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Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants

Nature Microbiology volume 1, Article number: 15010 (2016) Cite this article

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Abstract

Atypical enteropathogenic Escherichia coli (aEPEC) is an umbrella term given to E. coli that possess a type III secretion system encoded in the locus of enterocyte effacement (LEE), but lack the virulence factors (stx, bfpA) that characterize enterohaemorrhagic E. coli and typical EPEC, respectively. The burden of disease caused by aEPEC has recently increased in industrialized and developing nations, yet the population structure and virulence profile of this emerging pathogen are poorly understood. Here, we generated whole-genome sequences of 185 aEPEC isolates collected during the Global Enteric Multicenter Study from seven study sites in Asia and Africa, and compared them with publicly available E. coli genomes. Phylogenomic analysis revealed ten distinct widely distributed aEPEC clones. Analysis of genetic variation in the LEE pathogenicity island identified 30 distinct LEE subtypes divided into three major lineages. Each LEE lineage demonstrated a preferred chromosomal insertion site and different complements of non-LEE encoded effector genes, indicating distinct patterns of evolution of these lineages. This study provides the first detailed genomic framework for aEPEC in the context of the EPEC pathotype and will facilitate further studies into the epidemiology and pathogenicity of EPEC by enabling the detection and tracking of specific clones and LEE variants.

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Figure 1: Phylogeny of E. coli based on SNPs within 1,810 core genes.
Figure 2: Detection of aEPEC diversity and temporal and geographic distribution of aEPEC clones across the GEMS sites.
Figure 3: Nucleotide similarity and selection pressures within the LEE.
Figure 4: Co-evolution of sub-networks of LEE genes.
Figure 5: Identification of 30 LEE subtypes within 252 genomes and characterization of Nle-effector gene repertoire.
Figure 6: Distribution of LEE subtypes among 252 E. coli isolates.

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Acknowledgements

This work was funded by the Australian NHMRC (project grant nos. 1009296 and 1067428 to R.M.R.-B., fellowship no. 1061409 to K.E.H.), the Wellcome Trust (grant no. 098051 to the Wellcome Trust Sanger Institute, WTSI), the Bill & Melinda Gates Foundation (grant ID no. 38874 to M.M.L.) and the Victorian Life Sciences Computation Initiative (grant no. VR0082). The authors thank the sequencing teams at the WTSI for genome sequencing.

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Authors and Affiliations

  1. Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 3010, Victoria, Australia

    Danielle J. Ingle, Marija Tauschek, Dianna M. Hocking, Kristy I. Azzopardi, Thakshila Amarasena, Vicki Bennett-Wood, Jaclyn S. Pearson & Roy M. Robins-Browne

  2. Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 3010, Victoria, Australia

    Danielle J. Ingle, David J. Edwards & Kathryn E. Holt

  3. Centre for Systems Genomics, The University of Melbourne, Parkville, 3010, Victoria, Australia

    Danielle J. Ingle, David J. Edwards & Kathryn E. Holt

  4. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, Cambridge, UK

    Derek J. Pickard & Gordon Dougan

  5. Centre pour le Développement des Vaccins du Mali, Bamako, Mali

    Boubou Tamboura

  6. Medical Research Council Unit (United Kingdom), Fajara, The Gambia

    Martin Antonio

  7. Kenya Medical Research Institute/Centers for Disease Control and Prevention, Kisumu, Kenya

    John B. Ochieng & Joseph Oundo

  8. Centro de Investigação em Saúde de Manhiça, (CISM), CP 1929, Maputo, Mozambique

    Inácio Mandomando

  9. Instituto Nacional de Saúde, Ministério da Saúde, Maputo, Mozambique

    Inácio Mandomando

  10. Department of Paediatrics and Child Health, The Aga Khan University, Karachi 74800, Pakistan

    Shahida Qureshi

  11. National Institute of Cholera and Enteric Diseases, Kolkata, 700010, West Bengal, India

    Thandavarayan Ramamurthy

  12. International Centre for Diarrhoeal Disease Research, Mohakhali, Dhaka, Bangladesh

    Anowar Hossain

  13. Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, 21201, Maryland, USA

    Karen L. Kotloff & Myron M. Levine

  14. Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, 22908, Virginia, USA

    James P. Nataro

  15. Murdoch Childrens Research Institute, Royal Children's Hospital, 3052, Victoria, Australia

    Roy M. Robins-Browne

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  1. Danielle J. Ingle
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Contributions

D.J.I., M.T., R.M.R.-B. and K.E.H. contributed to the design of the study and data interpretation. K.I.A., T.A., V.B.-W., J.S.P., D.H. and D.J.I. performed the experimental analyses. D.J.P. and G.D. sequenced the isolates. D.J.I. performed the majority of bioinformatics analyses with input from K.E.H. D.J.E. developed the mapping pipeline RedDog. R.M.R.-B., M.T. and K.E.H. supervised. B.T., M.A., J.B.O., J.A.H., S.Q., T.R., A.H., K.L.K., J.P.N. and M.M.L. were responsible for the experimental analyses at the GEMS sites and K.L.K., J.P.N. and M.M.L. for the design of GEMS. All authors contributed to the writing of the manuscript.

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Correspondence to Danielle J. Ingle, Roy M. Robins-Browne or Kathryn E. Holt.

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The authors declare no competing financial interests.

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Ingle, D., Tauschek, M., Edwards, D. et al. Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants. Nat Microbiol 1, 15010 (2016). https://doi.org/10.1038/nmicrobiol.2015.10

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