Acquisition of Genes in Water Habitats and Development of Antibiotic Resistances
Acquisition of heterologous genes by lateral transfer largely facilitate the adaptive evolution of bacteria, especially under strong selective pressures. Transfer of exogenous DNA in bacteria may be mediated by plasmids, phages, transposons, genomic islands, or captation of free DNA by transformation. Sengelov and Sorensen (1998) have found that in environments such as bulk water, plasmid transfer from a donor to a recipient cell occur, even at a low frequency. Taylor et al. (2011) have observed that several factors could, not only influence, but also promote gene transfer among bacteria in water environment. One such factor is filter feeding organisms that collect bacteria belonging to different species and concentrate them at high density in a reduced space, facilitating gene exchange. Biofilm matrix in water habitats also creates favorable conditions both for plasmid exchange and transformation process (Molin and Tolker-Nielsen, 2003). Interestingly, Meibom et al. (2005) have demonstrated how chitin present in the crustacean exoskeletons is able to activate the competence status of Vibrio cholerae, and thus enhance transformation by acquisition of exogenous DNA. Although they are not classified as mobile genetic elements, integrons are platforms for genes aggregation, and thus contribute to MDR development. Furthermore, the abundance of integrons in bacterial communities of water habitats seems to be associated with the degree of water bodies’ pollution (Wright et al., 2008). Many findings support the crucial role of genetic transfer in water habitats mediated by phages (Ripp and Miller, 1995).

Integrons
Several studies have highlighted the crucial role of integrons, particularly class 1 integrons, in the evolution of antibiotic resistances in clinics (Cambray et al., 2010). Indeed, class 1 integrons are not only platforms for genes aggregation, leading to the establishment of multi-drug resistance, but their localization on mobile genetic elements such as plasmids and transposons favor the spread of several genes in a unique transfer event. Recently, studies on environmental microbial communities have demonstrated that integrons of class 1 are largely present in the environment. Gillings et al. (2008) have provided evidences that the clinical class 1 integrons originated from environmental bacterial communities. The authors observed that class 1 integrons isolated from environmental samples do not carry any antibiotic resistance gene and harbored the qac gene cassettes, which is responsible for the bacterial resistance to quaternary ammoniums by efflux. Clinical class 1 integrons would have arisen from environmental ones by integration on a Tn402-like transposon, which then disseminated in human commensals and pathogens. The presence of the qac gene has conferred a selective advantage to adapt in clinical environments, where bacteria are often challenged by disinfectants. The establishment of class 1 integrons in clinical strains has later on enabled the acquisition of antibiotic resistances positively selected by the usage of drugs. This hypothesis is also supported by the fact that clinical class 1 integrons demonstrated similar structures among them, in terms of integrases and recombination site, inferring a common ancestor. Gaze et al. (2005) have demonstrated how pollution of water bodies and their sediments with quaternary ammonium compounds, directly select for bacteria harboring qacE gene cassettes, located on the class 1 integrons. Furthermore, evidence of selection of bacteria harboring class 1 integrons in water bodies contaminated by industrial waste has been provided by Wright et al. (2008). The authors demonstrated that the contamination of freshwater with heavy metals correlated positively with a higher abundance of class 1 integrons in the bacterial community. More recently, Gaze et al. (2011) showed in sewage sludge and pig slurry that the prevalence of class 1 integrons and of qac genes was higher in bacteria exposed to detergents and/or antibiotic residues. All these studies demonstrate that pollution of water bodies with different agents increases the risk of selection and spread of integron structures. These genetic structures may be acquired by bacterial species that play role as shuttle between environment and clinics, constituting gene vectors for further dissemination in nosocomial bacteria.

Phages
Phages are major constituents of environmental ecosystems, in particular freshwater (Weinbauer, 2004; Srinivasiah et al., 2008). Their abundance is usually higher than bacterial abundance and, since a significant fraction of the prokaryotic community is infected with phages in aquatic systems, phages are likely to play an important role in horizontal gene transfer. Parsley et al. (2010) have proven the presence of β-lactamases genes in the viral metagenome of an activated sludge, confirming that transduction events may be responsible for the propagation of antibiotic resistance genes in these environments. Interestingly, Colomer-Lluch et al. (2011) demonstrated the presence of blaTEM and blaCTX-M, the most common genes conferring β-lactams resistance in Enterobacteriaceae, and mecA, responsible for methicillin resistance in Staphylococcus aureus, in phage DNA isolated from a waste water treatment plant and the natural water of the receiving river.
The presence of mecA in the phage fraction of natural freshwater is of great sanitary concern because of the threat represented by methicillin resistant Staphylococcus aureus (MRSA) infections, both in hospitals and communities (Campanile et al., 2011). This finding is also of interest for the understanding of the propagation of this gene. mecA codes for a protein with a low affinity to penicillin (PBP2a), conferring methicillin resistance. This gene is located on a mobile genomic element, the staphylococcal cassette chromosome (SCCmec), and has been reported only from the Staphylococcus genus from clinics. Baba et al. (2009) have characterized a methicillin resistance gene complex, mecIRAm, which could be the progenitor of SCCmec observed in clinical MRSA, from a strain of Macrococcus caseolyticus (closely related to S. aureus), isolated from animal meat. Interestingly, Tsubakishita et al. (2010) found a mecA gene in S. fleurettii chromosomally located and not associated to the SCCmec element. Thus, the authors advanced the hypothesis that S. fleurettii, an animal related species, is the progenitor of this resistance mechanism. The mecA gene has been reported rarely from natural water, but Schwartz et al. (2003) detected mecA in hospital waste waters. Later, Bockelmann et al. (2009) have reported the sporadic presence of mecA in a ground water recharge system. Kassem et al. (2008) described the presence of the mecA gene in 18 Proteus vulgaris, four M. morganii, and three Enterococcus faecalis isolated from surface water. A ca. 250 bp-sequence of mecA from one representative isolate of P. vulgaris, M. morganii, and E. faecalis was found to exhibit 100% similarity with the S. aureus mecA gene. However, this result, which is the first report of MecA in non-staphylococcal organisms, has never been confirmed by other studies or investigated further. Acquisition by transduction of heterologous genes, particularly of antibiotic resistance genes, might represent an important mechanism of horizontal gene transfer in water bodies. Considering the high concentration of phages in such environments (Weinbauer, 2004; Srinivasiah et al., 2008), transduction constitutes probably one of the main gene transfer mechanisms and of genome evolution for bacteria in water habitats. More studies are needed to understand the impact of phage communities on bacterial evolution and antibiotic resistance spread within the water bodies.