Skip to main content
NCBI home page
Frontiers in Microbiology logoLink to Frontiers in Microbiology
. 2012 Apr 9;3:119. doi: 10.3389/fmicb.2012.00119

Integron Involvement in Environmental Spread of Antibiotic Resistance

Thibault Stalder 1,2,3, Olivier Barraud 1,2, Magali Casellas 3, Christophe Dagot 3, Marie-Cécile Ploy 1,2,*
PMCID: PMC3321497  PMID: 22509175

Abstract

The spread of antibiotic-resistant bacteria is a growing problem and a public health issue. In recent decades, various genetic mechanisms involved in the spread of resistance genes among bacteria have been identified. Integrons – genetic elements that acquire, exchange, and express genes embedded within gene cassettes (GC) – are one of these mechanisms. Integrons are widely distributed, especially in Gram-negative bacteria; they are carried by mobile genetic elements, plasmids, and transposons, which promote their spread within bacterial communities. Initially studied mainly in the clinical setting for their involvement in antibiotic resistance, their role in the environment is now an increasing focus of attention. The aim of this review is to provide an in-depth analysis of recent studies of antibiotic-resistance integrons in the environment, highlighting their potential involvement in antibiotic-resistance outside the clinical context. We will focus particularly on the impact of human activities (agriculture, industries, wastewater treatment, etc.).

Keywords: integron, antibiotic resistance, soil, aquatic ecosystems, wastewater, agriculture, water

Bacterial evolution has largely been shaped by the high plasticity of bacterial genomes, leading to their adaptation to most ecosystems. This ability to exchange and rearrange genomic sequences to gain new traits has been extensively demonstrated with the bacterial resistance to antibiotics. Today, the increasing rate of antibiotic resistant bacteria is a major public health issue (Davies and Davies, 2010). During the last decade, several studies have underlined the environmental resistome as a source of resistance genes of clinical interest (D’Costa et al., 2006; Aminov and Mackie, 2007; Martínez, 2008; Wright, 2010). While mutation events contribute to the bacterial adaptation, horizontal gene transfer seems to be the main cause of the rapid proliferation of antibiotic-resistance genes across a wide diversity of bacteria. Much of this horizontal gene transfers have been shown to occur in the environment (Aminov, 2011). Nevertheless, the diversity of mobile genetic elements currently described (Wozniak and Waldor, 2010; Bertels and Rainey, 2011), shows that beyond horizontal gene transfer, the loss and acquisition of functional modules are an important part in the processes of rapid bacterial adaptation and development of resistance. Integrons are one of the genetic elements involved in the adaptation of bacteria. We address the question of the involvement of integrons in the environmental spread of antibiotic resistance. More specifically, the anthropogenic impacts, which have been shown to be involved in the antibiotic-resistance spread in the environment, and the role of integrons in this process.

Integrons: Generalities

Integrons are bacterial genetic elements able to promote acquisition and expression of genes embedded within gene cassettes (GCs; Stokes and Hall, 1989). The definition of an integron is based on a functional platform (also called 5′ conserved segment, 5′CS), composed of three key elements: the intI gene, a specific recombination site attI, and a promoter, Pc (Hall and Collis, 1995; Boucher et al., 2007; Figure 1). The intI gene encodes an integrase protein IntI, which belongs to the family of tyrosine recombinases (Nunes-Düby et al., 1998).

Figure 1.

Figure 1

Open in a new tab

General organization of an integron and gene cassette (GC) recombination mechanism. The IntI1 protein catalyzes the insertion (A) and excision (B) of the GC in the integron, with GC integration occurring at the attI recombination site. In example (A), the circularized GC3 is integrated in linear form inside the integron platform via a specific recombination mechanism between the attI site and the attC3 site of the GC3. GC excision preferentially occurs between two attC sites. In example (B), the GC1 is excised following the recombination between the two attC1 and attC3 sites. Pc: gene cassette promoter; attI: integron recombination site; attC1, attC2, and attC3: attC GC recombination sites; intI: the integrase gene; GC1, GC2, GC3 are the gene cassettes, and arrows indicate the direction of coding sequences (Barraud and Ploy, 2011).

The GCs are non-replicative mobile elements, which generally couple an open reading frame (ORF) with an attC site. GCs are integrated or excised from the functional platform by a site-specific recombination mechanism catalyzed by the IntI integrase. Two types of recombination can occur (Figure 1): (i) between attI and attC sites, resulting in the insertion of GCs at the attI site, and (ii) between two attC sites, leading to excision of the GCs (Mazel, 2006). The GCs can be found either as a linear form, included in an integron, or as a covalently closed circular free intermediate (Collis and Hall, 1992). GCs are usually promoterless and require the Pc promoter for their expression as in an operon. The consequence of this system is that the last integrated cassette is the closest to the Pc promoter (Collis et al., 1993; Collis and Hall, 2004), leading to the highest level of expression in the integron.

Two major groups of integrons have been described: “chromosomal integrons” (CIs), and “mobile integrons” (MIs). CIs are located on the chromosome of hundreds of bacterial species; in silico analysis showed that 17% of sequenced bacterial genomes exhibited such genetic arrangements (Cambray et al., 2010). CIs are often described in bacteria from marine or terrestrial ecosystems, such as Vibrio spp. and Xanthomonas spp., CIs have also been termed “super-integrons” (SIs) as they can carry up to 200 cassettes that mainly encode proteins with unknown functions. CIs may also carry cassettes without functional reading frames. MIs are not self-transposable elements but are located on mobile genetic elements such as transposons and plasmids, which promote their dissemination among bacteria. MIs contain a limited number of GCs (less than 10 GCs; Naas et al., 2001; GenBank DQ112222). The GCs described to date in these MIs usually encode antibiotic-resistance determinants. MIs are therefore sometimes also called “resistant integrons” (RIs) or “multidrug resistance integrons” (MRIs).

In this review, we will focus on MIs.

Classes of MIs

Most MIs have been described in a wide range of Gram-negative bacteria, and only sporadically in Gram-positive bacteria (Martin et al., 1990; Nesvera et al., 1998; Nandi et al., 2004; Shi et al., 2006; Xu et al., 2010; Barraud et al., 2011). Based on the amino-acid sequence of the IntI protein, five classes of MIs have been described (Cambray et al., 2010). Classes 1, 2, and 3 are the most commonly detected. Classes 4 and 5 have only been detected once (Hochhut et al., 2001; GenBank AJ277063).

Class 1 MIs have been extensively studied due to their broad distribution among Gram-negative bacteria of clinical interest and are the most reported in human and animals. They have been described to be mainly associated with functional and non-functional transposons derived from Tn402. The non-functional type is the main common structural organization described in clinical isolates, and led some authors to call these class 1 MIs, “clinical integrons” (Gillings et al., 2008c). In addition, these structures are frequently embedded in plasmids or larger transposons, such as those of the Tn3 family (Tn21, Tn1696) allowing their dispersion (Labbate et al., 2009). The intI1 gene sequence is highly conserved among MIs found in clinical isolates, while it shows variability in MIs-containing environmental isolates (Gillings et al., 2008b). Furthermore, many class 1 MIs exhibit a 3′ region usually called 3′-conserved segment (3′CS). However, some authors consider using this 3′CS to detect MIs could create a bias in detection, since some MIs lack this sequence (Betteridge et al., 2011). The 3′CS is composed of a qacEΔ1 gene, a functional deletion of the qacE gene still conferring resistance to quaternary ammonium compounds (QACs; Paulsen et al., 1993), followed by a sul1 gene conferring resistance to sulfonamides, and orf5 encoding a protein of unknown function.

Class 2 MIs are the second most described group. In most class 2 MIs, the intI2 gene is interrupted by a stop codon, resulting in a truncated and non-functional protein. This results in a stable GCs array, mainly composed of the GC dfrA1 (involved in the resistance to trimethoprim), sat2 (involved in the resistance to streptothricin), aadA1 (involved in the resistance to streptomycin and spectinomycin), and orfX (unknown function; Hansson et al., 2002). However, some class 2 MIs with a different GCs array have been described, probably resulting from the ability of the integrase of class 1 MIs to catalyze recombination at the attI2 site (Biskri and Mazel, 2003; Ahmed et al., 2005; Ramírez et al., 2005, 2010; Gassama Sow et al., 2010). Class 2 MIs are almost always associated with the Tn7 transposon and their derivatives, hence promoting their dissemination. Two class 2 MIs have been described recently with a functional integrase, one containing nine GCs encoding unknown function and the second one harbored the dfrA14 GC followed by a second novel GC in which a lipoprotein signal peptidase gene has been predicted (Barlow and Gobius, 2006; Márquez et al., 2008).

Only few class 3 MIs have been described. Although their role in clinical antimicrobial resistance is less important, environmental ecosystems could harbor an important pool of these elements (see below).

MIs Dissemination and Their Involvement in Antibiotic Resistance

Antibiotic pressure has probably played an important role in the MIs selection and dissemination in bacteria. More than 130 GCs conferring resistance to antibiotics and more than 60 GCs of unknown functions have been described in MIs (Partridge et al., 2009). Genes involved in resistance to almost all antibiotic families are embedded in GCs, including beta-lactams, aminoglycosides, trimethoprim, chloramphenicol, fosfomycin, macrolides, lincosamides, rifampicin, and quinolones. In addition, the qac GCs, encoding resistance determinants to antiseptics of the QACs family, are commonly found in MIs. Studies have suggested that MIs were more prevalent in bacterial communities subjected to direct or indirect antibiotic pressure in clinical, agricultural, and environmental settings (Skurnik et al., 2005; Daikos et al., 2007; Barlow et al., 2009; Luo et al., 2010; Kristiansson et al., 2011). Other factors, such as QACs or heavy metals have also been shown to be involved in the MIs dissemination, and thus probably playing a role in their spread before the antibiotic era (see below). More generally, it has been shown, when studying animal fecal E. coli, that human activity in the near vicinity increased the prevalence of MIs in these bacteria (Skurnik et al., 2006). Concerning the role of the antibiotic selective pressure, no published studies have demonstrated the direct in vivo selection of resistance through the acquisition of an integron. One study has demonstrated the in vivo selection of resistance through a rearrangement of the GCs array within a class 1 MI under antibiotic selective pressure (Hocquet et al., 2011).

Recent in vitro studies have shown that antibiotics are able to induce integrase transcription, both in CIs and MIs, via the SOS response. The SOS response is a global regulatory network controlled by the transcriptional repressor LexA and induced by stress leading to direct or indirect DNA damage, such as damage resulting from exposure to some widely used antibiotics (fluoroquinolones, beta-lactams, trimethoprim, aminoglycosides; Guerin et al., 2009; Baharoglu et al., 2010; Cambray et al., 2011). The activation of the SOS response in bacteria results in integrase overexpression, which leads to the raise of GCs recombination events.

Clinical, veterinary, and environmental surveys have shown that bacteria harboring MIs are often associated with multidrug-resistant (MDR) phenotypes (Bass et al., 1999; Leverstein-van Hall et al., 2003; Biyela et al., 2004; Nijssen et al., 2005; Laroche et al., 2009). However, the MDR profile could not be linked only to the antibiotic-resistance GCs carried by the MIs, but also to other resistance genes located on MIs-containing plasmids and transposons. This way, MIs could be co-selected with the plasmid- and/or transposon-associated antibiotic-resistance genes (Laroche et al., 2009; Li et al., 2010). For example, co-selection of class 1 MIs on plasmids harboring a tet gene (involved in the tetracycline resistance) in oxytetracycline-contaminated environments has been reported (Li et al., 2010).

The link between MIs and antibiotic resistance is still controversial since several studies present divergent conclusions (Hoyle et al., 2006; Smith et al., 2007). Furthermore many data have to be interpreted with caution. Indeed, biases in the study of links between MIs and antibiotic resistance could be generated by the selective choice of antibiotic-specific resistant strains, leading to misinterpretation. Finally, this relationship between MIs and antibiotic resistance has mainly been studied in bacteria of clinical or veterinary interest, such as those within the family Enterobacteriaceae.

