**2. Transposable elements or transposons**

Transposable elements (TEs) or transposons have a significant role in the genome evolution and organization [12]. TEs are DNA fragments, which are able to change their position within the genome, in the process called transposition [13]. Bacterial transposable elements or bacterial transposons are divided into three different types: (i) insertion sequence elements, (ii) composite transposons, and (iii) noncomposite transposons. Insertion sequence elements, or in short, insertion sequences (ISs) are the simplest version of the transposable elements. ISs have not genetic information apart from necessary for their mobility. Composite and noncomposite transposons, on the other hand, also they have additional genetic material unrelated with transposition, for example, antibiotic resistance genes [14]. Composite transposons are flanked by the insertion sequences [12]. *E. coli* has various transposable elements carrying antibiotic resistance genes, including Tn*3*, Tn*5*, Tn*7*, Tn*9*, and Tn*10* encoding ampicillin, kanamycin, trimethoprim, chloramphenicol, and tetracycline, respectively [13, 15]. A transposon, Tn*6306*, encoding imipenem-hydrolyzing β-lactamase that mediates dissemination of the *blaIM*<sup>I</sup> among *Enterobacteriaceae* reported in 2017 [16]. The gene conferring resistance


**71**

*Insight into the mobilome of Escherichia coli DOI: http://dx.doi.org/10.5772/intechopen.82799*

inserted into a self-transferable plasmid [21].

elements of *E. coli* are listed.

**3. Plasmids**

to colistin, *mcr-1* gene is carried by the ISApl1 transposon [17]. Moreover, trimethoprim resistance gene *dfrA* was rapidly disseminated in Nigeria and Ghana via Tn*21*-type transposon in *E. coli* [18]. In **Table 1**, the most important transposable

Sometimes transposable elements comprise integrons, which are genetic elements that can capture genes including antibiotic resistance from different sources [19]. And integrons can be located on transposons, but also on plasmids, and in the bacterial chromosome [20]. Integrons are genetic elements that include the gene for the enzyme integrase together with gene cassettes encoding antibiotic resistance genes. A study reported a novel integron, In*53*, which is located on transposon

Plasmids are extrachromosomal DNA elements, which are self-replicating. Apart from the genetic information needed for the autonomous replication, they can also carry additional genetic information like antibiotic resistance genes and the genes encoding resistance to heavy metals, virulence, and other metabolic functions [22, 29]. Thanks to their specific functions, certain plasmids are used as cloning vectors in the recombinant DNA technology [30]. Plasmids are grouped into different Inc families/ groups. Inc groups are based on the inability of two plasmids to co-exist together in a bacterial cell [31]. Inc plasmids of the same Inc group have same type of replication region and thus have incompatible replication and partition mechanisms and hence cannot co-exist in a bacterial cell [32]. Plasmids belonging to the IncX family encode various resistance genes, mainly distributed among members of *Enterobacteriaceae* [33]. For example, recently, an emerging IncX plasmid, which is encoding *blaSHV-12* β-lactamase gene was reported in *E. coli*. The *blaIMI-2* gene, encoding an imipenemhydrolyzing β-lactamase, is carried by pRJ18, an IncFIB plasmid [16]. The ESBLencoding plasmids belonging to the Inc F, A/C, N, H12, 11 and K type were reported from The European Union. And one of the significant ESBL enzyme genes, CTX-M-1, is generally located on the Inc1 or IncN plasmids. For instance, CTX-M-1 ß-lactamase

originated from an animal is transmitted via Inc1 ST3 plasmid [34].

gene and also an IncFII plasmid carrying *blaNDM-5* [41].

