Influence of industrial contamination on mobile genetic elements: class 1 integron abundance and gene cassette structure in aquatic bacterial communities

Abstract

The acquisition of new genetic material via horizontal gene transfer allows bacteria to rapidly evolve. One key to estimating the contribution of horizontal gene transfer to bacterial evolution is to quantify the abundance of mobile genetic elements (MGEs) in bacterial communities under varying degrees of selective pressure. We quantified class 1 integrase (intI1) gene abundance in total community DNA extracted from contaminated and reference riverine and estuarine microhabitats, and in metal-or antibiotic-amended freshwater microcosms. The intI1 gene was more abundant in all contaminant-exposed communities indicating that relative gene transfer potential is higher in these communities. A second key to assessing the contributions of MGEs to bacterial evolution is to examine the structure and function of the MGE-associated gene pool. We determined that the gene cassette pool is a novel and diverse resource available for bacterial acquisition, but that contamination has no discernible effect on cassette richness. Gene cassette profiles were more similar within sites than among sites, yet bacterial community profiles were not, suggesting that selective pressures can shape the structure of the gene cassette pool. Of the 46 sequenced gene cassette products, 37 were novel sequences, while the 9 gene cassettes with similarity to database sequences were primarily to hypothetical proteins. That class 1 integrons are ubiquitous and abundant in environmental bacterial communities indicates that this group of MGEs can play a substantial role in the acquisition of a diverse array of gene cassettes beyond their demonstrated impact in mediating multidrug resistance in clinical bacteria.

Quantitative and qualitative impact of hospital effluent on dissemination of the integron pool

“…Class 1 integrons were the most frequent integrons in all samples, and their concentrations in the WWTP influent and effluent were similar to those previously reported in such samples (Zhang et al, 2009a, b). The high normalized copy number of class 1 integrons in wastewater samples supports the view that human activities are a major source of class 1 integrons (Wright et al, 2008;Moura et al, 2010;Rosewarne et al, 2010). Moreover, the marked diversity of antibiotic-resistance gene cassettes identified here, including gene cassettes previously found in bacteria from wastewater environments and others only detected in clinical strains (Supplementary Table S6), supports the important role of class 1 integrons in the dissemination of antibiotic resistance.…”

“…Global sludge stress constitutes an ideal system for activation of the SOS response, leading to continuous IntI expression and, thus, to a high rate of gene cassette rearrangement via excision, increasing the probability of empty RIs. The normalized copy number of integrons in the discharged river water was similar to that found in previous studies (Hardwick et al, 2008;Gillings et al, 2008b;Wright et al, 2008;Rosewarne et al, 2010), in which bacteria harboring class 1 integrons represented between 1% and 10% of total bacteria in various environmental samples. These low values seem to represent the basal integron background occurring naturally in bacterial communities not subjected to anthropogenic activities.…”

Integrons: Past, Present, and Future

“…As an example, selection for resistance to quaternary ammonium compounds is thought to have fixed the clinical class 1 integron in a human commensal bacterium (113), and these disinfectants are known to coselect for elements carrying antibiotic resistance genes (129). Similarly, exposure to heavy metals can coselect for antibiotic resistance when resistance genes are carried on mobile DNA elements that also carry genes for resistance to those heavy metals (28,(233)(234)(235). In environments containing diverse resistance elements and diverse selective agents, plasmids can acquire genes for resistance to multiple antibiotics, disinfectants, and metals and at the same time assemble genes for degradative pathways capable of acting upon other xenobiotics (236).…”

Natural transformation with synthetic gene cassettes: new tools for integron research and biotechnology

“…Integrons are common in bacteria, and diverse in their phylogeny and predicted functions (Boucher et al, 2007a; Elsaied et al, 2007;Gillings et al, 2005;Holmes et al, 2003a;Nield et al, 2001;Rowe-Magnus & Mazel, 2001;Rowe-Magnus et al, 2003). Integrons increasingly seem to have a role as general-purpose agents of adaptation, not just enablers of antibiotic resistance (Koenig et al, 2009(Koenig et al, , 2011Rosewarne et al, 2010;Wright et al, 2008).…”

“…Integrons are common in bacteria, and diverse in their phylogeny and predicted functions (Boucher et al, 2007a; Elsaied et al, 2007;Gillings et al, 2005;Holmes et al, 2003a;Nield et al, 2001;Rowe-Magnus & Mazel, 2001;Rowe-Magnus et al, 2003). Integrons increasingly seem to have a role as general-purpose agents of adaptation, not just enablers of antibiotic resistance (Koenig et al, 2009(Koenig et al, , 2011Rosewarne et al, 2010;Wright et al, 2008).Previous studies have used excision assays (Collis & Hall, 1992;Drouin et al, 2002; Léon & Roy, 2003) or cointegrate assays (Biskri et al, 2005;Collis et al, 2002Collis et al, , 2001Holmes et al, 2003b;Martinez & de la Cruz, 1988) to quantify integron recombination. Improvements to these assays include the use of mobilizable suicide plasmids to deliver single-stranded recombination templates , and using quantitative PCR to simplify the cointegrate assay (Shearer & Summers, 2009;Wei et al, 2011;Yang et al, 2009).…”