Otherwise, the environment contains a wide range of bacterial species and cultivation methods only permit the isolation of a small fraction (around 1%; Amann et al., 1995). Techniques based on the study of the metagenome have thus been developed to avoid this limitation. The combination of culturing and metagenomics approaches on environmental ecosystems has highlighted the roles of MIs in antibiotic-resistance dissemination. Tables 1 and 2 present an extensive list of the studies that have quantified the occurrence of MIs in the environment, using either cultivation methods (Table 1) or cultivation independent methods (Table 2). Genetic methods presented in this review quantify the abundance of integrase genes in the total DNA from different ecosystems. In order to normalize the quantity of gene to the total bacterial communities, most authors have used quantification of the ubiquitous bacterial 16S rRNA encoding genes. By dividing the abundance of integrase genes by the number of 16S rRNA genes, authors were able to demonstrate relative abundance. This ratio corresponds to the integrase genes proportion in the total bacterial communities. However, some authors have multiplying the ratio by the average number of copies of the 16S rRNA encoding genes per bacteria; which is approximately four (Klappenbach et al., 2001), and other authors present their results as percentages. In order to integrate all relative abundance data from diverse studies, results have been normalized to the same ratio for the purpose of this review and the relative abundance corresponds to the percentage of MIs per bacterial cell (Table 2).

Table 1.

Bacterial prevalence of class 1 and 2 MIs in different ecosystems (results from cultivation-dependent studies).

Ecosystem Sample Class 1 MIs% (n) Class 2 MIs% (n) Taxonomic affiliation Reference
Clean area Lake Sediment 2.1 (n = 192) – NS Stokes et al. (2006)
1–3 (n = 192) – Gillings et al. (2008a)
Soil/lake Sediment 2–4 (n = 200) – NS Stokes et al. (2006)
Soil Forest soil 45.8 (n = 24) – Enterobacteriaceae Srinivasan et al. (2008)
Agricultural land 0 (n = 262) – NS and QACsR Gaze et al. (2005)
Karst Drinking water source 0 (n = 436) E. coli Laroche et al. (2010)
Anthropogenic impacted*** River US from the WWTP 0 (n = 75) a – NS Li et al. (2009)
3 (n = 65) b – Li et al. (2010)
4.4 (n = 45) 2.2 (n = 45) E. coli Oberlé et al. (2012)
6 (n = 301) c Koczura et al. (2012)
DS from the WWTP 8 (n = 50) 0 (n = 50) Oberlé et al. (2012)
14 (n = 322) c Koczura et al. (2012)
9.1 (n = 163) a – NS Li et al. (2009)
86.2 (n = 87) b – Li et al. (2010)
Water 17.1 (n = 117) 4.3 (n = 117) E. coli** Figueira et al. (2011)
41 (n = 500) – E. coli Chen et al. (2011)
58.1 (n = 43) – MDR Enterobacteriaceae Biyela et al. (2004)
7.6 (n = 183) 2.7 (n = 183) Enterobacteriaceae Ozgumus et al. (2009)
23 (n = 87) – Enterobacteriaceae R and Aeromonas spp.R Guo et al. (2011)
27.7 (n = 65) –
Water/sediment 13 (n = 32) 3.1 (n = 32) MDR E. coli Roe et al. (2003)
44 (n = 313) – Aeromonas sp. Schmidt et al. (2001)
Lake Water 21 (n = 14) 0 MDR E. coli Dolejská et al. (2009)
Estuaries Water 8.9 (n = 279) 1.4 (n = 279) E. coli Laroche et al. (2009)
29.6 (n = 54) 7.4 (n = 54) ampR Enterobacteriaceae** Henriques et al. (2006)
21 (n = 57) – ampRAeromonas sp.**
3.6 (n = 3000) – colif., Pseudo. And Vibrio.* Rosser and Young (1999)
Hospital wastewater 54.9 (n = 302) – Enterobacteriaceae R and Aeromonas spp.R Guo et al. (2011)
48.4 (n = 184)
6 (n = 50) 0 (n = 50) E. coli Oberlé et al. (2012)
Retirement home wastewater 36 (n = 50) 0 (n = 50) E. coli Oberlé et al. (2012)
WWTP Raw effluent 15.1 (n = 643) c E. coli Koczura et al. (2012)
Treated effluent 11.5 (n = 174) c
Activated sludge 3.7 (n = 378) c
Raw effluent 10 (n = 61) 8 (n = 61) Enterobacteriaceae and Aeromonas spp.** Moura et al. (2007)
Treated effluent 40 (n = 94) 2 (n = 94)
Activated sludge 61 (n = 35) 6 (n = 35)
Raw effluent 7.4 (n = 95) 0 (n = 95) Enterobacteriaceae and Aeromonas spp.** Moura et al. (2012)
Treated effluent 4.6 (n = 131) 0 (n = 131)
Activated sludge ≈3 (n = 169) 0.6 (n = 169)
Raw effluent 20.4 (n = 54) – LF Enterobacteriaceae and Aeromonas spp.** Ma et al. (2011a)
Treated effluent 38.9 (n = 54) –
Activated sludge 30.9 (n = 81) –
Raw effluent 10 – E. coli** Ferreira da Silva et al. (2007)
Treated effluent 9.6 –
Raw effluent 19.1 (n = 204) 4.9 (n = 204) E. coli** Figueira et al. (2011)
Treated effluent 22.3 (n = 117) 4.3 (n = 117)
Raw effluent 16.4 (n = 49) 0 (n = 49) E. coli Oberlé et al. (2012)
Treated effluent 8.5 (n = 49) 2 (n = 49)
Treated effluenta 14 (n = 179) – NS Li et al. (2009)
Treated effluentb 97.4 (n = 189) – Li et al. (2010)
Activated sludge 33 (n = 109) – LF Enterobacteriaceae** Zhang et al. (2009b)
Activated sludge 1 (n = 193) – E. coli sulR Díaz-Mejía et al. (2008)
Reed bed Sediment 14.9 (n = 127) – NS and QACsR Gaze et al. (2005)
GWTP AC biofilm 30 (n = 192) – NS Gillings et al. (2008a)
Soil 6.6 (n = 500) 10.2 (n = 500) NS + antibioticR Byrne-Bailey et al. (2010)
6.6 (n = 213) – tetR strains Agerso and Sandvang (2005)
Manured soil 89.3 (n = 56) – Enterobacteriaceae Srinivasan et al. (2008)
Soil/pig slurry 6.2 (n = 531) 9.6 (n = 531) NS + antibioticR Byrne-Bailey et al. (2009)
Compost 7.6 (n = 136) – E. coli ** Heringa et al. (2010)
Urban dust Indoor ≈2 (n = 183) – E. coli sulR Díaz-Mejía et al. (2008)
outdoor ≈15 (n = 116) –
Open in a new tab

n, Number of isolated strains; LF, lactose fermenting; GWTP, ground water treatment plant; AC, activated carbon; NS, non-selective; US and DS, upstream (US) or downstream (DS) from the WWTP discharge in the receiving river; MDR, multidrug resistant; *coliform, Pseudomonas-like and Vibrio-like; **the taxonomic affiliation is based on 16S rRNA gene sequencing; ***impacted environment by urban and/or agricultural activities (sewage/industrial/WWTP/animal husbandaries facilities/fishponds/organic amendment); athe WWTP specifically treated effluents from a penicillin production facilities; bthe WWTP specifically treated effluent from an oxytetracycline production facilities; cprevalence comprise both class 1 and 2 MIs; QACsR, quaternary ammonium compounds resistant strains; Enterobacteriaceae and Aeromonas spp.R refer to selected strains resistant to at least one antibiotic; ampR, ampicillin resistant, sulR, sulfonamide resistant, tetR, tetracycline resistant; “≈”: values have been extracted from graph.

Table 2.

Concentration and relative abundance of class 1 MIs in total community DNA from different ecosystems.

Samples Characteristics Class 1 MIs (intI1· L−1 or g−1) Class 1 MIs relative abundance given by authors Relative abundance recalculated (%)* Reference
Clean area a River/lake Waters ≈104 ≈0.01 c 4 Wright et al. (2008)
Sediments ≈103–104** ≈0.001 c 0.4
Biofilm ≈101–103** ≈0.0001 c 0.04
Sediments – 2.65 (max = 8) d 2.65 (max = 8) Hardwick et al. (2008)
Creek, GWTP, and pond biofilms – 4.5 (min = 1/max = 9) d 4.5 (min = 1/max = 9) Gillings et al. (2008c)
River water <106 <0.0001 c  < 0.04 Lapara et al. (2011)
Estuary Waters ≈103–104 ≈0.00005–0.0001 c 0.02–0.04 Wright et al. (2008)
Sediments ≈104** ≈0.00005 c 0.02
Soil – 0.0036 e 0.00576 Gaze et al. (2011)
Anthropogenic-impacted area b River/lake Waters Industrial polluted ≈103–104 ≈0.01 or 0.05 c 2 and 4 Wright et al. (2008)
Sediments Industrial polluted ≈103–104** ≈0.1 or 0.005 c 2 and 40
Biofilm Industrial polluted ≈102–104** ≈0.0005 c 0.2
Waters microcosms Initial (day 0) ≈104 ≈0.0001 c 0.04
incubated at 23°C Cadmium, 0.1 mM ≈104–105 ≈0.001 c 0.4
during 7 days Tetracycline, 30 mg L−1 ≈103–105 ≈0.01 c 4
Control ≈102–103 ≈0.0001 c 0.04
Sediments Industrial area – ≈1.5 (max = 4.294 for 6 (max = 17) Rosewarne et al. (2010)
residential area the sewage input) f
DS a sewage output
Agricultural/clean area – ≈0.1 (mini = 0.02) f 0.4
Waters Urban and agricultural influenced ≈107–108 ≈0.000005–0.005 c 0.002–2 Luo et al. (2010)
Sediments Urban and agricultural influenced ≈1011**
River Waters Urban and industrial polluted ≈105 between 102 and 103 g – Zhang et al. (2009a)
Lake Waters Urban and industrial polluted ≈106 between 103 and 104 g –
Lake Sediments Urban and industrial polluted ≈1011 between 103 and 104 g –
River Water DS of a sewage output ≈1–6 × 106 ≈0.0005–0.005c 0.2–2 Lapara et al. (2011)
River sediment DS of a sewage output 2.4–2.5 × 106** – 0.05
Lake water Far DS of a sewage output ND ND ND
Lake sediment 4.9–7.7 × 105** – 0.02
Estuary Waters Industrial polluted ≈104 ≈0.001 c 0.4 Wright et al. (2008)
Sediments Industrial polluted ≈104** ≈0.0001 c 0.04
WWTP Raw effluent CAS 2.04 × 1010 1.46 × 105g – Zhang et al. (2009a)
Treated effluent CAS 1.20 × 109 1.48 × 105g –
Activated sludge CAS 2.49 × 1012 1.17 × 105g –
Raw effluent CAS ≈1011 and 1012 ≈106 g – Zhang et al. (2009b)
Treated effluent CAS ≈109 ≈105 and 106 g –
≈107 ≈104 g –
After disinfection step ≈106 ≈103 g –
Activated sludge ≈109 ≈102–105g –
Digested sludge ≈108 and 1011 ≈101 and 102 g –
Treated effluent ≈1.8 × 107 0.009 c 3.6 Lapara et al. (2011)
Sludges 5.13 × 109** ≈0.01 c 4 Ma et al. (2011b)
– ≈0.0004–0.0015 c 0.16–0.6 Ghosh et al. (2009)
1.0 and 1.3 × 1012 ≈0.01–0.1 c 4–40 Diehl and Lapara (2010)
Digested sludge QACs + ATB polluted – 1.01 e 1.616 Gaze et al. (2011)
Treated sludges limed and dewatered – 0.56 e 0.896
Reed bed cores QACs polluted – 0.65 e 1.04
GWTP Biofilter Raw influent 8.0 and 9.28 × 104 287.0 and 309.3 g – Zhang et al. (2009a)
Treated effluent 1.29 and 1.39 × 104 194.9 and 177.4 g –
Biofilms ND 856.9 and 823 g –
Soil Pig slurry Initial – 0.0002 e 0.00032 Byrne-Bailey et al. (2010)
amendment 1 day PA – 0.01 e 0.016
experiments 21 day PA – 0.008 e 0.0128
90 day PA – 0.003 e 0.0048
289 day PA – 0.004 e 0.0064
1 month PA – 0.36 e 0.576 Gaze et al. (2011)
12 month PA – 0.02 e 0.032
24 month PA – 0.01 e 0.016
Animal waste Pig slurry Antibiotic (tylosin) – 0.21 e 0.336
treated pig – 0.21 e 0.336 Byrne-Bailey et al. (2010)
Open in a new tab

