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.

Piklu Roy Chowdhury,Steven P Djordjevic,Ian G Charles,Willem Van Schaik

doi:10.1371/journal.pone.0115781

Piklu Roy Chowdhury, Steven P Djordjevic + Show 2 more

Open Access

https://doi.org/10.1371/journal.pone.0115781

Copy DOI

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.

Highlights

The German outbreak of E. coli O104:H4, and a smaller number of sporadic cases of E. coli O104:H4 infections that followed a few weeks later in France, resulted in an unusually high incidence of haemolytic uremic syndrome (HUS) (850 cases) (as well as bloody diarrhoea (4320PLOS ONE | DOI:10.1371/journal.pone.0115781 February 12, 2015Complex Antibiotic Resistance Gene Loci in enteroaggregative hemorrhagic Escherichia coli (EAHEC) O104:H4 cases) and 82 deaths) [1]
We propose an evolutionary model for the complex antibiotic resistance gene loci (CRL) seen in EAHEC O104:H4 isolates, based on the genetic signatures we identified from the closed genomes and iterative BLASTn searches of the microbial genome database
Our analysis showed that the basic backbone of the CRL that defines region of divergence 1 (RD1) in O104:H4 strains comprise a chimeric Tn21/Tn1721 structure with a Tn1721-associated tetA-tetR-pecM module adjacent to a mercury resistance module from Tn21

Summary

Introduction

Complex Antibiotic Resistance Gene Loci in EAHEC O104:H4 cases) and 82 deaths (total numbers)) [1]. Isolates from these outbreaks, including 2011C-3493 isolated from a US patient with a history of travel to Germany, express Shiga toxin 2, (stx2) which is typically associated with enterohemorrhagic (EHEC) strains. Strains isolated from the German outbreak and the ones from the sporadic infections in France form a separate clade (Clade 1) distinct from historical enteroaggregative O104:H4 isolates,- such as strain O104:H4 55989 recovered from Central Africa in 1995 [2,3,4]. Strains isolated in 2009 from the Republic of Georgia (2009EL–2050, 2009EL–2071) are closely related to the Clade 1 strains but cluster distinctly from them and the historical isolates [2]

Methods

Results

Conclusion