In 1983 Barbara McClintock earned her Nobel prize after discovering jumping genes or transposons in maize. At the time of the discovery of transposons, there was much speculation about their credibility because they conferred elasticity to the genome, much contradictory to the genetic stability proven by Gregor Mendel [1]. But now, almost seven decades later, owing to the astonishing advances in molecular techniques, the structure and function of the transposons and their role in genomic evolution have been proven beyond any doubt [2].

{(TE(s)} are DNA sequences that are capable of changing their positions within the genome, creating new mutations and may change the cell’s genome size and often result in the duplication of the individual TE [2]. In general, they are considered as junk DNA and they make up a large proportion of the C-value of the eukaryotic cell and are useful in research to modify the DNA inside the living organisms [3]. TEs possess two main characteristics that differentiate them from other genetic elements. As they are mobile, they are capable of changing their genetic environment and in doing so they alter the genetic environment of the locus into which they insert [4]. Since they have the intrinsic ability to multiply during the transposition process, they are automatically amplified, with a large copy number, restricted only by the carrying capacity of their environment (i.e. the genome) [1]. Transposons often persist in genomes over millions of years. This requires an exquisite balance between replication and suppression of their activity. In fact, transposons often have specific targeting mechanisms that exploit “safe havens” in the genome, such as noncoding or transcriptionally repressed regions, that help them survive for longer periods [5].

Several types of transposable elements are present. One of those is mobile genetic elements which includes two classes based on their mechanism of transposition, and can best be described as either “copy and paste” (for Class I TEs) or “cut and paste” (for Class II TEs) [6].

Antimicrobial drugs have played an important role in alleviating illness and death associated with infectious diseases in animals and humans. However, selective pressure exerted by antimicrobial drug use and also irrational use of antibiotics also have been the major factors behind the emergence and spread of drug-resistance traits among pathogenic and commensal bacteria [12]. In addition, resistance has developed after invention of every major class of antimicrobial drugs, varying in time from as short as 1 year (penicillin) to >10 years (vancomycin) [13].

The development of multi-drug resistance in E. coli is of major concern worldwide. Although prevalence rates for resistant E. coli strains are significantly distinct for various populations and environments and the impact of resistance to antimicrobial drugs is ubiquitous [14]. Erb et al., [15] reviewed the emergence trends in E. coli antimicrobial resistance from 1970 to 2006 and observed that the prevalence of resistance to specific antibiotics was highly variable in different populations and in different countries, ranging from 0% to 100%. The prevalence of resistance to a wide range of antibiotics reported in studies from Middle and South America, Spain, and Turkey was higher than that reported in the USA and Central Europe. Moreover, a tendency towards higher prevalence rates of resistance in recent years was observed.

Widespread antibiotic resistance has been recognized in E. coli isolates from human, animal and environmental sources [16]. A very recent study by Adachi et al., [17] showed the occurrence of fluoroquinolones and fluoroquinolone-resistance genes in E. coli in the aquatic environment in Japan. This is the first report of plasmid-mediated quinolone resistance determinant qnrS1 in the aquatic environment. Another recent study by Ryu et al., [18] on antimicrobial resistance and resistance genes in E. coli strains isolated from commercial fish and seafood in Korea showed that Class 1 and Class 2 integrons were associated with conferring resistance of these strains to a wide range of antibiotics. Another bothersome area is the infectious E. coli of animal origin that are multi drug resistant. Because of the intensive use of antimicrobial agents in food animal production, meat is frequently contaminated with antimicrobial-resistant E. coli. Humans can be colonized with E. coli of animal origin and because of resistance to commonly used antimicrobial agents, these bacteria may cause infections for which limited therapeutic options are available. This may lead to treatment failure and can have serious consequences for the patient. Furthermore, E. coli of animal origin may act as a donor of antimicrobial resistance genes for other pathogenic E. coli [16]. There are numerous reports that address most recent findings and indicate the severity and magnitude of antimicrobial resistance in E. coli from a wide spectrum of environments and enumerating them here would neither be possible nor pertinent. The aim of this review is to focus on the role of transposable elements and the underlying molecular mechanisms that aid in development of versatility in E. coli in acquiring and disseminating antimicrobial resistance.

Bacterial evolution has been largely influenced by the high plasticity of bacterial genomes, thus leading to their adaptation to most ecosystems. This ability to exchange and rearrange genomic sequences to gain new traits has been extensively documented with the development of resistance to antibiotics [19]. Today, the increasing rate of antibiotic resistant bacteria is a major public health issue [20]. During the last decade, several studies have highlighted the environmental resistance as a source of resistance genes of clinical interest [21-24].