*The relative abundance was calculated using the formula: [(intI/16S) × 4 × 100], with four being the average number of copies of the gene encoding 16S rRNA per bacterial cell, according to the ribosomal RNA database (Klappenbach et al., 2001). **The results are expressed as copies·g−1.

aRepresent natural environments without hospital proximity, WWTP, agriculture or animal husbandries facilities or no historical organic amendment practice; bimpacted environment by urban and/or agricultural activities (sewage/industrial/WWTP/animal husbandries facilities/fishponds/organic amendment); cthe relative abundance of integron was calculated per 16S rRNA encoding gene (intI/16S); dthe relative abundance of integron was calculated per percent of bacterial cells [(intI/16S) × 4 × 100]; ethe relative abundance of integron was calculated per percent of bacterial cells [(intI/16S) × 2.5 × 100]; fthe relative abundance of integron was calculated per percent of 16S rRNA encoding gene [(intI/16S) × 100]; gthe relative abundance was calculated by dividing the number of gene per the amount of total extracted DNA; PA, post-application; ND, not detected; GWTP, ground water treatment plant; QACs, quaternary ammonium compounds; ATB, antibiotic; DS, downstream; CAS, conventional activated sludge system; “≈”: values have been extracted from graphs.

MIs in the Environment

There is growing evidence that the environment plays a role in the spread of antibiotic resistance among pathogenic strains. Many questions have been raised concerning the impact of the release of antibiotics and antibiotic-resistant bacteria on the environment or on human and animal health (Aminov, 2010). The distribution of MIs, and especially the class 1 MIs, in the environment is a growing focus of attention, as illustrated by the recent publications presented in Tables 1 and 2.

MIs have been described in a wide range of natural ecosystems, both aquatic (e.g., lakes, rivers, estuaries) and terrestrial. However, their distribution has been investigated mainly in human-impacted environments such as amended soils and aquatic ecosystems influenced by urbanization, agriculture, aquaculture, industrial waste, and even in indoor and outdoor dust.

MI occurrence in “natural” environments

Different authors have investigated the occurrence of class 1 MIs in ecosystems considered to be untouched or barely affected by anthropogenic influence, these are often termed “reference sites” and correspond in Tables 1 and 2 to the “clean area.”

Only a few teams have studied MIs abundance in soils. Gaze et al. (2011) reported a class 1 MIs relative abundance of 0.00576% (Table 2) by a metagenomic approach in soils with no history of organic amendment, whereas the same authors previously found no class 1 MIs in the bacterial culturable fraction, which was composed of Bacillaceae, Paenibacillaceae, and Pseudomonadaceae (Gaze et al., 2005). In a study on forest soils, 11 out of 24 isolated Enterobacteriaceae strains (45%) were found to contain class 1 MIs, but these MIs harbored no GCs (Srinivasan et al., 2008).

In aquatics environments, Wright et al. (2008) and Hardwick et al. (2008) found, using metagenomics approaches, a relative class 1 MIs abundance recovery from 0.02 to 4%, in estuarine and stream water/sediments/biofilms, and 2.65% in creek sediments (Table 2). Using cultivation-dependent methods, class 1 MIs were found in lake sediments, with a prevalence of 1–4% (Stokes et al., 2006; Gillings et al., 2008a). Some studies investigated the GCs content of class 1 MIs. More often, one to three GCs were present, mainly encoding unknown function. GCs implied in the resistance to QACs (qac alleles) were also frequently described and antibiotic-resistance GCs were rarely found (Gillings et al., 2008c, 2009a).

Environmental source of MIs

The class 1 MIs are ubiquitous elements naturally occurring in the environment, and different studies suggest that these elements emerged from ancestral environmental CIs (Rowe-Magnus et al., 2001; Mazel, 2006). Following the discovery of several class 1 MIs lacking resistance genes in environmental samples and located on the bacterial chromosome (Stokes et al., 2006; Gillings et al., 2008a), an evolutionary model was proposed and is now well documented (Gillings et al., 2008a; Labbate et al., 2009; Cambray et al., 2010; Stokes and Gillings, 2011). This model involves a succession of evolutionary recombination events, which facilitated the spread of class 1 MIs among pathogenic bacteria. These events led to the association of an “ancient” chromosomal class 1 MI with mobile functions of a Tn402-like transposon, and the acquisition of a qacE and sul1 genes. During this evolution, deletions, insertions, and other rearrangements finally shaped the 3′CS of current class 1 MIs found in clinical isolates, as well as their inclusion in larger mobile platforms (plasmids and transposons), resulting in the spread of these elements among a broad range of bacteria, including pathogenic species (Gillings et al., 2008a; Labbate et al., 2009). Finally, it has been suggested that the class 1 MIs were probably widely distributed in Proteobacteria before the antibiotic era (Stokes and Gillings, 2011). These authors suggested that these class 1 MIs were unlikely to have GCs encoding antibiotic resistant determinants, and that they further evolved by acquisition of the 3′CS and antibiotic-resistance GCs. Nevertheless, a class 1 MI found in a Pseudomonas isolate recently recovered from 15,000- to 40,000-years-old Siberian permafrost with all the characteristics of a typical clinical class 1 MI, i.e., 5′CS and 3′CS, an antibiotic resistant GC (aadA2 encoding resistance determinants to streptomycin and spectinomycin), localization on a mobile element (Tn5045 transposon), contradicts this hypothesis (Petrova et al., 2011).

Anthropogenic impact on MIs distribution

Rivers, seas, and lakes

Water is the main vector of pollutants in the environment and thus has received most attention. Furthermore, water bodies have been underlined as ideal vectors for the antibiotic-resistance dissemination (Lupo et al., 2012). Indeed, compared to the “natural” waters previously described, the prevalence of class 1 MIs-containing strains is higher in known polluted waters (Table 1). The variation of results observed among studies may depend on many factors, such as the selected bacterial species, the applied culture method (selective or not selective), as well as the sample characteristics (e.g., sediment or water, occurrence of rain events before sampling, close location of a wastewater discharged site). Using metagenomic approaches, urban and agricultural activities were positively associated with class 1 MIs. High concentrations of class 1 MIs were found in a Chinese river located in an urban and agriculturally influenced region, with around 107–108 copies · L−1 and 1011 copies · g−1 of sediment (Luo et al., 2010), whereas in a clean area, concentrations of class 1 MIs were found to be around 104 copies · L−1 and 103–104 copies · g−1 of sediments (Wright et al., 2008). Zhang et al. (2009b) found a significant enrichment of class 1 MIs into the Yangtze river along its course through the Nanjing city, highlighting the impact of urban areas on rivers. Also, the relative abundance of class 1 MIs has been strongly correlated with the contribution of treated sewage output flow in the receiving river sediment (Rosewarne et al., 2010). This has been confirmed in a recent study carried out by Lapara et al. (2011), underlining the role of the wastewater treatment plant (WWTP) in the dissemination of class 1 MIs in the environment. Otherwise, fish farming has been shown to significantly elevate the prevalence of class 1 MIs in motile Aeromonads in river waters. The MIs identified contained dfr GCs encoding trimethoprim determinants, and their occurrence correlated with the administration of combined sulfonamide/trimethoprim drugs in freshwater fish farms (Schmidt et al., 2001). In polluted estuaries, the prevalence of class 1 MIs appears to be less important than in the aquatic ecosystems previously described, with values ranging between 2.7 and 14.7% (Laroche et al., 2009). Nevertheless, it has been observed that in anthropogenically impacted estuaries the relative abundance was around 10 times more than in an unpolluted reference estuary (Wright et al., 2008; Table 2). The authors did not show any influence of the tide, the relative MIs abundance being similar during ebb or flood tides.

Studies involving effluents of factories which produce antibiotics showed that antibiotic production could have an effect on the prevalence of MI-containing bacteria in the receiving river (Li et al., 2009, 2010). In these two studies, the impact differed according to the industry production, although the effluent treatment processes were equivalent in the two industries (anaerobic digestion following by activated sludge process without disinfection step). Indeed, the penicillin production effluents elevated the prevalence of class 1 MIs-harboring strains in the river, from 0% upstream of the discharge to 9.1% after the treated effluent was discharged whereas the oxytetracycline production effluents elevated the MIs prevalence in the river from 3% upstream of the discharge to 86.2% downstream (Li et al., 2009, 2010). Moreover, the authors suggested that some Pseudomonas sp. and Bacillus sp. isolates harbored simultaneously up to seven different class 1 MIs per bacteria, from the effluent of the oxytetracycline factory, as well as in the receiving river. In comparison, the bacteria from upstream of the WWTP harbored only one class 1 MI. More recently in a metagenomics study, authors observed a 6.7-fold enrichment of class 1 MIs in river sediments downstream of a treated WWTP effluent discharge point from an antibiotic production complex (Kristiansson et al., 2011).

However, the impact of anthropogenic activities is not limited to antibiotic pressure alone, since similar observations have been made in environments without sources of antibiotics input. An Australian study has correlated the rise of the relative abundance of class 1 MIs with environmental parameters (Hardwick et al., 2008). When the environmental conditions were more stressful to the bacteria, the relative abundance of class 1 MIs was higher. Industrial activities (mainly resulting in heavy metal contamination) also have been shown specifically to contribute to the increase of class 1 MIs relative abundance (Wright et al., 2008; Rosewarne et al., 2010). It has been shown that adding tetracycline or cadmium to a water stream in microcosm experiments increased the MIs relative abundance by a factor of between 10- and 100-fold (Wright et al., 2008). The co-selection of resistance genes with heavy metal such as mercury resistance has been previously described (Aminov and Mackie, 2007). Class 1 MIs have been described on the Tn21 transposon which also contains a mercury resistance operon (Liebert et al., 1999). Antiseptic agents as QACs have also been shown to be associated with a higher prevalence of class 1 MIs (Gillings et al., 2008c). In QACs contaminated reed bed, it was shown that 95% of the isolated strains with class 1 MIs harbored a qac gene (Gaze et al., 2005). Heavy metals and QACs are thus probably involved in MIs dissemination and may have contributed to the MIs selection before the antibiotic era (Stokes and Gillings, 2011).

