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

Abstract

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 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.

Lateral gene transfer, bacterial genome evolution, and the Anthropocene

“…This increased the size, complexity, and diversity of the ICEs. Expansion of the gene content of ICEs and genomic islands expands the number of phenotypes with relevance for human welfare, and has done so in many species of clinical importance, including Pseudomonas aeruginosa , Acinetobacter baumannii , and Escherichia coli …”

Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia

“…The insertion sequence IS26 of the IS6 family plays a significant role in the capture, assembly and mobilization of drug resistance genes found on plasmids (Dionisi et al, 2009;Cain et al, 2010;Shahid, 2010;Venturini et al, 2010Venturini et al, , 2013Lai et al, 2013;Abbo and Hooton, 2014;Chavda et al, 2015;Reid et al, 2015;Garcia et al, 2016) and in the chromosome (Roy Chowdhury et al, 2015. IS26 may promote plasmid stability and persistence by mediating deletions of plasmid backbone sequence, the expression of which incurs a burden to the host (Porse et al, 2016).…”

Genomics and the evolution of antibiotic resistance

“…Tn 916 appears to be undergoing a radiation into a range of commensals and pathogens, possibly driven by their extraordinary ability to acquire cargo genes that encode antibiotic resistance . In a similar manner, transposon Tn 6029 has interacted with integrons, IS elements, and diverse antibiotic‐resistance genes to generate a series of complex assembly events in Escherichia coli 0104:H4 …”

“…113 In a similar manner, transposon Tn6029 has interacted with integrons, IS elements, and diverse antibiotic-resistance genes to generate a series of complex assembly events in Escherichia coli 0104:H4. 114 Genome sequencing continues to expand the discovery of modular ICEs and genomic islands that contain mobile elements and antibiotic resistance determinants and to document their spread into new hosts such as the opportunistic pathogens Pseudomonas aeruginosa 115 and Acinetobacter baumannii. 116 These mosaic assemblies have almost certainly been fixed in new species by antibiotic selection.…”

“…DNA sequencing technologies have helped us to reconstruct the likely origins of many of the resistance genes currently circulating and evolving in human pathogens. 3,89,111,114 While there are genes found in the human commensal flora that can confer resistance to antimicrobial agents, 120 these are generally not the genes of concern in clinical contexts. In contrast, soil bacteria carry genes with 100% identity to genes that confer resistance to major antibiotic classes in a range of human pathogens.…”