A variety of genetic elements are strongly associated with the exchange and transfer of antimicrobial resistance genes among gram-negative bacteria. Transposons can transfer resistance genes intracellularly. On the other hand, integrons are genetic elements that can acquire several resistance genes in the form of gene cassettes. These genetic elements sometimes co-exist and work cooperatively. For example, integrons, which are not mobile by themselves, can acquire an ability to transfer when they are incorporated into transposons [25]. In this section, we are reviewing the individual contribution of integrons and transposons in acquiring antimicrobial resistance and genomic evolution of E. coli.

E. coli is known to harbour a wide range of transposons such as Tn3, Tn5, Tn7, Tn9 and Tn10, each conferring resistance to antibiotics, namely, Tn3 to ampicillin, Tn5 to kanamycin, Tn7 to trimethoprim, streptothricin, spectinomycin, streptomycin, Tn9 to chloramphenicol and Tn10 to tetracycline respectively [26]. Some of the common E. coli transposons and their antibiotic resistance are listed in Table 2. The Tn5 transposon is known to harbour a gene cassette of three genes conferring resistance to three antibiotics: the ble gene for bleomycin resistance, the neo gene for neomycin and the str gene for streptomycin resistance [27].

Among the numerous and important classes of transposons are the conjugative transposons. As their name implies, conjugative transposons are mobile elements that possess the genetic machinery to facilitate their own transfer between bacterial cells. Referring back at some pioneering work in this field about two decades ago, several prototypes of conjugative transposons have been described [35]. An earlier misconception was that these transposons were largely found only on Gram-positive bacteria but later on it was observed that the transposon groups Tn916 and Tn1545 transfer readily to a wide

Table 2. Common E. coli transposons.

variety of gram-positive and gram-negative bacteria in the laboratory. In one report, Enterococcus faecalis readily transferred plasmid-borne Tn916 to Alcaligenes eutrophus, Citrobacter freundii, and E. coli, conferring selectable levels of tetracycline resistance [1]. It has been assumed that acquiring antimicrobial resistance mediated by transposons bestows upon the bacteria a fitness impact enabling it to survive better under selection pressure. E. coli is known to have acquired resistance to chloramphenicol, tetracycline and kanamycin from genes carried on transposons [36]. Therefore, as is evidenced by the above reports, starting from earlier antibiotics such as tetracycline, kanamycin and chloramphenicol to the new generation trimethoprim and sulfonamides, a wide array of transposons are involved in imparting resistance [37]. The broad-spectrum antibacterial trimethoprim is heavily used worldwide, most commonly in combination with sulphonamides. Trimethoprim inhibits the enzyme dihydrofolate reductase (Dfr). E. coli most commonly becomes resistance acquiring one of over 30 known dfr genes encoding resistant variants, most of which belong to the dfrA category [38]. Recently, Labar et al., [39] found the regional dissemination of a trimethoprim-resistance gene cassette via a successful transposable element. They observed a 50% increase in the prevalence of trimethoprim resistance among fecal E. coli from healthy Nigerian students between 1998 and 2005, a trend to increase that continued in 2009. In this study 16.3% isolates carried transposons conferring trime-thoprim resistance, indicating transposition as a principal mechanism for disseminating dfrA7 among E. coli from Nigeria and Ghana.

With the recent innovations in technology for analyzing the molecular genetics of bacterial pathogens, understanding of the role of transposons in the dissemination of antimicrobial resistance has expanded significantly. Although a lot of attention has been focused on transposon mediated transfer of antibiotic resistance, the wide spread involvement of integrons in conferring multi drug resistance is being strongly asserted in recent studies. Integrons are genetic elements that can collect several resistance genes in the form of gene cassettes. These genetic elements sometimes co-exist and work cooperatively. For example, integrons, which are not mobile by themselves, can obtain an ability to transfer when they are incorporated into transposons. It thus becomes very important to focus on this class of transposable elements, which seem to have relied initially on transposons to mobilise them, but have rapidly evolved in their ability to rapidly disseminate wider range of resistance to various antimicrobials in E. coli. Hence the next section is aimed at documenting some of the recent evidences for integron mediated antimicrobial resistance in E. coli from different environments.