In anthropogenic-impacted waters, an important diversity of GCs has been recovered (Rosser and Young, 1999; Roe et al., 2003; Henriques et al., 2006; Taviani et al., 2008; Laroche et al., 2009; Li et al., 2009; Ozgumus et al., 2009; Verner-Jeffreys et al., 2009; Kumar et al., 2010; Rosewarne et al., 2010; Chen et al., 2011). Resistance to almost all families of antimicrobials has been recovered with various GCs: aad, aac (conferring resistance to aminoglycosides); blaCARB-2, blaOXA, blaP1 (conferring resistance to beta-lactams); dfr (conferring resistance to trimethoprim); catB (conferring resistance to chloramphenicol); ereA (conferring resistance to erythromycin); arr (conferring resistance to rifampicin); and qac (conferring resistance to QACs). Moreover, GCs with unknown function have been also commonly found. Several studies have characterized the total pool of integron GCs from environmental samples by using a PCR approach targeting only the GCs (attC sites) and not the integrase genes. They showed a huge GCs diversity mostly encoding unknown functions, and underlined the effect of both environmental and anthropogenic conditions on the GCs pool composition (Koenig et al., 2008, 2009, 2011; Huang et al., 2009; Elsaied et al., 2011). Anthropogenic activity thus increases the prevalence of class 1 MIs in microbial communities. These anthropogenic environmental changes result in an increase in transferable genetic elements potentially harboring resistance genes, and an ability to capture new resistance genes from autochthonous hosts. Antibiotic-resistance genes located in mobile genetic elements (plasmids, transposons, integrons) have been suggested to be “genetic pollutants” representative of human activities (Martinez, 2009a). Moreover, anthropogenic stresses has been suggested to facilitate the possible transfer of chromosomal resistance genes to the mobile gene pool accelerating the evolution and the possible spread in human-pathogenic strains (Cattoir et al., 2008; Picão et al., 2008; Martinez, 2009a,b; Rahube and Yost, 2010).

Class 2 MIs are less prevalent than class 1 in polluted waters (0–7.4%), Table 1. In a culture-independent method survey, the low relative abundance rate of class 2 MIs from river has been underlined (Luo et al., 2010). These results suggest that their role in aquatic ecosystems is probably minor.

Sewage and wastewater treatment plants

Wastewater treatment plants are the interface between human waste and both the aquatic and soil environments (Figure 2). They collect effluents from diverse sources (such as hospital, private household, industries, animal husbandries), which contribute to the final ecosystem of the WWTP. These include the organics, chemicals, and microbiological wastes. Finally the WWTP ecosystem constitutes a “broth” where each element interacts with each other under a physical and chemical constraint resulting mainly in an organic degradation in the aqueous and solid phase. Microorganisms are key to the process resulting in organic and chemical degradation or transformation. The bacterial communities are organized in free biofilm entities (called bacterial flocs), which constitute the total biomass (the sludge). As suggested by many authors, the high bacterial density, due to the nutritional richness, indicates that WWTP are hot spots for horizontal gene transfer (Tennstedt et al., 2003). Moreover, the antibiotics potentially present in the WWTP could select antibiotic-resistant bacteria, as shown for erythromycin (Louvet et al., 2010), thereby enabling the persistence of antibiotic-resistance plasmids. It has been shown that sulfamethoxazole or amoxicillin at sub-inhibitory concentrations in activated sludge improved the stability of the pB10 plasmid in E. coli (Merlin et al., 2011). This co-existence of bacteria and antibiotics in WWTP increases the frequency of genetic variations (as recombination events) and the possible emergence of novel mechanisms of resistance (Baquero et al., 2008).

Figure 2.

Figure 2

Open in a new tab

Main route of MIs dissemination from anthropogenic sources to the environment (pictures derived from PILLS project: http://www.pills-project.eu).

The highest concentrations of class 1 MIs ever described have been recovered from raw effluents with values comprised between 1010 and 1012 copies · L−1 (Table 2). Class 1 MIs have been described at all stages of the WWTP process with variable prevalence or relative abundance (Tables 1 and 2), nevertheless their relative abundance in the final treated effluents highlights the inefficiency of the process to remove bacteria harboring these genetic elements (this will be described below in more details). In activated sludge, 3–61% of the isolated strains harbored a class 1 MI (Table 1). By metagenomics approach, the relative abundance of class 1 MIs varied (Table 2). These variations could be explained by the different methods of nucleic acids extraction as well as the primers used to detect the MIs. Nevertheless relative abundance up to 40% has been found suggesting that the activated sludge is a hot spot for class 1 MIs selection and/or dissemination. In addition, two studies showed that 12% of isolated plasmids from WWTP sludge carried MIs (Tennstedt et al., 2003; Moura et al., 2007), among which more than half were broad-host-range plasmids displaying very high transfer frequencies (Tennstedt et al., 2003).

As previously described in the aquatic ecosystems, the low prevalence of class 2 MIs in WWTP suggests that their role is probably minor. Although less than 10 publications have reported class 3 MIs, 2 of them have been described in Delftia sp. (D. acidovorans and D. tsuruhatensis) isolated from activated sludge (Xu et al., 2007). These class 3 MIs contained GCs of unknown function. Moreover, using molecular approach, class 3 MIs were detected in effluents from an urban WWTP and a slaughter house WWTP (Moura et al., 2010). These findings suggest that even if class 3 MIs play a minor role in clinical microbiology, their role in the environment is probably more extensive.

The analysis of GCs content from wastewater ecosystems showed a huge diversity of genes encoding antibiotic resistance: resistances to aminoglycosides with aad, aacA GCs; to beta-lactams with blaOXA, blaVIM-2, blaIMP, blaP1, blaGES-5, and blaGES-7 GCs; to trimethoprim with dfr gene GCs; to chloramphenicol with cat and cml GCs; to erythromycin with ereA and estX GCs; to rifampicin with arr GCs; and to quinolones with qnrVC4 GC (Tennstedt et al., 2003; Ferreira da Silva et al., 2007; Moura et al., 2007, 2012; Taviani et al., 2008; Li et al., 2009, 2010; Pellegrini et al., 2009, 2011; Zhang et al., 2009b; Xia et al., 2010; Girlich et al., 2011; Guo et al., 2011; Ma et al., 2011a; Scotta et al., 2011). A molecular approach describing the global pool of GCs in WWTP have shown a great diversity of GCs, mainly encoding for determinants implied in metabolic functions or unknown functions, suggesting the wide potential reservoir of GCs in WWTP (Moura et al., 2010).

Efficiency of WWTP process to remove MIs

While the WWTP reduced the bacterial load, it appears that the treatment is inefficient to remove both antibiotic resistant bacteria (Novo and Manaia, 2010; Luczkiewicz et al., 2010), and MIs-harboring bacteria.

As presented in Tables 1 and 2, the prevalence or relative abundance of MIs after the activated sludge process is not reduced, and is even often higher than in the raw effluent (Ferreira da Silva et al., 2007; Moura et al., 2007; Figueira et al., 2011; Ma et al., 2011a). These authors often concluded that activated process can remove bacteria, but do not reduce significantly the bacteria harboring class 1 MIs. When using abundance normalized to the total DNA amount, same observation have been done (Zhang et al., 2009a), however in another study, these authors found that the effluent treatment process decreased the MIs rate (Zhang et al., 2009b). Nevertheless, normalization to DNA amount is critical as total community DNA usually contains DNA of non-bacterial origin. The removal of bacteria bearing antibiotic-resistance genetics elements by the WWTP is a new challenge for the future. Several studies have investigated the efficiency of different advanced processes such as UV treatment, membrane biological reactors, and chlorination, to remove bacteria carrying antibiotic-resistance genes (Auerbach et al., 2007; Garcia et al., 2007; Kim et al., 2010; Huang et al., 2011; Munir et al., 2011), but no studies have examined the effects on MIs. Recently, hospital effluents were shown to be potential sources of dissemination of MIs in the sewage network (Guo et al., 2011). Oberlé et al. (2012) noted a decrease of the prevalence of class 1 MIs in E. coli along the effluents treatment from the hospital to the WWTP and the receiving river continuum. As treatment of hospital effluents onsite is a growing and controversial question (Pauwels and Verstraete, 2006; Kümmerer, 2008; Ort et al., 2010; Escher et al., 2011), these data need confirmation by further studies in order to assess the impact of these specific effluents on the release of MIs in the WWTP.

Activated sludges are often used in agriculture as organic amendment (Figure 2). However, before their use, treatments in order to reduce their volume and improve stability are applied. Several studies have specifically investigated the potential of aerobic and anaerobic treatments to reduce class 1 MIs in activated sludges, demonstrating a better performance of anaerobic thermophilic process (50–60°C) to decrease the relative abundance of class 1 MIs (Ghosh et al., 2009; Diehl and Lapara, 2010). However, dissimilar results have been obtained in same conditions by Ma et al. (2011b), suggesting that other factors may influence the MIs occurrence during the sludge digestion. Evidence of horizontal gene transfers in WWTP sludge has been shown by Merlin et al. (2011). They have shown that, horizontal transfer of pB10 plasmid occurred in sludge from the anaerobic digesters or from fixed biofilm reactors, with higher efficiency in fixed biofilm conditions.

Soil ecosystem and the animal wastes as sources of MIs

While the soil “resistome” is a vast original reservoir of resistance genes (D’Costa et al., 2006; Allen et al., 2010), manure has been shown to significantly increase the mobile genetic resistance elements pool (Heuer et al., 2011). Recent studies have highlighted the role of the amendment practice on the input of MIs in soil (Heuer and Smalla, 2007; Binh et al., 2009; Byrne-Bailey et al., 2010; Gaze et al., 2011), see Table 2. Moreover, studies on sewage sludge and pig slurry amendment showed that even if the prevalence of class 1 MIs decreased after the particular amendment (2 years and 10 months, respectively), the prevalence was still higher than in control soils without amendment (around 100 times more; Byrne-Bailey et al., 2010; Gaze et al., 2011). Some authors studied the GCs array of class 1 MIs introduced in soil via manure amendment and mainly found streptomycin and spectinomycin resistance aadA GCs (Heuer and Smalla, 2007; Binh et al., 2009). Class 2 MIs have been also identified from amended soils with relative high rates (Byrne-Bailey et al., 2009, 2010; Rodríguez-Minguela et al., 2009). The high antibiotics consumption in some animal husbandries, and their systemic application as food additives in the past, had probably significantly contributed to MIs dissemination in amended soils. Tschäpe (1994) showed that the streptothricin usage as food additive contributed to the dissemination of sat genes in amended soils via mobile genetic structures, such as the Tn7 transposon carrying a class 2 MI usually bearing a streptothricin-resistant sat2 GC.

Animal wastes (e.g., manure, poultry litter, and slurry) are the main vectors of MIs dissemination in soil. As recently reviewed by Heuer et al. (2011), only a few studies have investigated the reduction of some resistance genes following different processes, such as storage, composting, and anaerobic digestion (Chen et al., 2007, 2010; Heuer et al., 2008). Only composting was efficient in reducing the prevalence and absolute amount of erythromycin resistance genes (Chen et al., 2007). Concerning the MIs, one study reported that after 57 days of storage of manure at 20°C, the class 1 MIs GCs array electrophoresis gel profiles were almost identical to that at the beginning of the experiment; however the GCs contents was not investigated (Heuer et al., 2008).

Role of the Food Chain

The food chain probably also takes place in the transit of MIs from the environments to the human. Indeed, bacteria harboring MIs have been recovered from a variety of aquatic living organisms, such as in prawns, with an Enterobacter cloacae harboring a class 1 MI (Gillings et al., 2009b); or in Corbicula with a class 1 MIs relative abundance of 4% (Wright et al., 2008); and in oysters where the uncommon class 3 MIs prevailed (Barkovskii et al., 2010). Transfers of MIs between animals and human occur and have been well reviewed by Stokes and Gillings (2011). Class 1 MIs have been also reported from biofilms of drinking water supplies (Tables 1 and 2; Gillings et al., 2008a; Zhang et al., 2009a). All these results underline the link, via the food chain, between the environmental MIs and the human or animal MIs.

Conclusion

As described in this review, MIs are efficient tools for bacterial adaptation and play a significant role in antibiotic resistance. Environmental studies demonstrated that anthropogenic impact lead to enrichment of class 1 MIs. More specifically, all factors leading to bacterial stress, such as antibiotics, QACs, or high concentrations of heavy metals resulted in the selection of class 1 MIs-harboring bacteria. Several hot spots of class 1 MIs dissemination have been identified, as agricultural manure amendment, WWTP, or industrial effluents. While these wastes are treated in varying degrees before their discharge, it appears that the current processes are inefficient to reduce MIs dissemination. This uncontrolled dissemination of MIs in the environment could represent a risk for human health.

