Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes

This article has been updated

Abstract

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.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Nomenclature of Lm cgMLST profiles.
Figure 2: Phylogenetic structure of the global Lm data set.
Figure 3: International distribution of Lm sublineages.
Figure 4: International groups of isolates classified into the same cgMLST type.
Figure 5: Temporal analysis of cgMLST profile evolution.
Figure 6: Virulence and resistance profiles across the phylogeny of the 1,696 Lm isolates.

Similar content being viewed by others

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.

References

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  3. Woolhouse, M. E. J., Rambaut, A. & Kellam, P. Lessons from Ebola: improving infectious disease surveillance to inform outbreak management. Sci. Transl. Med. 7, 307rv5 (2015).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  5. Bogner, P., Capua, I., Cox, N. J., Lipman, D. J. & Others. A global initiative on sharing avian flu data. Nature 442, 981–981 (2006).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

  12. Haase, J. K., Didelot, X., Lecuit, M., Korkeala, H. & Achtman, M. The ubiquitous nature of Listeria monocytogenes clones: a large-scale multilocus sequence typing study. Environ. Microbiol. 16, 405–416 (2014).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  16. Bergholz, T. M. 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).

    Article  Google Scholar 

  17. Schmid, D. 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).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  19. Ruppitsch, W. 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).

    Article  CAS  Google Scholar 

  20. Stasiewicz, M. J., Oliver, H. F., Wiedmann, M. & den Bakker, H. C. Whole genome sequencing allows for improved identification of persistent Listeria monocytogenes in food associated environments. Appl. Environ. Microbiol. 81, 6024–6037 (2015).

    Article  CAS  Google Scholar 

  21. Fretz, R. 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. Pightling, A. W., Petronella, N. & Pagotto, F. 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).

    Article  Google Scholar 

  23. Jolley, K. A. & Maiden, M. C. J. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11, 595 (2010).

    Article  Google Scholar 

  24. Pightling, A. W., Petronella, N. & Pagotto, F. The Listeria monocytogenes core-genome sequence typer (LmCGST): a bioinformatic pipeline for molecular characterization with next-generation sequence data. BMC Microbiol. 15, 29 (2015).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  26. Cantinelli, T. et al. ‘Epidemic clones’ of Listeria monocytogenes are widespread and ancient clonal groups. J. Clin. Microbiol. 51, 3770–3779 (2013).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  28. Ferreira, V., Wiedmann, M., Teixeira, P. & Stasiewicz, M. J. Listeria monocytogenes persistence in food-associated environments: epidemiology, strain characteristics, and implications for public health. J. Food Prot. 77, 150–170 (2014).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  34. Verghese, B. 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).

    Article  CAS  Google Scholar 

  35. Rabinovich, L., Sigal, N., Borovok, I., Nir-Paz, R. & Herskovits, A. A. Prophage excision activates Listeria competence genes that promote phagosomal escape and virulence. Cell 150, 792–802 (2012).

    Article  CAS  Google Scholar 

  36. Müller, A. 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).

    Article  Google Scholar 

  37. Schmitz-Esser, S., Müller, A., Stessl, B. & Wagner, M. Genomes of sequence type 121 Listeria monocytogenes strains harbor highly conserved plasmids and prophages. Front. Microbiol. 6, 380 (2015).

    Article  Google Scholar 

  38. Acciari, V. A. 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).

    Google Scholar 

  39. Leclercq, A., Charlier, C. & Lecuit, M. Global burden of listeriosis: the tip of the iceberg. Lancet Infect. Dis. 14, 1027–1028 (2014).

    Article  Google Scholar 

  40. Kuenne, C. 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).

    Article  CAS  Google Scholar 

  41. Holch, A. 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).

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

Download references

Acknowledgements

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

Authors and Affiliations

Authors

Contributions

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.

Corresponding authors

Correspondence to Marc Lecuit or Sylvain Brisse.

Ethics declarations

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.

Supplementary information

Supplementary information

Legends for Supplementary Tables 1–8, Supplementary Text, Supplementary Figures 1–11, Supplementary References (PDF 1366 kb)

Supplementary Table 1

Characteristics of the 1,696 Listeria monocytogenes isolates used in this study. (XLSX 224 kb)

Supplementary Table 2

Loci (n = 43) excluded from the initial set of 1,791 core genes. (XLSX 10 kb)

Supplementary Table 3

Characteristics of the 1,748 loci included in the cgMLST scheme. (XLSX 236 kb)

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 (XLSX 15 kb)

Supplementary Table 5

Historical SL1 and SL9 isolates used for temporal analyses. (XLSX 11 kb)

Supplementary Table 6

International clusters of isolates belonging to the same cgMLST type. (XLSX 11 kb)

Supplementary Table 7

Detection of recombination regions within major sublineages. (XLSX 9 kb)

Supplementary Table 8

Frameshifts and mutations identified in this study leading to premature stop codons (PMSC) in inlA gene. (XLSX 12 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Moura, A., Criscuolo, A., Pouseele, H. et al. Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes. Nat Microbiol 2, 16185 (2017). https://doi.org/10.1038/nmicrobiol.2016.185

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1038/nmicrobiol.2016.185

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing