Distribution of Class 1 Integrons with IS26-Mediated Deletions in Their 3′-Conserved Segments in Escherichia coli of Human and Animal Origin

Fay E Dawes,Karl A Bettelheim,Alexander Kuzevski,Steven P Djordjevic,Michael A Hornitzky,Mark J Walker,Christophe Herman

doi:10.1371/journal.pone.0012754

Abstract

Class 1 integrons play a role in the emergence of multi-resistant bacteria by facilitating the recruitment of gene cassettes encoding antibiotic resistance genes. 512 E. coli strains sourced from humans (n = 202), animals (n = 304) and the environment (n = 6) were screened for the presence of the intI1 gene. In 31/79 integron positive E. coli strains, the gene cassette regions could not be PCR amplified using standard primers. DNA sequence analysis of 6 serologically diverse strains revealed atypical integrons harboured the dfrA5 cassette gene and only 24 bp of the integron 3′-conserved segment (CS) remained, due to the insertion of IS26. PCR targeting intI1 and IS26 followed by restriction fragment length polymorphism (RFLP) analysis identified the integron-dfrA5-IS26 element in 27 E. coli strains of bovine origin and 4 strains of human origin. Southern hybridization and transformation studies revealed the integron-dfrA5-IS26 gene arrangement was either chromosomally located or plasmid borne. Plasmid location in 4/9 E. coli strains and PCR linkage of Tn21 transposition genes with the intI1 gene in 20/31 strains, suggests this element is readily disseminated by horizontal transfer.

Highlights

The emergence and spread of antibiotic resistance is an escalating global health concern
PCR screening for intI1 identified 79/512 (15.4%) E. coli strains contained class 1 integrons
In 31/79 integron positive E. coli strains, the cassette arrays could not be PCR amplified using standard L1 and R1 primers. These E. coli strains were sourced from cattle with clinical cases of infection (n = 27) and human patients suffering from urinary tract infections (UTI) (n = 2) and bloody diarrhoea (n = 2)

Summary

Introduction

The emergence and spread of antibiotic resistance is an escalating global health concern. Monitoring and surveillance of antibiotic resistance genes in the community is essential for developing strategies to minimize the spread of antimicrobial resistance and evaluating their impact. Class 1 integrons play an important role in the emergence of multi-resistant bacteria via the stockpiling of resistance determinants [2,3,4]. Essential features of the 59-CS are the integrase gene (intI1), the product of which mediates orientation specific integration and excision of gene cassettes [6], a promoter region, containing the potential promoter, Pc to allow expression of the inserted cassette genes [7], and an integration site (attI1) for the site-specific insertion of gene cassettes [8]. The 39-CS of class 1 integrons typically contains the qacED1 gene, mediating low-level resistance to quaternary ammonium compounds [9], the sulfonamide resistance gene, sul1 [10] and ORF5 of unknown function [3]

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Results

Conclusion