Conflict of Interest Statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Acknowledgments

This work was supported by the regional council of Limousin. The authors wish to thank Colin Hunter and William Rawlinson for their help in critical reading of the manuscript.

References

  1. Agerso Y., Sandvang D. (2005). Class 1 integrons and tetracycline resistance genes in Alcaligenes, Arthrobacter, and Pseudomonas spp. isolated from pigsties and manured soil. Appl. Environ. Microbiol. 71, 7941–7947 10.1128/AEM.71.12.7941-7947.2005 [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Ahmed A. M., Nakano H., Shimamoto T. (2005). Molecular characterization of integrons in non-typhoid Salmonella serovars isolated in Japan: description of an unusual class 2 integron. J. Antimicrob. Chemother. 55, 371–374 10.1093/jac/dkh534 [DOI] [PubMed] [Google Scholar]
  3. Allen H. K., Donato J., Wang H. H., Cloud-Hansen K. A., Davies J., Handelsman J. (2010). Call of the wild: antibiotic resistance genes in natural environments. Nat. Rev. Microbiol. 8, 251–259 10.1038/nrmicro2312 [DOI] [PubMed] [Google Scholar]
  4. Amann R. I., Ludwig W., Schleifer K. H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143–169 [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Aminov R. I. (2010). A brief history of the antibiotic era: lessons learned and challenges for the future. Front. Microbiol. 1:134. 10.3389/fmicb.2010.00134 [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Aminov R. I. (2011). Horizontal gene exchange in environmental microbiota. Front. Microbiol. 2:158. 10.3389/fmicb.2011.00158 [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Aminov R. I., Mackie R. I. (2007). Evolution and ecology of antibiotic resistance genes. FEMS Microbiol. Lett. 271, 147–161 10.1111/j.1574-6968.2007.00757.x [DOI] [PubMed] [Google Scholar]
  8. Auerbach E. A., Seyfried E. E., McMahon K. D. (2007). Tetracycline resistance genes in activated sludge wastewater treatment plants. Water Res. 41, 1143–1151 10.1016/j.watres.2006.11.045 [DOI] [PubMed] [Google Scholar]
  9. Baharoglu Z., Bikard D., Mazel D. (2010). Conjugative DNA transfer induces the bacterial SOS response and promotes antibiotic resistance development through integron activation. PLoS Genet. 6, e1001165. 10.1371/journal.pgen.1001165 [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Baquero F., Martínez J. L., Cantón R. (2008). Antibiotics and antibiotic resistance in water environments. Curr. Opin. Biotechnol. 19, 260–265 10.1016/j.copbio.2008.05.006 [DOI] [PubMed] [Google Scholar]
  11. Barkovskii A. L., Green C., Hurley D. (2010). The occurrence, spatial and temporal distribution, and environmental routes of tetracycline resistance and integrase genes in Crassostrea virginica beds. Mar. Pollut. Bull. 60, 2215–2224 10.1016/j.marpolbul.2010.08.016 [DOI] [PubMed] [Google Scholar]
  12. Barlow R. S., Fegan N., Gobius K. S. (2009). Integron-containing bacteria in faeces of cattle from different production systems at slaughter. J. Appl. Microbiol. 107, 540–545 10.1111/j.1365-2672.2009.04240.x [DOI] [PubMed] [Google Scholar]
  13. Barlow R. S., Gobius K. S. (2006). Diverse class 2 integrons in bacteria from beef cattle sources. J. Antimicrob. Chemother. 58, 1133–1138 10.1093/jac/dkl423 [DOI] [PubMed] [Google Scholar]
  14. Barraud O., Badell E., Denis F., Guiso N., Ploy M.-C. (2011). Antimicrobial drug resistance in Corynebacterium diphtheriae mitis. Emerging Infect. Dis. 17, 2078–2080 10.3201/eid1711.110282 [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Barraud O., Ploy M.-C. (2011). Actualités sur les intégrons de résistance aux antibiotiques: mise au point. J. Anti-infectieux 13, 133–144 10.1016/j.antinf.2011.03.001 [DOI] [Google Scholar]
  16. Bass L., Liebert C. A., Lee M. D., Summers A. O., White D. G., Thayer S. G., Maurer J. J. (1999). Incidence and characterization of integrons, genetic elements mediating multiple-drug resistance, in avian Escherichia coli. Antimicrob. Agents Chemother. 43, 2925–2929 [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Bertels F., Rainey P. B. (2011). Within-genome evolution of REPINs: a new family of miniature mobile DNA in bacteria. PLoS Genet. 7, e1002132. 10.1371/journal.pgen.1002132 [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Betteridge T., Partridge S. R., Iredell J. R., Stokes H. W. (2011). Genetic context and structural diversity of class 1 integrons from human commensal bacteria in a hospital intensive care unit. Antimicrob. Agents Chemother. 55, 3939–3943 10.1128/AAC.01831-10 [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Binh C. T. T., Heuer H., Kaupenjohann M., Smalla K. (2009). Diverse aadA gene cassettes on class 1 integrons introduced into soil via spread manure. Res. Microbiol. 160, 427–433 10.1016/j.resmic.2009.06.005 [DOI] [PubMed] [Google Scholar]
  20. Biskri L., Mazel D. (2003). Erythromycin esterase gene ere(A) is located in a functional gene cassette in an unusual class 2 integron. Antimicrob. Agents Chemother. 47, 3326–3331 10.1128/AAC.47.10.3326-3331.2003 [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Biyela P. T., Lin J., Bezuidenhout C. C. (2004). The role of aquatic ecosystems as reservoirs of antibiotic resistant bacteria and antibiotic resistance genes. Water Sci. Technol. 50, 45–50 [PubMed] [Google Scholar]
  22. Boucher Y., Labbate M., Koenig J. E., Stokes H. W. (2007). Integrons: mobilizable platforms that promote genetic diversity in bacteria. Trends Microbiol. 15, 301–309 10.1016/j.tim.2007.05.004 [DOI] [PubMed] [Google Scholar]
  23. Byrne-Bailey K. G., Gaze W. H., Kay P., Boxall A. B. A., Hawkey P. M., Wellington E. M. H. (2009). Prevalence of sulfonamide resistance genes in bacterial isolates from manured agricultural soils and pig slurry in the United Kingdom. Antimicrob. Agents Chemother. 53, 696–702 10.1128/AAC.00652-07 [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Byrne-Bailey K. G., Gaze W. H., Zhang L., Kay P., Boxall A., Hawkey P. M., Wellington E. M. H. (2010). Integron prevalence and diversity in manured soil. Appl. Environ. Microbiol. 77, 684–687 10.1128/AEM.01425-10 [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Cambray G., Guerout A.-M., Mazel D. (2010). Integrons. Annu. Rev. Genet. 44, 141–166 10.1146/annurev-genet-102209-163504 [DOI] [PubMed] [Google Scholar]
  26. Cambray G., Sanchez-Alberola N., Campoy S., Guerin E., Da Re S., Gonzalez-Zorn B., Ploy M.-C., Barbe J., Mazel D., Erill I. (2011). Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons. Mob. DNA 2, 6. 10.1186/1759-8753-2-6 [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Cattoir V., Poirel L., Aubert C., Soussy C.-J., Nordmann P. (2008). Unexpected occurrence of plasmid-mediated quinolone resistance determinants in environmental Aeromonas spp. Emerging Infect. Dis. 14, 231–237 10.3201/eid1402.070677 [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Chen B., Zheng W., Yu Y., Huang W., Zheng S., Zhang Y., Guan X., Zhuang Y., Chen N., Topp E. (2011). Class 1 integrons, selected virulence genes, and antibiotic resistance in Escherichia coli isolates from the Minjiang River, Fujian Province, China. Appl. Environ. Microbiol. 77, 148–155 10.1128/AEM.00375-11 [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Chen J., Michel F. C., Jr, Sreevatsan S., Morrison M., Yu Z. (2010). Occurrence and persistence of erythromycin resistance genes (erm) and tetracycline resistance genes (tet) in waste treatment systems on swine farms. Microb. Ecol. 60, 479–486 10.1007/s00248-010-9700-z [DOI] [PubMed] [Google Scholar]
  30. Chen J., Yu Z., Michel F. C., Jr, Wittum T., Morrison M. (2007). Development and application of real-time PCR assays for quantification of erm genes conferring resistance to macrolides-lincosamides-streptogramin B in livestock manure and manure management systems. Appl. Environ. Microbiol. 73, 4407–4416 10.1128/AEM.01577-06 [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Collis C. M., Grammaticopoulos G., Briton J., Stokes H. W., Hall R. M. (1993). Site-specific insertion of gene cassettes into integrons. Mol. Microbiol. 9, 41–52 10.1111/j.1365-2958.1993.tb01667.x [DOI] [PubMed] [Google Scholar]
  32. Collis C. M., Hall R. M. (1992). Gene cassettes from the insert region of integrons are excised as covalently closed circles. Mol. Microbiol. 6, 2875–2885 10.1111/j.1365-2958.1992.tb01467.x [DOI] [PubMed] [Google Scholar]
  33. Collis C. M., Hall R. M. (2004). Comparison of the structure-activity relationships of the integron-associated recombination sites attI3 and attI1 reveals common features. Microbiology 150, 1591–1601 10.1099/mic.0.26596-0 [DOI] [PubMed] [Google Scholar]
  34. Daikos G. L., Kosmidis C., Tassios P. T., Petrikkos G., Vasilakopoulou A., Psychogiou M., Stefanou I., Avlami A., Katsilambros N. (2007). Enterobacteriaceae Bloodstream infections: presence of integrons, risk factors, and outcome. Antimicrob. Agents Chemother. 51, 2366–2372 10.1128/AAC.00044-07 [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Davies J., Davies D. (2010). Origins and evolution of antibiotic resistance. Microbiol. Mol. Biol. Rev. 74, 417–433 10.1128/MMBR.00016-10 [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. D’Costa V. M., McGrann K. M., Hughes D. W., Wright G. D. (2006). Sampling the antibiotic resistome. Science 311, 374–377 10.1126/science.1120800 [DOI] [PubMed] [Google Scholar]
  37. Díaz-Mejía J. J., Amábile-Cuevas C. F., Rosas I., Souza V. (2008). An analysis of the evolutionary relationships of integron integrases, with emphasis on the prevalence of class 1 integrons in Escherichia coli isolates from clinical and environmental origins. Microbiology 154, 94–102 10.1099/mic.0.2007/008649-0 [DOI] [PubMed] [Google Scholar]
  38. Diehl D. L., Lapara T. M. (2010). Effect of temperature on the fate of genes encoding tetracycline resistance and the integrase of class 1 integrons within anaerobic and aerobic digesters treating municipal wastewater solids. Environ. Sci. Technol. 44, 9128–9133 10.1021/es102765a [DOI] [PubMed] [Google Scholar]
  39. Dolejská M., Bierosová B., Kohoutová L., Literák I., Cízek A. (2009). Antibiotic-resistant i and Escherichia coli isolates with integrons and extended-spectrum beta-lactamases in surface water and sympatric black-headed gulls. J. Appl. Microbiol. 106, 1941–1950 10.1111/j.1365-2672.2009.04155.x [DOI] [PubMed] [Google Scholar]