The paradigm F plasmid, found among members of *Enterobacteriaceae,* is an IncF plasmid [35]. F-like plasmids can be detected in pathogenic as well as in nonpathogenic *E. coli* strains of different origins. The whole genome sequencing data of *E. coli* ST131 indicated that the acquisition of the CTX-M resistance gene was transferred via the conjugative F plasmid [36]. However, with the F plasmid, another significant antibiotic resistance gene is transferred, the *mcr-1* gene conferring resistance to colistin. Moreover, this *mcr-1* gene was found to be carried by 13 different plasmid incompatibility groups, among them are the Incl2, IncX4, and IncHI2 [37]. Although it has been reported that *mcr-1* gene has been carried by a transposon, it was shown that the *mcr-1* gene was transported via the plasmid, firstly. Moreover, it was found that the other *mcr* genes including *mcr-2, mcr-3, mcr-4, mcr-5,* and variants are carried by plasmids [38–40]. Recently, a new international outbreak was reported in Denmark. This outbreak was caused by *E. coli* ST410, an extraintestinal pathogenic *E. coli* resistant to fluoroquinolones, third-generation, cephalosporins, and carbapenems. This strain has acquired an IncX3 plasmid carrying *blaOXA-181*

Sometimes, plasmids are transferred among bacteria with conjugation, a genetic transfer that occurs between donor and recipient cell that is in a direct cell-to-cell contact [42]. Conjugative plasmids can carry integrons and/or transposons, and such genetic information can be transferred then horizontally via conjugation [43].

#### **Table 1.**

*Transposable elements in* E. coli *strains.*

*Insight into the mobilome of Escherichia coli DOI: http://dx.doi.org/10.5772/intechopen.82799*

to colistin, *mcr-1* gene is carried by the ISApl1 transposon [17]. Moreover, trimethoprim resistance gene *dfrA* was rapidly disseminated in Nigeria and Ghana via Tn*21*-type transposon in *E. coli* [18]. In **Table 1**, the most important transposable elements of *E. coli* are listed.

Sometimes transposable elements comprise integrons, which are genetic elements that can capture genes including antibiotic resistance from different sources [19]. And integrons can be located on transposons, but also on plasmids, and in the bacterial chromosome [20]. Integrons are genetic elements that include the gene for the enzyme integrase together with gene cassettes encoding antibiotic resistance genes. A study reported a novel integron, In*53*, which is located on transposon inserted into a self-transferable plasmid [21].

### **3. Plasmids**

*The Universe of Escherichia coli*

**2. Transposable elements or transposons**

the incompatibility and conjugative features. Plasmids have a big contribution to the bacterial cell in terms of acquiring antibiotic resistance genes and virulence genes [7, 8]. Bacteriophages are viruses that infect bacteria and replicate within bacterial cells. Bacteriophages can transfer genes among bacterial cells with the mechanism, called transduction. Specialized transduction can include only specific genes, however, generalized transduction can transfer any fragment of the bacterial DNA [6]. In a similar manner, some bacteriophages also carry genes, which are advantageous for bacteria such as resistance and virulence-associated genes. Among them, Shiga-toxin coding genes are one of the most significant phage-associated genes that is transferred to *E. coli* O157 : H7 [9]. Important mobile genetic elements are also genomic islands (GIs), which are genomic regions of gene clusters, often acquired by horizontal gene transfer and inserted into tRNA genes [10]. GIs can contain phage- or plasmid-derived sequences. GIs in *E. coli* strains carry genes associated with metabolism, pathogenesis as well as antimicrobial resistance [11].

Transposable elements (TEs) or transposons have a significant role in the genome evolution and organization [12]. TEs are DNA fragments, which are able to change their position within the genome, in the process called transposition [13]. Bacterial transposable elements or bacterial transposons are divided into three different types: (i) insertion sequence elements, (ii) composite transposons, and (iii) noncomposite transposons. Insertion sequence elements, or in short, insertion sequences (ISs) are the simplest version of the transposable elements. ISs have not genetic information apart from necessary for their mobility. Composite and noncomposite transposons, on the other hand, also they have additional genetic material unrelated with transposition, for example, antibiotic resistance genes [14]. Composite transposons are flanked by the insertion sequences [12]. *E. coli* has various transposable elements carrying antibiotic resistance genes, including Tn*3*, Tn*5*, Tn*7*, Tn*9*, and Tn*10* encoding ampicillin, kanamycin, trimethoprim, chloramphenicol, and tetracycline, respectively [13, 15]. A transposon, Tn*6306*, encoding imipenem-hydrolyzing β-lactamase that mediates dissemination of the *blaIM*<sup>I</sup> among *Enterobacteriaceae* reported in 2017 [16]. The gene conferring resistance

