Identification and analysis of integrons and cassette arrays in bacterial genomes

Abstract

Integrons recombine gene arrays and favor the spread of antibiotic resistance. Their broader roles in bacterial adaptation remain mysterious, partly due to lack of computational tools. We made a program -IntegronFinder -to identify integrons with high accuracy and sensitivity. IntegronFinder is available as a standalone program and as a web application. It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching. We searched for integrons, integron-integrases lacking attC sites, and clusters of attC sites lacking a neighboring integron-integrase in bacterial genomes. All these elements are especially frequent in genomes of intermediate size. They are missing in some key phyla, such as ␣-Proteobacteria, which might reflect selection against cell lineages that acquire integrons. The similarity between attC sites is proportional to the number of cassettes in the integron, and is particularly low in clusters of attC sites lacking integron-integrases. The latter are unexpectedly abundant in genomes lacking integron-integrases or their remains, and have a large novel pool of cassettes lacking homologs in the databases. They might represent an evolutionary step between the acquisition of genes within integrons and their stabilization in the new genome.

Structural and functional characterization of three Type B and C chloramphenicol acetyltransferases from Vibrio species

“…Gram‐negative bacteria use integrons to pick up and express genes found in mobile genetic elements . There are two types of integrons: mobile integrons and sedentary chromosomal integrons, including superintegrons . Mobile integrons have been associated with antibiotic resistance, whereas superintegrons are chromosomal, are not mobile, and have a very large number of gene cassettes that can include antibiotic resistance determinants (reviewed in Reference ).…”

“…15 There are two types of integrons: mobile integrons and sedentary chromosomal integrons, including superintegrons. 16 Mobile integrons have been associated with antibiotic resistance, whereas superintegrons are chromosomal, are not mobile, and have a very large number of gene cassettes that can include antibiotic resistance determinants (reviewed in Reference 15). While mobile integrons have been shown to have a direct role in antibiotic resistance, less is known about the roles of antibiotic genes found in superintegrons since it appears they may only be functionally expressed under specific pressures or environmental conditions.…”

A megaplasmid family responsible for dissemination of multidrug resistance inPseudomonas

“…Isolates genome annotation was complemented with the Sma3s tool v.2 (30) and by integrating data from conserved domains searches performed with InterProScan v.5.30-69.0 (31,32) . Integrons occuring in the Thai megaplasmids were identified using the Integron Finder package v.1.5.1 (33)(34)(35)(36) .…”

High diversity and rapid spatial turnover of integron gene cassettes in soil

“…Integron gene cassettes appear to be ubiquitous, having been recovered from every environment surveyed, including soil and aquatic sediments, the microbiota of plants and animals, aquatic biofilms, seawater and deep-sea hydrothermal vents (Goldstein et al, 2001;Gillings et al, 2005;Elsaied et al, 2007;Gillings et al, 2009;Bailey et al, 2010;Elsaied et al, 2011;Ghaly et al, 2017). Further, in silico analysis has detected integron gene cassettes in the sequenced genomes of a range of major bacterial taxa, including γ-Proteobacteria, β-Proteobacteria, Spirochaetes, Chloroflexi, Chlorobi and Planctomycetes (Cury et al, 2016). However, the diversity, richness and biogeography of the cassette metagenome remain unknown.…”