  40. Elsaied H., Stokes H. W., Kitamura K., Kurusu Y., Kamagata Y., Maruyama A. (2011). Marine integrons containing novel integrase genes, attachment sites, attI, and associated gene cassettes in polluted sediments from Suez and Tokyo Bays. ISME J. 5, 1162–1177 10.1038/ismej.2010.208 [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Escher B. I., Baumgartner R., Koller M., Treyer K., Lienert J., McArdell C. S. (2011). Environmental toxicology and risk assessment of pharmaceuticals from hospital wastewater. Water Res. 45, 75–92 10.1016/j.watres.2010.08.019 [DOI] [PubMed] [Google Scholar]
  42. Ferreira da Silva M., Vaz-Moreira I., Gonzalez-Pajuelo M., Nunes O. C., Manaia C. M. (2007). Antimicrobial resistance patterns in Enterobacteriaceae isolated from an urban wastewater treatment plant. FEMS Microbiol. Ecol. 60, 166–176 10.1111/j.1574-6941.2006.00268.x [DOI] [PubMed] [Google Scholar]
  43. Figueira V., Serra E., Manaia C. M. (2011). Differential patterns of antimicrobial resistance in population subsets of Escherichia coli isolated from waste- and surface waters. Sci. Total Environ. 409, 1017–1023 10.1016/j.scitotenv.2010.12.011 [DOI] [PubMed] [Google Scholar]
  44. Garcia S., Wade B., Bauer C., Craig C., Nakaoka K., Lorowitz W. (2007). The effect of wastewater treatment on antibiotic resistance in Escherichia coli and Enterococcus sp. Water Environ. Res. 79, 2387–2395 10.2175/106143007X183826 [DOI] [PubMed] [Google Scholar]
  45. Gassama Sow A., Aïdara-Kane A., Barraud O., Gatet M., Denis F., Ploy M. C. (2010). High prevalence of trimethoprim-resistance cassettes in class 1 and 2 integrons in Senegalese Shigella spp isolates. J. Infect. Dev. Ctries. 4, 207–212 10.3855/jidc.583 [DOI] [PubMed] [Google Scholar]
  46. Gaze W. H., Abdouslam N., Hawkey P. M., Wellington E. M. H. (2005). Incidence of class 1 integrons in a quaternary ammonium compound-polluted environment. Antimicrob. Agents Chemother. 49, 1802–1807 10.1128/AAC.49.5.1802-1807.2005 [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Gaze W. H., Zhang L., Abdouslam N. A., Hawkey P. M., Calvo-Bado L., Royle J., Brown H., Davis S., Kay P., Boxall A. B. A., Wellington E. M. (2011). Impacts of anthropogenic activity on the ecology of class 1 integrons and integron-associated genes in the environment. ISME J. 5, 1253–1261 10.1038/ismej.2011.15 [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Ghosh S., Ramsden S. J., LaPara T. M. (2009). The role of anaerobic digestion in controlling the release of tetracycline resistance genes and class 1 integrons from municipal wastewater treatment plants. Appl. Microbiol. Biotechnol. 84, 791–796 10.1007/s00253-009-2125-2 [DOI] [PubMed] [Google Scholar]
  49. Gillings M. R., Boucher Y., Labbate M., Holmes A., Krishnan S., Holley M., Stokes H. W. (2008a). The evolution of class 1 integrons and the rise of antibiotic resistance. J. Bacteriol. 190, 5095–5100 10.1128/JB.00152-08 [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Gillings M. R., Krishnan S., Worden P. J., Hardwick S. A. (2008b). Recovery of diverse genes for class 1 integron-integrases from environmental DNA samples. FEMS Microbiol. Lett. 287, 56–62 10.1111/j.1574-6968.2008.01291.x [DOI] [PubMed] [Google Scholar]
  51. Gillings M. R., Xuejun D., Hardwick S. A., Holley M. P., Stokes H. W. (2008c). Gene cassettes encoding resistance to quaternary ammonium compounds: a role in the origin of clinical class 1 integrons? ISME J. 3, 209–215 10.1038/ismej.2008.98 [DOI] [PubMed] [Google Scholar]
  52. Gillings M. R., Holley M. P., Stokes H. W. (2009a). Evidence for dynamic exchange of qac gene cassettes between class 1 integrons and other integrons in freshwater biofilms. FEMS Microbiol. Lett. 296, 282–288 10.1111/j.1574-6968.2009.01646.x [DOI] [PubMed] [Google Scholar]
  53. Gillings M. R., Labbate M., Sajjad A., Giguère N. J., Holley M. P., Stokes H. W. (2009b). Mobilization of a Tn402-like class 1 integron with a novel cassette array via flanking miniature inverted-repeat transposable element-like structures. Appl. Environ. Microbiol. 75, 6002–6004 10.1128/AEM.01033-09 [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Girlich D., Poirel L., Szczepanowski R., Schlüter A., Nordmann P. (2011). Carbapenem-hydrolyzing GES-5-encoding gene on different plasmid types from a sewage treatment plant. Appl. Environ. Microbiol. 78, 1292–1295 10.1128/AEM.06841-11 [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Guerin E., Cambray G., Sanchez-Alberola N., Campoy S., Erill I., Da Re S., Gonzalez-Zorn B., Barbé J., Ploy M.-C., Mazel D. (2009). The SOS response controls integron recombination. Science 324, 1034. 10.1126/science.1172914 [DOI] [PubMed] [Google Scholar]
  56. Guo X., Xia R., Han N., Xu H. (2011). Genetic diversity analyses of class 1 integrons and their associated antimicrobial resistance genes in Enterobacteriaceae strains recovered from aquatic habitats in China. Lett. Appl. Microbiol. 52, 667–675 10.1111/j.1472-765X.2011.03059.x [DOI] [PubMed] [Google Scholar]
  57. Hall R. M., Collis C. M. (1995). Mobile gene cassettes and integrons: capture and spread of genes by site-specific recombination. Mol. Microbiol. 15, 593–600 10.1111/j.1365-2958.1995.tb02368.x [DOI] [PubMed] [Google Scholar]
  58. Hansson K., Sundström L., Pelletier A., Roy P. H. (2002). IntI2 integron integrase in Tn7. J. Bacteriol. 184, 1712–1721 10.1128/JB.184.6.1712-1721.2002 [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Hardwick S. A., Stokes H. W., Findlay S., Taylor M., Gillings M. R. (2008). Quantification of class 1 integron abundance in natural environments using real-time quantitative PCR. FEMS Microbiol. Lett. 278, 207–212 10.1111/j.1574-6968.2007.00992.x [DOI] [PubMed] [Google Scholar]
  60. Henriques I. S., Fonseca F., Alves A., Saavedra M. J., Correia A. (2006). Occurrence and diversity of integrons and beta-lactamase genes among ampicillin-resistant isolates from estuarine waters. Res. Microbiol. 157, 938–947 10.1016/j.resmic.2006.09.003 [DOI] [PubMed] [Google Scholar]
  61. Heringa S., Kim J., Shepherd M. W., Jr, Singh R., Jiang X. (2010). The presence of antibiotic resistance and integrons in Escherichia coli isolated from compost. Foodborne Pathog. Dis. 7, 1297–1304 10.1089/fpd.2010.0544 [DOI] [PubMed] [Google Scholar]
  62. Heuer H., Focks A., Lamshöft M., Smalla K., Matthies M., Spiteller M. (2008). Fate of sulfadiazine administered to pigs and its quantitative effect on the dynamics of bacterial resistance genes in manure and manured soil. Soil Biol. Biochem. 40, 1892–1900 10.1016/j.soilbio.2008.03.014 [DOI] [Google Scholar]
  63. Heuer H., Schmitt H., Smalla K. (2011). Antibiotic resistance gene spread due to manure application on agricultural fields. Curr. Opin. Microbiol. 14, 236–243 10.1016/j.mib.2011.04.009 [DOI] [PubMed] [Google Scholar]
  64. Heuer H., Smalla K. (2007). Manure and sulfadiazine synergistically increased bacterial antibiotic resistance in soil over at least two months. Environ. Microbiol. 9, 657–666 10.1111/j.1462-2920.2006.01185.x [DOI] [PubMed] [Google Scholar]
  65. Hochhut B., Lotfi Y., Mazel D., Faruque S. M., Woodgate R., Waldor M. K. (2001). Molecular analysis of antibiotic resistance gene clusters in Vibrio cholera O139 and O1 SXT constins. Antimicrob. Agents Chemother. 45, 2991–3000 10.1128/AAC.45.11.2991-3000.2001 [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Hocquet D., Llanes C., Thouverez M., Kulasekara H., Legrand F., Bertrand X., Plésiat P., Mazel D., Miller S. (2011). “A Pseudomonas aeruginosa clinical isolate with antibiotic resistance promoted by the SOS response in a patient,” in ASM 111th General Meeting, New Orleans, LA [Google Scholar]
  67. Hoyle D. V., Davison H. C., Knight H. I., Yates C. M., Dobay O., Gunn G. J., Amyes S. G. B., Woolhouse M. E. J. (2006). Molecular characterisation of bovine faecal Escherichia coli shows persistence of defined ampicillin resistant strains and the presence of class 1 integrons on an organic beef farm. Vet. Microbiol. 115, 250–257 10.1016/j.vetmic.2006.01.006 [DOI] [PubMed] [Google Scholar]
  68. Huang J.-J., Hu H.-Y., Tang F., Li Y., Lu S.-Q., Lu Y. (2011). Inactivation and reactivation of antibiotic-resistant bacteria by chlorination in secondary effluents of a municipal wastewater treatment plant. Water Res. 45, 2775–2781 10.1016/j.watres.2011.06.003 [DOI] [PubMed] [Google Scholar]
  69. Huang L., Cagnon C., Caumette P., Duran R. (2009). First gene cassettes of integrons as targets in finding adaptive genes in metagenomes. Appl. Environ. Microbiol. 75, 3823–3825 10.1128/AEM.02188-08 [DOI] [PMC free article] [PubMed] [Google Scholar]
  70. Kim S., Park H., Chandran K. (2010). Propensity of activated sludge to amplify or attenuate tetracycline resistance genes and tetracycline resistant bacteria: a mathematical modeling approach. Chemosphere 78, 1071–1077 10.1016/j.chemosphere.2009.12.068 [DOI] [PubMed] [Google Scholar]
  71. Koczura R., Mokracka J., Jabłońska L., Gozdecka E., Kubek M., Kaznowski A. (2012). Antimicrobial resistance of integron-harboring Escherichia coli isolates from clinical samples, wastewater treatment plant and river water. Sci. Total Environ. 414, 680–685 [DOI] [PubMed] [Google Scholar]
  72. Klappenbach J. A., Saxman P. R., Cole J. R., Schmidt T. M. (2001). rrndb: the Ribosomal RNA operon copy number database. Nucleic Acids Res. 29, 181–184 10.1093/nar/29.1.181 [DOI] [PMC free article] [PubMed] [Google Scholar]
  73. Koenig J. E., Boucher Y., Charlebois R. L., Nesbø C., Zhaxybayeva O., Bapteste E., Spencer M., Joss M. J., Stokes H. W., Doolittle W. F. (2008). Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments. Environ. Microbiol. 10, 1024–1038 10.1111/j.1462-2920.2007.01524.x [DOI] [PubMed] [Google Scholar]
  74. Koenig J. E., Bourne D. G., Curtis B., Dlutek M., Stokes H. W., Doolittle W. F., Boucher Y. (2011). Coral-mucus-associated Vibrio integrons in the Great Barrier Reef: genomic hotspots for environmental adaptation. ISME J. 5, 962–972 10.1038/ismej.2010.193 [DOI] [PMC free article] [PubMed] [Google Scholar]
  75. Koenig J. E., Sharp C., Dlutek M., Curtis B., Joss M., Boucher Y., Doolittle W. F. (2009). Integron gene cassettes and degradation of compounds associated with industrial waste: the case of the Sydney Tar Ponds. PLoS ONE 4, e5276. 10.1371/journal.pone.0005276 [DOI] [PMC free article] [PubMed] [Google Scholar]
