Listeria monocytogenes genotypes unique to individual meat and poultry processing plants and a model for rapid niche-specific adaptation, biofilm formation, and persistence. Appl. Environ. Microbiol. 77, 3279–3292 (2011).

  35. 35.

    , , , & Prophage excision activates Listeria competence genes that promote phagosomal escape and virulence. Cell 150, 792–802 (2012).

  36. 36.

    et al. The Listeria monocytogenes transposon Tn6188 provides increased tolerance to various quaternary ammonium compounds and ethidium bromide. FEMS Microbiol. Lett. 361, 166–173 (2014).

  37. 37.

    , , & Genomes of sequence type 121 Listeria monocytogenes strains harbor highly conserved plasmids and prophages. Front. Microbiol. 6, 380 (2015).

  38. 38.

    et al. Tracing sources of Listeria contamination in traditional Italian cheese associated with a US outbreak: investigations in Italy. Epidemiol. Infect. 2, 1–9 (2015).

  39. 39.

    , & Global burden of listeriosis: the tip of the iceberg. Lancet Infect. Dis. 14, 1027–1028 (2014).

  40. 40.

    et al. Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome. BMC Genomics 14, 47 (2013).

  41. 41.

    et al. Genome sequencing identifies two nearly unchanged strains of persistent Listeria monocytogenes isolated at two different fish processing plants sampled 6 years apart. Appl. Environ. Microbiol. 79, 2944–2951 (2013).

  42. 42.

    SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics 7, 88 (2006).

  43. 43.

    Phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217–223 (2012).

  44. 44.

    et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 10, e1003537 (2014).

  45. 45.

    et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 43, e15 (2015).

Download references


The authors thank K. Jolley (Oxford University) for assistance with BIGSdb implementation, PulseNet International Network members for continuous surveillance and data sharing, the Genomics platform (PF1, Institut Pasteur) for assistance with sequencing, D. Mornico (Institut Pasteur) for assistance with the submission of raw data, J. Haase and M. Achtman (Environmental Research Institute, Ireland) for providing cultures of historical isolates of SL1. The authors also thank N. Tessaud-Rita, G. Vales and P. Thouvenot (National Reference Centre for Listeria, Institut Pasteur) for recovering and extracting DNA from historical isolates of SL9.

This work was supported by Institut Pasteur, INSERM, Public Health France, French government's Investissement d'Avenir program Laboratoire d'Excellence “Integrative Biology of Emerging Infectious Diseases” (grant ANR-10-LABX-62-IBEID), European Research Council, Swiss National Fund for Research and the Advanced Molecular Detection (AMD) initiative at CDC.

Author information


  1. National Reference Centre and World Health Organization Collaborating Center for Listeria, Institut Pasteur, 75724 Paris, France

    • Alexandra Moura
    • , Mylène M. Maury
    • , Alexandre Leclercq
    • , Hélène Bracq-Dieye
    • , Thomas Cantinelli
    • , Viviane Chenal-Francisque
    •  & Marc Lecuit
  2. Biology of Infection Unit, Institut Pasteur, 75724 Paris, France

    • Alexandra Moura
    • , Mylène M. Maury
    • , Alexandre Leclercq
    • , Hélène Bracq-Dieye
    •  & Marc Lecuit
  3. Inserm U1117, 75015 Paris, France

    • Alexandra Moura
    • , Mylène M. Maury
    •  & Marc Lecuit
  4. Microbial Evolutionary Genomics Unit, Institut Pasteur, 75724 Paris, France

    • Alexandra Moura
    • , Mylène M. Maury
    • , Elise Larsonneur
    • , Marie Touchon
    • , Eduardo P. C. Rocha
    •  & Sylvain Brisse
  5. CNRS, UMR 3525, 75015 Paris, France

    • Alexandra Moura
    • , Mylène M. Maury
    • , Marie Touchon
    • , Eduardo P. C. Rocha
    •  & Sylvain Brisse
  6. Institut Pasteur–Hub Bioinformatique et Biostatistique–C3BI, USR 3756 IP CNRS, 75724 Paris, France

    • Alexis Criscuolo
    • , Elise Larsonneur
    •  & Louis Jones
  7. Applied-Maths, 9830 Sint-Martens-Latem, Belgium

    • Hannes Pouseele
    •  & Bruno Pot
  8. Sorbonne Paris Cité, Cellule Pasteur, Paris Diderot University, 75013 Paris, France

    • Mylène M. Maury
  9. Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA

    • Cheryl Tarr
    • , Heather Carleton
    • , Lee S. Katz
    • , Steven Stroika
    • , Zuzana Kucerova
    •  & Peter Gerner-Smidt
  10. Statens Serum Institut, 2300 Copenhagen, Denmark

