A Role for Tn6029 in the Evolution of the Complex Antibiotic Resistance Gene Loci in Genomic Island 3 in Enteroaggregative Hemorrhagic Escherichia Coli O104:H4

PLoS One. 2015 Feb 12;10(2):e0115781. doi: 10.1371/journal.pone.0115781. eCollection 2015.


In enteroaggregative hemorrhagic Escherichia coli (EAHEC) O104 the complex antibiotic resistance gene loci (CRL) found in the region of divergence 1 (RD1) within E. coli genomic island 3 (GI3) contains blaTEM-1, strAB, sul2, tet(A)A, and dfrA7 genes encoding resistance to ampicillin, streptomycin, sulfamethoxazole, tetracycline and trimethoprim respectively. The precise arrangement of antibiotic resistance genes and the role of mobile elements that drove the evolutionary events and created the CRL have not been investigated. We used a combination of bioinformatics and iterative BLASTn searches to determine the micro-evolutionary events that likely led to the formation of the CRL in GI3 using the closed genome sequences of EAHEC O104:H4 strains 2011C-3493 and 2009EL-2050 and high quality draft genomes of EAHEC E. coli O104:H4 isolates from sporadic cases not associated with the initial outbreak. Our analyses indicate that the CRL in GI3 evolved from a progenitor structure that contained an In2-derived class 1 integron in a Tn21/Tn1721 hybrid backbone. Within the hybrid backbone, a Tn6029-family transposon, identified here as Tn6029C abuts the sul1 gene in the 3'-Conserved Segment (-CS) of a class 1 integron generating a unique molecular signature that has only previously been observed in pASL01a, a small plasmid found in commensal E. coli in West Africa. From this common progenitor, independent IS26-mediated events created two novel transposons identified here as Tn6029D and Tn6222 in 2011C-3493 and 2009EL-2050 respectively. Analysis of RD1 within GI3 reveals IS26 has played a crucial role in the assembly of regions within the CRL.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / pharmacology*
  • Biological Evolution*
  • Computational Biology
  • DNA Transposable Elements
  • Drug Resistance, Bacterial / genetics*
  • Enterohemorrhagic Escherichia coli / drug effects*
  • Enterohemorrhagic Escherichia coli / genetics*
  • Gene Order
  • Genome, Bacterial
  • Genomic Islands*
  • Genomics
  • Homologous Recombination
  • Mutagenesis, Insertional
  • Quantitative Trait Loci*


  • Anti-Bacterial Agents
  • DNA Transposable Elements

Grant support

This work was supported by a joint collaboration between the NSW Department of Primary Industries and the ithree Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.