  76. Kristiansson E., Fick J., Janzon A., Grabic R., Rutgersson C., Weijdegård B., Söderström H., Larsson D. G. J. (2011). Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements. PLoS ONE 6, e17038. 10.1371/journal.pone.0017038 [DOI] [PMC free article] [PubMed] [Google Scholar]
  77. Kumar A., Mukherjee S., Chakraborty R. (2010). Characterization of a novel trimethoprim resistance gene, dfrA28, in class 1 integron of an oligotrophic Acinetobacter johnsonii strain, MB52, isolated from River Mahananda, India. Microb. Drug Resist. 16, 29–37 10.1089/mdr.2009.0111 [DOI] [PubMed] [Google Scholar]
  78. Kümmerer K. (2008). Pharmaceuticals in the Environment Sources, Fate, Effects, and Risks, 3rd Edn. Heidelberg: Springer [Google Scholar]
  79. Labbate M., Case R. J., Stokes H. W. (2009). The integron/gene cassette system: an active player in bacterial adaptation. Methods Mol. Biol. 532, 103–125 10.1007/978-1-60327-853-9_6 [DOI] [PubMed] [Google Scholar]
  80. Lapara T. M., Burch T. R., McNamara P. J., Tan D. T., Yan M., Eichmiller J. J. (2011). Tertiary-treated municipal wastewater is a significant point source of antibiotic resistance genes into Duluth-Superior Harbor. Environ. Sci. Technol. 45, 9543–9549 10.1021/es202775r [DOI] [PubMed] [Google Scholar]
  81. Laroche E., Pawlak B., Berthe T., Skurnik D., Petit F. (2009). Occurrence of antibiotic resistance and class 1, 2 and 3 integrons in Escherichia coli isolated from a densely populated estuary (Seine, France). FEMS Microbiol. Ecol. 68, 118–130 10.1111/j.1574-6941.2009.00655.x [DOI] [PubMed] [Google Scholar]
  82. Laroche E., Petit F., Fournier M., Pawlak B. (2010). Transport of antibiotic-resistant Escherichia coli in a public rural karst water supply. J. Hydrol. 392, 12–21 10.1016/j.jhydrol.2010.07.022 [DOI] [Google Scholar]
  83. Leverstein-van Hall M. A., Blok H. E. M., Donders A. R. T., Paauw A., Fluit A. C., Verhoef J. (2003). Multidrug resistance among Enterobacteriaceae is strongly associated with the presence of integrons and is independent of species or isolate origin. J. Infect. Dis. 187, 251–259 10.1086/345880 [DOI] [PubMed] [Google Scholar]
  84. Li D., Yang M., Hu J., Zhang J., Liu R., Gu X., Zhang Y., Wang Z. (2009). Antibiotic-resistance profile in environmental bacteria isolated from penicillin production wastewater treatment plant and the receiving river. Environ. Microbiol. 11, 1506–1517 10.1111/j.1462-2920.2008.01810.x [DOI] [PubMed] [Google Scholar]
  85. Li D., Yu T., Zhang Y., Yang M., Li Z., Liu M., Qi R. (2010). Antibiotic resistance characteristics of environmental bacteria from an oxytetracycline production wastewater treatment plant and the receiving river. Appl. Environ. Microbiol. 76, 3444–3451 10.1128/AEM.02214-09 [DOI] [PMC free article] [PubMed] [Google Scholar]
  86. Liebert C. A., Hall R. M., Summers A. O. (1999). Transposon Tn21, flagship of the floating genome. Microbiol. Mol. Biol. Rev. 63, 507–522 [DOI] [PMC free article] [PubMed] [Google Scholar]
  87. Louvet J. N., Giammarino C., Potier O., Pons M. N. (2010). Adverse effects of erythromycin on the structure and chemistry of activated sludge. Environ. Pollut. 158, 688–693 10.1016/j.envpol.2009.10.021 [DOI] [PubMed] [Google Scholar]
  88. Luczkiewicz A., Jankowska K., Fudala-Ksiazek S., Olanczuk-Neyman K. (2010). Antimicrobial resistance of fecal indicators in municipal wastewater treatment plant. Water Res. 44, 5089–5097 10.1016/j.watres.2010.08.007 [DOI] [PubMed] [Google Scholar]
  89. Luo Y., Mao D., Rysz M., Zhou Q., Zhang H., Xu L., Alvarez P. J. J. (2010). Trends in antibiotic resistance genes occurrence in the Haihe River, China. Environ. Sci. Technol. 44, 7220–7225 10.1021/es1002814 [DOI] [PubMed] [Google Scholar]
  90. Lupo A., Coyne S., Berendonk T. U. (2012). Origin and evolution of antibiotic resistance: the common mechanisms of emergence and spread in water bodies. Front. Microbiol. 3:18. 10.3389/fmicb.2012.00018 [DOI] [PMC free article] [PubMed] [Google Scholar]
  91. Ma L., Zhang X.-X., Cheng S., Zhang Z., Shi P., Liu B., Wu B., Zhang Y. (2011a). Occurrence, abundance and elimination of class 1 integrons in one municipal sewage treatment plant. Ecotoxicology 20, 968–973 10.1007/s10646-011-0652-y [DOI] [PubMed] [Google Scholar]
  92. Ma Y., Wilson C. A., Novak J. T., Riffat R., Aynur S., Murthy S., Pruden A. (2011b). Effect of various sludge digestion conditions on sulfonamide, macrolide, and tetracycline resistance genes and class I integrons. Environ. Sci. Technol. 45, 7855–7861 10.1021/es201808e [DOI] [PubMed] [Google Scholar]
  93. Márquez C., Labbate M., Ingold A. J., Roy Chowdhury P., Ramírez M. S., Centrón D., Borthagaray G., Stokes H. W. (2008). Recovery of a functional class 2 integron from an Escherichia coli strain mediating a urinary tract infection. Antimicrob. Agents Chemother 52, 4153–4154 10.1128/AAC.00710-08 [DOI] [PMC free article] [PubMed] [Google Scholar]
  94. Martin C., Timm J., Rauzier J., Gomez-Lus R., Davies J., Gicquel B. (1990). Transposition of an antibiotic resistance element in mycobacteria. Nature 345, 739–743 10.1038/345739a0 [DOI] [PubMed] [Google Scholar]
  95. Martínez J. L. (2008). Antibiotics and antibiotic resistance genes in natural environments. Science 321, 365–367 10.1126/science.1159483 [DOI] [PubMed] [Google Scholar]
  96. Martinez J. L. (2009a). Environmental pollution by antibiotics and by antibiotic resistance determinants. Environ. Pollut. 157, 2893–2902 10.1016/j.envpol.2009.05.051 [DOI] [PubMed] [Google Scholar]
  97. Martinez J. L. (2009b). The role of natural environments in the evolution of resistance traits in pathogenic bacteria. Proc. Biol. Sci. 276, 2521–2530 10.1098/rspb.2009.0320 [DOI] [PMC free article] [PubMed] [Google Scholar]
  98. Mazel D. (2006). Integrons: agents of bacterial evolution. Nat. Rev. Microbiol. 4, 608–620 10.1038/nrmicro1462 [DOI] [PubMed] [Google Scholar]
  99. Merlin C., Bonot S., Courtois S., Block J.-C. (2011). Persistence and dissemination of the multiple-antibiotic-resistance plasmid pB10 in the microbial communities of wastewater sludge microcosms. Water Res. 45, 2897–2905 10.1016/j.watres.2011.03.002 [DOI] [PubMed] [Google Scholar]
  100. Moura A., Henriques I., Ribeiro R., Correia A. (2007). Prevalence and characterization of integrons from bacteria isolated from a slaughterhouse wastewater treatment plant. J. Antimicrob. Chemother. 60, 1243–1250 10.1093/jac/dkm340 [DOI] [PubMed] [Google Scholar]
  101. Moura A., Henriques I., Smalla K., Correia A. (2010). Wastewater bacterial communities bring together broad-host range plasmids, integrons and a wide diversity of uncharacterized gene cassettes. Res. Microbiol. 161, 58–66 10.1016/j.resmic.2009.11.004 [DOI] [PubMed] [Google Scholar]
  102. Moura A., Pereira C., Henriques I., Correia A. (2012). Novel gene cassettes and integrons in antibiotic-resistant bacteria isolated from urban wastewaters. Res. Microbiol. 163, 92–100 10.1016/j.resmic.2011.10.010 [DOI] [PubMed] [Google Scholar]
  103. Munir M., Wong K., Xagoraraki I. (2011). Release of antibiotic resistant bacteria and genes in the effluent and biosolids of five wastewater utilities in Michigan. Water Res. 45, 681–693 10.1016/j.watres.2010.08.033 [DOI] [PubMed] [Google Scholar]
  104. Naas T., Mikami Y., Imai T., Poirel L., Nordmann P. (2001). Characterization of In53, a class 1 plasmid- and composite transposon-located integron of Escherichia coli which carries an unusual array of gene cassettes. J. Bacteriol. 183, 235–249 10.1128/JB.183.1.235-249.2001 [DOI] [PMC free article] [PubMed] [Google Scholar]
  105. Nandi S., Maurer J. J., Hofacre C., Summers A. O. (2004). Gram-positive bacteria are a major reservoir of class 1 antibiotic resistance integrons in poultry litter. Proc. Natl. Acad. Sci. U.S.A. 101, 7118–7122 10.1073/pnas.0306466101 [DOI] [PMC free article] [PubMed] [Google Scholar]
  106. Nesvera J., Hochmannová J., Pátek M. (1998). An integron of class 1 is present on the plasmid pCG4 from Gram-positive bacterium Corynebacterium glutamicum. FEMS Microbiol. Lett. 169, 391–395 10.1111/j.1574-6968.1998.tb13345.x [DOI] [PubMed] [Google Scholar]
  107. Nijssen S., Florijn A., Top J., Willems R., Fluit A., Bonten M. (2005). Unnoticed spread of integron-carrying Enterobacteriaceae in intensive care units. Clin. Infect. Dis. 41, 1–9 10.1086/429488 [DOI] [PubMed] [Google Scholar]
  108. Novo A., Manaia C. (2010). Factors influencing antibiotic resistance burden in municipal wastewater treatment plants. Appl. Microbiol. Biotechnol. 87, 1157–1166 10.1007/s00253-010-2583-6 [DOI] [PubMed] [Google Scholar]
  109. Nunes-Düby S. E., Kwon H. J., Tirumalai R. S., Ellenberger T., Landy A. (1998). Similarities and differences among 105 members of the Int family of site-specific recombinases. Nucleic Acids Res. 26, 391–406 10.1093/nar/26.2.391 [DOI] [PMC free article] [PubMed] [Google Scholar]
  110. Oberlé K., Capdeville M.-J., Berthe T., Budzinski H., Petit F. (2012). Evidence for a complex relationship between antibiotics and antibiotic-resistant Escherichia coli: from medical center patients to a receiving environment. Environ. Sci. Technol. 46, 1859–1868 10.1021/es203399h [DOI] [PubMed] [Google Scholar]
  111. Ort C., Lawrence M. G., Reungoat J., Eaglesham G., Carter S., Keller J. (2010). Determining the fraction of pharmaceutical residues in wastewater originating from a hospital. Water Res. 44, 605–615 10.1016/j.watres.2009.08.002 [DOI] [PubMed] [Google Scholar]
  112. Ozgumus O. B., Sandalli C., Sevim A., Celik-Sevim E., Sivri N. (2009). Class 1 and class 2 integrons and plasmid-mediated antibiotic resistance in coliforms isolated from ten rivers in northern Turkey. J. Microbiol. 47, 19–27 10.1007/s12275-008-0206-z [DOI] [PubMed] [Google Scholar]
  113. Partridge S. R., Tsafnat G., Coiera E., Iredell J. R. (2009). Gene cassettes and cassette arrays in mobile resistance integrons. FEMS Microbiol. Rev. 33, 757–784 10.1111/j.1574-6976.2009.00175.x [DOI] [PubMed] [Google Scholar]
  114. Paulsen I. T., Littlejohn T. G., Rådström P., Sundström L., Sköld O., Swedberg G., Skurray R. A. (1993). The 3′ conserved segment of integrons contains a gene associated with multidrug resistance to antiseptics and disinfectants. Antimicrob. Agents Chemother. 37, 761–768 [DOI] [PMC free article] [PubMed] [Google Scholar]