    • Jonas T. Björkman
    •  & Eva M. Nielsen
  11. Public Health England, London NW9 5EQ, UK

    • Timothy Dallman
    •  & Kathie Grant
  12. Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada

    • Aleisha Reimer
    • , Matthew Walker
    •  & Celine Nadon
  13. Pasteur International Bioresources network (PIBnet), Mutualized Microbiology Platform (P2M), Institut Pasteur, 75724 Paris, France

    • Vincent Enouf
  14. CNRS, UMS 3601 IFB-Core, 91198 Gif-sur-Yvette, France

    • Elise Larsonneur
  15. Public Health France, 94415 Saint-Maurice, France

    • Mathieu Tourdjman
  16. Sorbonne Paris Cité, Institut Imagine, 75006 Paris, Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Paris Descartes University, 75015 Paris, France

    • Marc Lecuit


  1. Search for Alexandra Moura in:

  2. Search for Alexis Criscuolo in:

  3. Search for Hannes Pouseele in:

  4. Search for Mylène M. Maury in:

  5. Search for Alexandre Leclercq in:

  6. Search for Cheryl Tarr in:

  7. Search for Jonas T. Björkman in:

  8. Search for Timothy Dallman in:

  9. Search for Aleisha Reimer in:

  10. Search for Vincent Enouf in:

  11. Search for Elise Larsonneur in:

  12. Search for Heather Carleton in:

  13. Search for Hélène Bracq-Dieye in:

  14. Search for Lee S. Katz in:

  15. Search for Louis Jones in:

  16. Search for Marie Touchon in:

  17. Search for Mathieu Tourdjman in:

  18. Search for Matthew Walker in:

  19. Search for Steven Stroika in:

  20. Search for Thomas Cantinelli in:

  21. Search for Viviane Chenal-Francisque in:

  22. Search for Zuzana Kucerova in:

  23. Search for Eduardo P. C. Rocha in:

  24. Search for Celine Nadon in:

  25. Search for Kathie Grant in:

  26. Search for Eva M. Nielsen in:

  27. Search for Bruno Pot in:

  28. Search for Peter Gerner-Smidt in:

  29. Search for Marc Lecuit in:

  30. Search for Sylvain Brisse in:


This study was designed by S.B., M.L., P.G.-S. and B.P. Selection of isolates was carried out by E.M.N., C.N., V.C.-F., A.L., A.R., K.G., T.D. and L.S.K. DNA preparation and sequencing was performed by H.B.-D., V.C.-F., A.L., C.T., H.C., S.S., Z.K., J.T.B., A.R., C.N., K.G., M.W. and V.E. PFGE analysis was performed by H.B.-D., V.C.-F., A.L. and A.M. Sequence analysis was carried out by A.M., H.P., T.C., L.S.K., H.C. and J.T.B. Definition of core genome was done by M.M.M., E.P.C.R., M.Touc. Validation and reproducibility of cgMLST loci was performed by A.M., H.P. and E.L. Phylogenetic and clustering analyses were carried out by A.M. and A.C. Online database implementation was done by L.J., A.M. and S.B. Epidemiological data analysis was performed by M.Tour. A.L., A.M., T.D., K.G., E.M.N. and C.T. A.M. and S.B. wrote the manuscript, with contributions and comments from all authors.

Competing interests

H.P. and B.P. are co-developers of the BioNumerics software mentioned in the manuscript. The remaining authors declare no competing interests.

Corresponding authors

Correspondence to Marc Lecuit or Sylvain Brisse.

Supplementary information

PDF files

  1. 1.

    Supplementary information

    Legends for Supplementary Tables 1–8, Supplementary Text, Supplementary Figures 1–11, Supplementary References

Excel files

  1. 1.

    Supplementary Table 1

    Characteristics of the 1,696 Listeria monocytogenes isolates used in this study.

  2. 2.

    Supplementary Table 2

    Loci (n = 43) excluded from the initial set of 1,791 core genes.

  3. 3.

    Supplementary Table 3

    Characteristics of the 1,748 loci included in the cgMLST scheme.

  4. 4.

    Supplementary Table 4

    Prevalence of sublineages (SL) identified in this study using cgMLST and correspondence with clonal complexes (CC) and sequence types (ST) defined based on conventional MLST

  5. 5.

    Supplementary Table 5

    Historical SL1 and SL9 isolates used for temporal analyses.

  6. 6.

    Supplementary Table 6

    International clusters of isolates belonging to the same cgMLST type.

  7. 7.

    Supplementary Table 7

    Detection of recombination regions within major sublineages.

  8. 8.

    Supplementary Table 8

    Frameshifts and mutations identified in this study leading to premature stop codons (PMSC) in inlA gene.

About this article

Publication history





Further reading