**Name Description Reference** Transposon-like element *blaCMY-2*-carrying element [22] Tn*21*-type transposon *dfrA* trimethoprim resistance [18] Tn*1999*-like element *blaOXA-48* gene encoding OXA-48 carbapenem [23] Tn*6306 blaIMI* [16] ISApl1 *mcr-1* [17] In*53 blaVEB-1* [21] Tn*3* Ampicillin resistance [24] Tn*5* Kanamycin resistance [25] Tn*7* Trimethoprim resistance [26] Tn*9* Chloramphenicol resistance [27] Tn*10* Tetracycline resistance [28]

**70**

**Table 1.**

*Transposable elements in* E. coli *strains.*

Plasmids are extrachromosomal DNA elements, which are self-replicating. Apart from the genetic information needed for the autonomous replication, they can also carry additional genetic information like antibiotic resistance genes and the genes encoding resistance to heavy metals, virulence, and other metabolic functions [22, 29]. Thanks to their specific functions, certain plasmids are used as cloning vectors in the recombinant DNA technology [30]. Plasmids are grouped into different Inc families/ groups. Inc groups are based on the inability of two plasmids to co-exist together in a bacterial cell [31]. Inc plasmids of the same Inc group have same type of replication region and thus have incompatible replication and partition mechanisms and hence cannot co-exist in a bacterial cell [32]. Plasmids belonging to the IncX family encode various resistance genes, mainly distributed among members of *Enterobacteriaceae* [33]. For example, recently, an emerging IncX plasmid, which is encoding *blaSHV-12* β-lactamase gene was reported in *E. coli*. The *blaIMI-2* gene, encoding an imipenemhydrolyzing β-lactamase, is carried by pRJ18, an IncFIB plasmid [16]. The ESBLencoding plasmids belonging to the Inc F, A/C, N, H12, 11 and K type were reported from The European Union. And one of the significant ESBL enzyme genes, CTX-M-1, is generally located on the Inc1 or IncN plasmids. For instance, CTX-M-1 ß-lactamase originated from an animal is transmitted via Inc1 ST3 plasmid [34].

The paradigm F plasmid, found among members of *Enterobacteriaceae,* is an IncF plasmid [35]. F-like plasmids can be detected in pathogenic as well as in nonpathogenic *E. coli* strains of different origins. The whole genome sequencing data of *E. coli* ST131 indicated that the acquisition of the CTX-M resistance gene was transferred via the conjugative F plasmid [36]. However, with the F plasmid, another significant antibiotic resistance gene is transferred, the *mcr-1* gene conferring resistance to colistin. Moreover, this *mcr-1* gene was found to be carried by 13 different plasmid incompatibility groups, among them are the Incl2, IncX4, and IncHI2 [37]. Although it has been reported that *mcr-1* gene has been carried by a transposon, it was shown that the *mcr-1* gene was transported via the plasmid, firstly. Moreover, it was found that the other *mcr* genes including *mcr-2, mcr-3, mcr-4, mcr-5,* and variants are carried by plasmids [38–40]. Recently, a new international outbreak was reported in Denmark. This outbreak was caused by *E. coli* ST410, an extraintestinal pathogenic *E. coli* resistant to fluoroquinolones, third-generation, cephalosporins, and carbapenems. This strain has acquired an IncX3 plasmid carrying *blaOXA-181* gene and also an IncFII plasmid carrying *blaNDM-5* [41].

Sometimes, plasmids are transferred among bacteria with conjugation, a genetic transfer that occurs between donor and recipient cell that is in a direct cell-to-cell contact [42]. Conjugative plasmids can carry integrons and/or transposons, and such genetic information can be transferred then horizontally via conjugation [43].