  115. Pauwels B., Verstraete W. (2006). The treatment of hospital wastewater: an appraisal. J. Water Health 4, 405–416 [PubMed] [Google Scholar]
  116. Pellegrini C., Celenza G., Segatore B., Bellio P., Setacci D., Amicosante G., Perilli M. (2011). Occurrence of class 1 and 2 integrons in resistant Enterobacteriaceae collected from a urban wastewater treatment plant: first report from central Italy. Microb. Drug Resist. 17, 229–234 10.1089/mdr.2010.0117 [DOI] [PubMed] [Google Scholar]
  117. Pellegrini C., Mercuri P. S., Celenza G., Galleni M., Segatore B., Sacchetti E., Volpe R., Amicosante G., Perilli M. (2009). Identification of bla(IMP-22) in Pseudomonas spp. in urban wastewater and nosocomial environments: biochemical characterization of a new IMP metallo-enzyme variant and its genetic location. J. Antimicrob. Chemother. 63, 901–908 10.1093/jac/dkp061 [DOI] [PubMed] [Google Scholar]
  118. Petrova M., Gorlenko Z., Mindlin S. (2011). Tn5045, a novel integron-containing antibiotic and chromate resistance transposon isolated from a permafrost bacterium. Res. Microbiol. 162, 337–345 10.1016/j.resmic.2011.01.003 [DOI] [PubMed] [Google Scholar]
  119. Picão R. C., Poirel L., Demarta A., Silva C. S. F., Corvaglia A. R., Petrini O., Nordmann P. (2008). Plasmid-mediated quinolone resistance in Aeromonas allosaccharophila recovered from a Swiss lake. J. Antimicrob. Chemother. 62, 948–950 10.1093/jac/dkn341 [DOI] [PubMed] [Google Scholar]
  120. Rahube T. O., Yost C. K. (2010). Antibiotic resistance plasmids in wastewater treatment plants and their possible dissemination into the environment. Afr. J. Biotechnol. 9, 9183–9190 [Google Scholar]
  121. Ramírez M. S., Piñeiro S., Centrón D. (2010). Novel insights about class 2 integrons from experimental and genomic epidemiology. Antimicrob. Agents Chemother. 54, 699–706 10.1128/AAC.01392-08 [DOI] [PMC free article] [PubMed] [Google Scholar]
  122. Ramírez M. S., Quiroga C., Centrón D. (2005). Novel rearrangement of a class 2 integron in two non-epidemiologically related isolates of Acinetobacter baumannii. Antimicrob. Agents Chemother. 49, 5179–5181 10.1128/AAC.49.10.4418-4420.2005 [DOI] [PMC free article] [PubMed] [Google Scholar]
  123. Rodríguez-Minguela C. M., Apajalahti J. H. A., Chai B., Cole J. R., Tiedje J. M. (2009). Worldwide prevalence of class 2 integrases outside the clinical setting is associated with human impact. Appl. Environ. Microbiol. 75, 5100–5110 10.1128/AEM.00133-09 [DOI] [PMC free article] [PubMed] [Google Scholar]
  124. Roe M. T., Vega E., Pillai S. D. (2003). Antimicrobial resistance markers of class 1 and class 2 integron-bearing Escherichia coli from irrigation water and sediments. Emerging Infect. Dis. 9, 822–826 [DOI] [PMC free article] [PubMed] [Google Scholar]
  125. Rosewarne C. P., Pettigrove V., Stokes H. W., Parsons Y. M. (2010). Class 1 integrons in benthic bacterial communities: abundance, association with Tn402-like transposition modules and evidence for coselection with heavy-metal resistance. FEMS Microbiol. Ecol. 72, 35–46 10.1111/j.1574-6941.2009.00823.x [DOI] [PubMed] [Google Scholar]
  126. Rosser S. J., Young H. K. (1999). Identification and characterization of class 1 integrons in bacteria from an aquatic environment. J. Antimicrob. Chemother. 44, 11–18 10.1093/jac/44.suppl_1.11 [DOI] [PubMed] [Google Scholar]
  127. Rowe-Magnus D. A., Guerout A. M., Ploncard P., Dychinco B., Davies J., Mazel D. (2001). The evolutionary history of chromosomal super-integrons provides an ancestry for multiresistant integrons. Proc. Natl. Acad. Sci. U.S.A. 98, 652–657 10.1073/pnas.98.2.652 [DOI] [PMC free article] [PubMed] [Google Scholar]
  128. Schmidt A. S., Bruun M. S., Dalsgaard I., Larsen J. L. (2001). Incidence, distribution, and spread of tetracycline resistance determinants and integron-associated antibiotic resistance genes among motile aeromonads from a fish farming environment. Appl. Environ. Microbiol. 67, 5675–5682 10.1128/AEM.67.12.5675-5682.2001 [DOI] [PMC free article] [PubMed] [Google Scholar]
  129. Scotta C., Juan C., Cabot G., Oliver A., Lalucat J., Bennasar A., Albertí S. (2011). Environmental microbiota represents a natural reservoir for dissemination of clinically relevant metallo-{beta}-lactamases. Antimicrob. Agents Chemother. 55, 5376–5379 10.1128/AAC.00716-11 [DOI] [PMC free article] [PubMed] [Google Scholar]
  130. Shi L., Zheng M., Xiao Z., Asakura M., Su J., Li L., Yamasaki S. (2006). Unnoticed spread of class 1 integrons in Gram-positive clinical strains isolated in Guangzhou, China. Microbiol. Immunol. 50, 463–467 [DOI] [PubMed] [Google Scholar]
  131. Skurnik D., Le Menac’h A., Zurakowski D., Mazel D., Courvalin P., Denamur E., Andremont A., Ruimy R. (2005). Integron-associated antibiotic resistance and phylogenetic grouping of Escherichia coli isolates from healthy subjects free of recent antibiotic exposure. Antimicrob. Agents Chemother. 49, 3062–3065 10.1128/AAC.49.7.3062-3065.2005 [DOI] [PMC free article] [PubMed] [Google Scholar]
  132. Skurnik D., Ruimy R., Andremont A., Amorin C., Rouquet P., Picard B., Denamur E. (2006). Effect of human vicinity on antimicrobial resistance and integrons in animal faecal Escherichia coli. J. Antimicrob. Chemother. 57, 1215–1219 10.1093/jac/dkl122 [DOI] [PubMed] [Google Scholar]
  133. Smith J. L., Drum D. J. V., Dai Y., Kim J. M., Sanchez S., Maurer J. J., Hofacre C. L., Lee M. D. (2007). Impact of antimicrobial usage on antimicrobial resistance in commensal Escherichia coli strains colonizing broiler chickens. Appl. Environ. Microbiol. 73, 1404–1414 10.1128/AEM.01193-06 [DOI] [PMC free article] [PubMed] [Google Scholar]
  134. Srinivasan V., Nam H.-M., Sawant A. A., Headrick S. I., Nguyen L. T., Oliver S. P. (2008). Distribution of tetracycline and streptomycin resistance genes and class 1 integrons in Enterobacteriaceae isolated from dairy and nondairy farm soils. Microb. Ecol. 55, 184–193 10.1007/s00248-007-9266-6 [DOI] [PubMed] [Google Scholar]
  135. Stokes H. W., Gillings M. R. (2011). Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram negative pathogens. FEMS Microbiol. Rev. 35, 790–819 10.1111/j.1574-6976.2011.00273.x [DOI] [PubMed] [Google Scholar]
  136. Stokes H. W., Hall R. M. (1989). A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons. Mol. Microbiol. 3, 1669–1683 10.1111/j.1365-2958.1989.tb00153.x [DOI] [PubMed] [Google Scholar]
  137. Stokes H. W., Nesbø C. L., Holley M., Bahl M. I., Gillings M. R., Boucher Y. (2006). Class 1 integrons potentially predating the association with tn402-like transposition genes are present in a sediment microbial community. J. Bacteriol. 188, 5722–5730 10.1128/JB.01950-05 [DOI] [PMC free article] [PubMed] [Google Scholar]
  138. Taviani E., Ceccarelli D., Lazaro N., Bani S., Cappuccinelli P., Colwell R. R., Colombo M. M. (2008). Environmental Vibrio spp., isolated in Mozambique, contain a polymorphic group of integrative conjugative elements and class 1 integrons. FEMS Microbiol. Ecol. 64, 45–54 10.1111/j.1574-6941.2008.00455.x [DOI] [PubMed] [Google Scholar]
  139. Tennstedt T., Szczepanowski R., Braun S., Pühler A., Schlüter A. (2003). Occurrence of integron-associated resistance gene cassettes located on antibiotic resistance plasmids isolated from a wastewater treatment plant. FEMS Microbiol. Ecol. 45, 239–252 10.1016/S0168-6496(03)00164-8 [DOI] [PubMed] [Google Scholar]
  140. Tschäpe H. (1994). The spread of plasmids as a function of bacterial adaptability. FEMS Microbiol. Ecol. 15, 23–31 10.1111/j.1574-6941.1994.tb00226.x [DOI] [Google Scholar]
  141. Verner-Jeffreys D. W., Welch T. J., Schwarz T., Pond M. J., Woodward M. J., Haig S. J., Rimmer G. S. E., Roberts E., Morrison V., Baker-Austin C. (2009). High prevalence of multidrug-tolerant bacteria and associated antimicrobial resistance genes isolated from ornamental fish and their carriage water. PLoS ONE 4, e8388. 10.1371/journal.pone.0008388 [DOI] [PMC free article] [PubMed] [Google Scholar]
  142. Wozniak R. A. F., Waldor M. K. (2010). Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat. Rev. Microbiol. 8, 552–563 10.1038/nrmicro2382 [DOI] [PubMed] [Google Scholar]
  143. Wright G. D. (2010). Antibiotic resistance in the environment: a link to the clinic? Curr. Opin. Microbiol. 13, 589–594 10.1016/j.mib.2010.08.005 [DOI] [PubMed] [Google Scholar]
  144. Wright M. S., Baker-Austin C., Lindell A. H., Stepanauskas R., Stokes H. W., McArthur J. V. (2008). Influence of industrial contamination on mobile genetic elements: class 1 integron abundance and gene cassette structure in aquatic bacterial communities. ISME J. 2, 417–428 10.1038/ismej.2008.8 [DOI] [PubMed] [Google Scholar]
  145. Xia R., Guo X., Zhang Y., Xu H. (2010). qnrVC-like gene located in a novel complex class 1 integron harboring the ISCR1 element in an Aeromonas punctata strain from an aquatic environment in Shandong Province, China. Antimicrob. Agents Chemother. 54, 3471–3474 10.1128/AAC.01668-09 [DOI] [PMC free article] [PubMed] [Google Scholar]
  146. Xu H., Davies J., Miao V. (2007). Molecular characterization of class 3 integrons from Delftia spp. J. Bacteriol. 189, 6276–6283 10.1128/JB.01808-06 [DOI] [PMC free article] [PubMed] [Google Scholar]
  147. Xu Z., Li L., Shirtliff M. E., Peters B. M., Peng Y., Alam M. J., Yamasaki S., Shi L. (2010). First report of class 2 integron in clinical Enterococcus faecalis and class 1 integron in Enterococcus faecium in South China. Diagn. Microbiol. Infect. Dis. 68, 315–317 10.1016/j.diagmicrobio.2010.05.014 [DOI] [PubMed] [Google Scholar]
  148. Zhang X., Wu B., Zhang Y., Zhang T., Yang L., Fang H. H. P., Ford T., Cheng S. (2009a). Class 1 integronase gene and tetracycline resistance genes tetA and tetC in different water environments of Jiangsu Province, China. Ecotoxicology 18, 652–660 10.1007/s10646-009-0344-z [DOI] [PubMed] [Google Scholar]
  149. Zhang X. X., Zhang T., Zhang M., Fang H. H. P., Cheng S.-P. (2009b). Characterization and quantification of class 1 integrons and associated gene cassettes in sewage treatment plants. Appl. Microbiol. Biotechnol. 82, 1169–1177 10.1007/s00253-009-1908-9 [DOI] [PubMed] [Google Scholar]

Articles from Frontiers in Microbiology are provided here courtesy of Frontiers Media SA

RESOURCES