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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  bla   TEM-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 Tn 21 /Tn 1721  hybrid backbone. Within the hybrid backbone, a Tn 6029 -family transposon, identified here as Tn 6029C  abuts the  sul1  gene in the 3´- C onserved  S egment (-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 IS 26 -mediated events created two novel transposons identified here as Tn 6029D  and Tn 6222  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.

plos one

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