Integrons contain an intI gene encoding a site-specific recombinase belonging to the integrase family and a recombination site attI. A gene cassette includes an open reading frame and, at the 3’-end, a recombination site attC. Integration or excision of cassettes occurs by a sitespecific recombination mechanism catalyzed by the integrase [40]. At least six classes of integrons have been determined according to their intl gene. Classes 1, 2 and 3 are the most studied and are largely associated with the dissemination of antibiotic resistance. Most gene cassettes encode antibiotic resistant determinants [41]. Integrons seem to play a major role in the spread of multidrug resistance in Gram-negative bacteria but recently they have been described in Gram-positive bacteria [20]. Moreover, the finding of super-integrons with gene cassettes coding for other determinants (biochemical functions, virulence factors) in different Gram negative bacteria suggests that integrons are probably involved in bacterial genome evolution [40]. More than 100 gene cassettes may be present, in contrast to resistance integrons where less than ten cassettes are present. Many species harbour super-integrons, which are species-specific, whereas particular resistance integrons can be found in a variety of species. In the last few years, a variety of new gene cassettes have been described. Many of these encode resistance against newer generation antibiotics such as cephalosporins and carbapenems [39].

With relation to acquisition of antimicrobial resistance, two major groups of integrons have been described: “chromosomal integrons” (CIs), and “mobile integrons” (MIs). They are located on the chromosome of hundreds of bacterial species; in fact, in silico analysis showed that 17% of sequenced bacterial genomes exhibit such genetic arrangements [38]. MIs are not self-transposable elements but are found on mobile genetic elements such as plasmids and transposons, which aid in their dissemination among bacteria. MIs contain a limited number of GCs (less than 10 GCs) [42]. 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).

Having discussed in detail the role of transposable elements in antimicrobial resistance, one is bound to highlight the recent concept of insertion sequence common region element (ISCR) and their role as a gene capture system in organisms. ISCR elements differ from the insertion sequences by lacking terminal inverted repeats (IRs), do not generate directly repeated sequence on insertion and are thought to be transposed by a mechanism defined as rolling-circle (RC) transposition [62]. ISCR elements are closely related to an unusual family of insertion sequences called the IS91 family. ISCR elements, as a novel gene-capturing system, are capable of mobilizing any piece of adjacent DNA sequences [63]. This powerful gene mobilization mechanism serves as a highly mobile vector or milieu in transferring antibiotic resistance genes between different species of bacteria

[64]. Nineteen members of the ISCR family have been discovered until now in many Gram-negative pathogens. The majority of these elements are found to be closely associated with antimicrobial resistance genes that are not necessary components of the host genome, suggesting that ISCR elements may be responsible for the rapid transmission of bacterial multi-drug resistance in the environment [65]. ISCR elements are now recognized as powerful antibiotic resistance gene capture and movement systems that also possess the ability to construct extended clusters of antibiotic resistance genes on plasmids as well as on chromosomes [66]. As a result, there is a lot of focus on these elements as major contributors to bacterial antimicrobial resistance and research in this area in the future would definitely provide deeper insights into this versatile phenomenon of genome evolution.

E. coli, usually a commensal bacterium of humans and animals is a highly versatile and ubiquitous bacterium. Pathogenic variants cause a wide range of infections such as intestinal and extraintestinal infections, including gastroenteritis, urinary tract infection, meningitis, peritonitis and septicemia [67]. Surveillance data show that resistance in E. coli is consistently highest for antimicrobial agents that have been in use the longest time in human and veterinary medicine [68]. The past two decades have witnessed major increases in emergence and spread of multidrug-resistant bacteria and increasing resistance to newer compounds such as fluoroquinolones and certain cephalosporins [14]. Intensive molecular analyses have shown multiple mechanisms in which E. coli attain the antimicrobial resistance, the chief contributions to this genomic fitness being horizontal gene transfer in terms of conjugative plasmids, transducing phages and transposable elements carrying resistance genes. Of the various contributing genetic elements, this review aims at assessing the recent information available on the role of transposable elements in dissemination of multidrug resistance traits to E. coli. The transposons and integrons, owing to their genomic plasticity have contributed a great deal to the fitness quotient and robustness of E. coli to survive in varying environments. The information presented here is an indication of the magnitude of genomic variation that has resulted due to the transposable elements and also fortifies the role of these elements in genomic evolution, thoroughly justifying the predictions of Barbara McClintok that trasnposons will play a major role in genomic diversity and evolution.