Therefore, the spreading of multiresistant genes is promoted [44]. For example, a conjugative *E. coli* plasmid from a swine incorporated a *cfr* gene, which conferred resistance to phenicol, lincosamides, oxazolidinones, pleuromutilins, streptogramin A, and also the *blaCTX-M-14b* ESBL gene [45]. Moreover, a colV plasmid (pCERC3) from a commensal *E. coli* ST95 carried virulence and antibiotic resistance genes including sulfonamide resistance encoded by sul3-associated with a class 1 integron [46]. The pE80 plasmid from a foodborne *E. coli* strain encodes multiple resistance determinants *oqxAB*, *fosA3*, *blaCTX-M-55*, and *blaTEM-1* and hence confers resistance to tetracycline, streptomycin, olaquindox/quinolone, and kanamycin [47].

In addition to carrying antibiotic resistance genes, plasmids have a major role in the transfer of virulence-associated genes. One of the most significant *E. coli* outbreaks was the hybrid enterohemorrhagic *E. coli* (EHEC)-enteroaggregative *E. coli* (EAEC) O104:H4 strain in Germany. This strain possesses three different plasmids: pAA (7.4 kb), pESBL (89 kb), and pG (1.5 kb) [48, 49]. pAA plasmid carries virulence factors including fimbriae for adherence, surface protein dispersion, Aat


**73**

virulence or resistance genes.

*Insight into the mobilome of Escherichia coli DOI: http://dx.doi.org/10.5772/intechopen.82799*

**4. Bacteriophages**

secretion system, protease, and the virulence regulator AggR [50]. Since the pAA plasmid is in the same cell as the pESBL, it increases both virulence and antibiotic resistance of this bacterium. Further, an EHEC O104:H7 strain that was isolated from cattle feces possessed IncB/O/K/Z and IncFIB plasmids carrying principal virulence genes, including, enterohemolysin and autotransporter [51]. Another significant serotype *for E. coli* is the O103 serotype, which is the second most common serogroup among the human foodborne illness. This serogroup has a pO157 plasmid encoding various virulence factors including enterohemolysin and type II secretion protein [8]. Recently, a characterized novel plasmid in a shiga-toxinproducing ETEC harbored *fae* locus encoding ETEC F4 fimbriae [7]. Some more

Viruses that are infecting bacteria are called bacteriophages. They have a significant impact on the dissemination of antibiotic resistance and virulenceassociated genes among foodborne pathogens, as they can transfer genes among bacteria in the process called phage-mediated transduction. Hence, they not only shape the bacterial evolution, but also cause the emergence of new pathogenic bacteria. On the other hand, in a good sense, phages protect against bacterial colonization of mucosal surfaces [56]. Moreover, viruses can be found everywhere in the world including soils, oceans, sewage, and different microbial communities [57, 58]. Transduction can be mediated via virulent or temperate phages. In the case of virulent phages, essentially any region of the bacterial DNA can be transferred (generalized transduction), while temperate phages can transfer only certain genes that are close to the attachment site of the lysogenic phage in the bacterial chromosome (specialized transduction). Specialized transduction happens when the prophage excision is inaccurate and some bacterial DNA co-excised with the prophage DNA [57]. Transduction is a significant process in terms of transferring antimicrobial resistance genes among bacterial cells [59]. For example, the phage called 933E transferred tetracycline resistance gene from the *E. coli* O157:H7 strain to the laboratory *E. coli* K12 AB1157 strain [60]. Similar to plasmids, phages have a crucial role in the acquisition of β-lactamase genes such as *blaCTX-M, blaSHV, blaTEM, qnrA, qnrB*, and *qnrS* [61]. A well-characterized P1-like bacteriophage, which lysogenizes bacteria, was reported, and it has encoded SHV-2 resistance in its genomic structure [62]. Furthermore, phages also have the ability to disseminate virulence factors such as staphylokinase, phospholipase or DNase, and superantigens [58]. Phages, which have been known for several years including bacteriophage , have been found to carry not only bacterial adhesion genes but also bacterial survival genes [63, 64]. Additionally, *E. coli* phage Ayreon carries the *cdt* gene cluster encoding the CdtA, CdtB, and CdtC subunits of the cdtI holotoxin [65]. Another significant toxin encoded by a temperate phage is the Shiga Toxin 2, which is a virulence factor in *E. coli* O157:H7 [9]. Moreover, some other Shiga Toxin variants including Shiga Toxin 2c can be encoded by phages of the pathogenic *E. coli* O157 strain [66]. However, some bacteriophages, for example, phiC119 can be used as biological control agents, as they can infect and lyse their bacterial hosts (phage therapy) [67]. Interestingly, genetic elements encoded by bacteriophages can also regulate gene expression in the bacterial host cell. For instance, transcription factor Cro has an effect on the regulation of virulence genes in enterohemorrhagic *E. coli* [68]. **Table 3** shows some well-known phages involved in the transduction of

