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

Authors

Danielle J. Ingle, The University of Melbourne, Australia
Marija Tauschek, The University of Melbourne, Australia
David J. Edwards, The University of Melbourne, Australia
Dianna M. Hocking, The University of Melbourne, Australia
Derek J. Pickard, Wellcome Trust Genome Campus,UK
Kristy I. Azzopardi, The University of Melbourne, Australia
Thakshila Amarasena, The University of Melbourne, Australia
Vicki Bennett-Wood, The University of Melbourne, Australia
Jaclyn S. Pearson, The University of Melbourne, Australia
Boubou Tamboura, Centre pour le Développement des Vaccins du ,Mali
Martin Antonio, Medical Research Council Unit,United Kingdom
John B. Ochieng, Kenya Medical Research Institute/Centers for Disease Control and Prevention,Kenya.
Joseph Oundo, Kenya Medical Research Institute/Centers for Disease Control and Prevention,Kenya.
Inácio Mandomando, Instituto Nacional de Saúde, Ministério da Saúde,Mozambique
Shahida Qureshi, Aga Khan UniversityFollow
Thandavarayan Ramamurthy, National Institute of Cholera and Enteric Diseases,India.
Anowar Hossain, International Centre for Diarrhoeal Disease Research,Bangladesh
Karen L. Kotloff, University of Maryland School of Medicine,USA
James P. Nataro, University of Virginia School of Medicine,USA
Gordon Dougan, Wellcome Trust Genome Campus,UK
Myron M. Levine, University of Virginia School of Medicine,USA
Roy M. Robins-Browne, Royal Children's Hospital,Australia.
Kathryn E. Holt, The University of Melbourne, Australia

Document Type

Article

Department

Paediatrics and Child Health

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.

Publication (Name of Journal)

Nature Microbiology

Recommended Citation

Ingle, D. J., Tauschek, M., Edwards, D. J., Hocking, D. M., Pickard, D. J., Azzopardi, K. I., Amarasena, T., Bennett-Wood, V., Pearson, J. S., Tamboura, B., Antonio, M., Ochieng, J. B., Oundo, J., Mandomando, I., Qureshi, S., Ramamurthy, T., Hossain, A., Kotloff, K. L., Nataro, J. P., Dougan, G., Levine, M. M., Robins-Browne, R. M., Holt, K. E. (2016). Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants. Nature Microbiology.
Available at: https://ecommons.aku.edu/pakistan_fhs_mc_women_childhealth_paediatr/282