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

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.

The influence of the accessory genome on bacterial pathogen evolution

“…[58][59][60]88,89 Integrons have been found in a wide range of non-pathogenic and pathogenic bacteria in environments ranging from marine to terrestrial organisms and niches. 73,77,83,[90][91][92][93][94][95][96][97][98][99][100][101] Two types of integrons, the chromosomal integron (CI) and mobile integron (MI) have been identified: 70 CIs appear to represent a "core" gene capture system in Gram negative bacteria to enable genome flexibility for adaptation to diverse environments. The five classes of MIs defined so far (based on intI sequence similarity) are associated with MGEs such as transposons and plasmids and thus provide a pool of elements for shuttling genes throughout microbial communities.…”

“…[70][71][72] Their common association with plasmids means they can be particularly promiscuous. [73][74][75][76][77][78][79] Integrons are essentially composed of: (1) a core stable platform of a site-specific tyrosine recombinase (integrase) gene (intI) with its own promoter (P int ) and an outward facing promoter (P C ) within the intI coding sequence that can express captured cassettes of gene(s), 80,81 and (2) an adjacent attI recombination site (Fig. 1).…”

Genetic Context and Structural Diversity of Class 1 Integrons from Human Commensal Bacteria in a Hospital Intensive Care Unit

“…Together with the nine isolates from which genetic contexts were not retrieved by the Tn21-specific primer HS1065, about one-third of integrons in this population are positioned in genetic elements additional to Tn21 and other previously identified relatives. The insertion sequences (ISs) IS26 and IS6100 can be inserted in or near class 1 integrons (3,5,15,29), and this can prevent amplification of the IRi boundary by using a primer analogous to HS1065 (18). Therefore, all 34 isolates were tested for the presence of these two ISs beyond IRi by using HS916 and different IS-specific primers ( Fig.…”

First description of food-borne Salmonella enterica resistance regions R1 and R3 associated with IS26 elements

“…[5,6,18], both in plasmids and in chromosomal genomic islands [19,20]. In this study, we described three different chromosomal regions containing antibiotic or mercury resistance genes that are flanked by, and eventually interspersed with, copies of IS26, including the new R3.…”

“…Indeed, a dfrA5-IS26 configuration was previously detected among Escherichia coli strains with different serotypes sourced from both humans and animals, acting as a conduit for the transfer of integron-related resistance genes to human pathogens [6]. In Salmonella strains, namely S. Typhimurium and the monophasic variant S. 4 [5],12:i:-, IS26 elements have been linked to the presence of resistance regions conferring an R-type ASSuT resistance pattern [7,8].…”