examples of important *E. coli* plasmids are given in **Table 2**.

**Table 2.** *Plasmids in* E. coli *strains.* *Insight into the mobilome of Escherichia coli DOI: http://dx.doi.org/10.5772/intechopen.82799*

secretion system, protease, and the virulence regulator AggR [50]. Since the pAA plasmid is in the same cell as the pESBL, it increases both virulence and antibiotic resistance of this bacterium. Further, an EHEC O104:H7 strain that was isolated from cattle feces possessed IncB/O/K/Z and IncFIB plasmids carrying principal virulence genes, including, enterohemolysin and autotransporter [51]. Another significant serotype *for E. coli* is the O103 serotype, which is the second most common serogroup among the human foodborne illness. This serogroup has a pO157 plasmid encoding various virulence factors including enterohemolysin and type II secretion protein [8]. Recently, a characterized novel plasmid in a shiga-toxinproducing ETEC harbored *fae* locus encoding ETEC F4 fimbriae [7]. Some more examples of important *E. coli* plasmids are given in **Table 2**.

### **4. Bacteriophages**

*The Universe of Escherichia coli*

Incl2, IncX4, and IncHI2

plasmid

Therefore, the spreading of multiresistant genes is promoted [44]. For example, a conjugative *E. coli* plasmid from a swine incorporated a *cfr* gene, which conferred resistance to phenicol, lincosamides, oxazolidinones, pleuromutilins, streptogramin A, and also the *blaCTX-M-14b* ESBL gene [45]. Moreover, a colV plasmid (pCERC3) from a commensal *E. coli* ST95 carried virulence and antibiotic resistance genes including sulfonamide resistance encoded by sul3-associated with a class 1 integron [46]. The pE80 plasmid from a foodborne *E. coli* strain encodes multiple resistance determinants *oqxAB*, *fosA3*, *blaCTX-M-55*, and *blaTEM-1* and hence confers resistance to tetracycline, streptomycin, olaquindox/quinolone, and kanamycin [47]. In addition to carrying antibiotic resistance genes, plasmids have a major role in the transfer of virulence-associated genes. One of the most significant *E. coli* outbreaks was the hybrid enterohemorrhagic *E. coli* (EHEC)-enteroaggregative *E. coli* (EAEC) O104:H4 strain in Germany. This strain possesses three different plasmids: pAA (7.4 kb), pESBL (89 kb), and pG (1.5 kb) [48, 49]. pAA plasmid carries virulence factors including fimbriae for adherence, surface protein dispersion, Aat

**Name or class Description/gene carried Reference** IncA/C plasmids Multiple antibiotic resistance [29] IncX3 plasmid *blaSHV-12* [33] IncA/C or IncI1 plasmid *blaCMY-2*-like genes [52] pRJ18 *blaIMI-2* [16]

MOBP131/IncL plasmids *blaOXA-48* [23] IncX3 plasmid *blaOXA-181* [41] IncFII plasmid *blaNDM-5* [41] pEC26 *mcr-1.9* [53] pCERC3 A colV plasmid carrying Sul3-related integron [46] pAA Encoding aggregative adherence fimbriae variant [48]

*mcr-1* [37]

*aap* gene encoding the surface protein dispersin [50] *aatPABCD* operon encoding Aat secretion system [50] Protease SepA [50]

[50]

[54]

[55]

[8]

[47]

*aggR* gene is encoding EAEC master virulence gene

Support of the translocation of the Stx2a across the

secretion protein, catalase, peroxidase, toxinB

pED1169 Encoding F4-like fimbriae [7] pGXEC3 Conjugative plasmid harboring *cfr* gene [45]

Inc1 ST131 *blaCTX-M-1* [34]

regulator AggR

epithelial cell

*cvaA*

pS88 Encoding virulence genes *ompTp*, *sitA*, *cia*, *iss*, *iroN, hlyF*,

pO157 Encoding enterohemolysin, serine protease, type II

pE80 Conjugative IncFII plasmid encoding *oqxAB*, *fosA3*, *blaCTX-M-55*, and *blaTEM-1*

**72**

**Table 2.**

*Plasmids in* E. coli *strains.*

Viruses that are infecting bacteria are called bacteriophages. They have a significant impact on the dissemination of antibiotic resistance and virulenceassociated genes among foodborne pathogens, as they can transfer genes among bacteria in the process called phage-mediated transduction. Hence, they not only shape the bacterial evolution, but also cause the emergence of new pathogenic bacteria. On the other hand, in a good sense, phages protect against bacterial colonization of mucosal surfaces [56]. Moreover, viruses can be found everywhere in the world including soils, oceans, sewage, and different microbial communities [57, 58]. Transduction can be mediated via virulent or temperate phages. In the case of virulent phages, essentially any region of the bacterial DNA can be transferred (generalized transduction), while temperate phages can transfer only certain genes that are close to the attachment site of the lysogenic phage in the bacterial chromosome (specialized transduction). Specialized transduction happens when the prophage excision is inaccurate and some bacterial DNA co-excised with the prophage DNA [57]. Transduction is a significant process in terms of transferring antimicrobial resistance genes among bacterial cells [59]. For example, the phage called 933E transferred tetracycline resistance gene from the *E. coli* O157:H7 strain to the laboratory *E. coli* K12 AB1157 strain [60]. Similar to plasmids, phages have a crucial role in the acquisition of β-lactamase genes such as *blaCTX-M, blaSHV, blaTEM, qnrA, qnrB*, and *qnrS* [61]. A well-characterized P1-like bacteriophage, which lysogenizes bacteria, was reported, and it has encoded SHV-2 resistance in its genomic structure [62].

Furthermore, phages also have the ability to disseminate virulence factors such as staphylokinase, phospholipase or DNase, and superantigens [58]. Phages, which have been known for several years including bacteriophage , have been found to carry not only bacterial adhesion genes but also bacterial survival genes [63, 64]. Additionally, *E. coli* phage Ayreon carries the *cdt* gene cluster encoding the CdtA, CdtB, and CdtC subunits of the cdtI holotoxin [65]. Another significant toxin encoded by a temperate phage is the Shiga Toxin 2, which is a virulence factor in *E. coli* O157:H7 [9]. Moreover, some other Shiga Toxin variants including Shiga Toxin 2c can be encoded by phages of the pathogenic *E. coli* O157 strain [66]. However, some bacteriophages, for example, phiC119 can be used as biological control agents, as they can infect and lyse their bacterial hosts (phage therapy) [67]. Interestingly, genetic elements encoded by bacteriophages can also regulate gene expression in the bacterial host cell. For instance, transcription factor Cro has an effect on the regulation of virulence genes in enterohemorrhagic *E. coli* [68]. **Table 3** shows some well-known phages involved in the transduction of virulence or resistance genes.

