**5. Genomic islands**

Genomic island (GI) is a large region of genomic DNA, more than 10 kb length, which can be frequently exchanged between bacterial isolates. GIs are encoding proteins for transfer, recombination, and restriction/modification or other proprieties, for example, gene clusters for metabolic adaptation, virulence, and or resistance of bacteria [11]. GIs involving virulence-associated genes are called pathogenicity islands (PAIs) [70]. PAI generally encodes genes related to virulence factors (VFs) including adhesins, toxins, invasins, capsule biosynthesis machinery, iron uptake system, and type III, IV, VI and or VII secretion apparatus [71]. Generally, the size of PAIs more than 10 kb and their GC content differs from the average genome. Their integration site is located in tRNA genes and repeated sequences, which is containing at least one mobile genetic element including remnants of plasmids, insertion sequences (ISs), and integrons, and associated gene cassettes [72]. tRNA-encoding genes are known as the hot spot for the integration of foreign DNA [71]. Several PAIs can be excised from bacterial chromosome by site-specific recombination [73].

PAIs have been reported firstly in the genome of uropathogenic *E. coli*, later also in other pathogenic bacteria [74]. PAIs are now found to be widely distributed among animal- and plant-associated bacterial pathogens and PAIs that can be horizontally transferred have great impact on the rapid evolution of virulent and antibiotic-resistant strains [71].

Enterocyte effacement locus (LEE) is one of the best known PAIs in *E. coli*. LEE is a 35-kb cluster of genes associated with bacterial adherence to intestinal epithelial cells and the formation of attaching and effacing lesions [75]. High-pathogenicity island (HPI), a PAI originally found in *Yersinia* species, but also widely spread among other *Enterobacteriaceae* including *E. coli*, encodes a siderophore iron uptake system (the *fyuA-irp* gene clusters), the so-called yersiniabactin. HPI was found among enteroaggregative *E. coli*, enteropathogenic *E. coli*, enteroinvasive *E. coli*, and enterotoxigenic *E. coli* (ETEC) [76]. HPI was also found in genomes of certain non-O157 STEC clonal lineages [77] (**Table 4**).

It was reported that UPEC strain 536 has at least four PAIs located on the chromosome. The sizes of the first two PAI I536 and PAI II536 are 70 and 120 kb. The significant virulence-associated genes encoded on these PAIs are hemolysin and P fimbriae. PAI III536 and PAI IV536 have S fimbriae and HPI analog gene clusters [78]. It was reported that an ExPEC strain causing neonatal meningitis possessed the HPI, suggesting that HPI was associated with the development of neonatal meningitis [79]. Moreover, capsule synthesis-associated genes can be

**75**

**6. Conclusion**

**Table 4.**

**Acknowledgements**

Technological Research Council of Turkey.

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

located on different PAIs in ExPEC [80]. Furthermore, it was shown that HPI in general contributes to ExPEC virulence [81]. Another novel PAI was found in an APEC strain integrated adjacent to the thrW tRNA gene encoding vacuolating autotransporter toxin. This PAI is known as Vat-encoding pathogenicity island and may contribute to APEC pathogenicity [82]. A novel function carried by a GI was reported recently—a GI located in the EHEC chromosome included the transcriptional activator GmrA that controls the motility of EHEC O157:H7 [83]. In addition, GIs have a role not only in virulence but also in the metabolic process of the bacterial cell. The *dnd* operon, which is a DNA modification system cluster encoding and catalyzing phosphorothioation of DNA in *E. coli* was found to be located on diverse

GI OI-29 Transcriptional activator GmrA [83]

AGI-3 PAI SelC-associated GI involved in carbohydrate uptake and

[86]

virulence

*Genomic islands and pathogenicity islands in* E. coli*.*

**Name Description Reference** LEE PAI locus of enterocyte effacement [75] Yersiniabactin-HPI Encoding an siderophore iron uptake system [77] PAI I536 and PAI II536 Hemolysin and P fımbriae [78] PAI III536 and PAI IV536 S fimbriae and HPI [78] PAI V536 K15 capsule determinant [80] Vat-encoding PAI Adjacent to the 3′ terminus-thrW tRNA gene [82] EPAI1 RTX family exoprotein [85] EPAI2 O-antigen polysaccharide (OPS) [85] EPAI3 EPAI3 [85] EPAI4 T3SS [85] EPAI5 O122 [85] EPAI6 LEE [85]

*E. coli* is one of the most studied bacteria all around the world. There are various pathotypes and subclones of *E. coli* as well as commensal strains. One of the most important reasons of emerging numerous pathotypes of *E. coli* is MGEs, including transposons, plasmids, bacteriophages, and genomic islands. MGEs are significant drivers of the horizontal gene transfer. Therefore, in order to understand the genome evolution, virulence and antibiotic resistance genes acquisition among *E. coli* strains

This study was supported by a fellowship from the Program (TUBITAK-2219- 2017-2nd term), and Elif Bozcal was awarded a fellowship by the Scientific and

GIs in *E. coli* [84]. **Table 4** shows some well-known GIs and PAIs.

from various sources is important to study MGEs and the mobilome.

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


#### **Table 4.**

*The Universe of Escherichia coli*

P1-like bacteriophage

(RCS47)

**Table 3.**

**5. Genomic islands**

*Bacteriophages of* E. coli*.*

Genomic island (GI) is a large region of genomic DNA, more than 10 kb length, which can be frequently exchanged between bacterial isolates. GIs are encoding proteins for transfer, recombination, and restriction/modification or other proprieties, for example, gene clusters for metabolic adaptation, virulence, and or resistance of bacteria [11]. GIs involving virulence-associated genes are called pathogenicity islands (PAIs) [70]. PAI generally encodes genes related to virulence factors (VFs) including adhesins, toxins, invasins, capsule biosynthesis machinery, iron uptake system, and type III, IV, VI and or VII secretion apparatus [71]. Generally, the size of PAIs more than 10 kb and their GC content differs from the average genome. Their integration site is located in tRNA genes and repeated sequences, which is containing at least one mobile genetic element including remnants of plasmids, insertion sequences (ISs), and integrons, and associated gene cassettes [72]. tRNA-encoding genes are known as the hot spot for the integration of foreign DNA [71]. Several PAIs can be excised from

**Name Description/gene carried Reference** Bacteriophage 933W *tet* [60]

Phage ayreon *cdt* gene cluster [65] Phage 2851 *Stx2c* [66]

Phage *bor* gene homologous to *iss* serum resistance locus [63]

Phage *lom* gene encoding K12 adhesion to human buccal epithelial cells

Phage PP01 Two tail fiber genes- 37 and 38 responsible for host-cell recognition

*blaSHV-2* [62]

[64]

[69]

PAIs have been reported firstly in the genome of uropathogenic *E. coli*, later also in other pathogenic bacteria [74]. PAIs are now found to be widely distributed among animal- and plant-associated bacterial pathogens and PAIs that can be horizontally transferred have great impact on the rapid evolution of virulent and

Enterocyte effacement locus (LEE) is one of the best known PAIs in *E. coli*. LEE is a 35-kb cluster of genes associated with bacterial adherence to intestinal epithelial cells and the formation of attaching and effacing lesions [75]. High-pathogenicity island (HPI), a PAI originally found in *Yersinia* species, but also widely spread among other *Enterobacteriaceae* including *E. coli*, encodes a siderophore iron uptake system (the *fyuA-irp* gene clusters), the so-called yersiniabactin. HPI was found among enteroaggregative *E. coli*, enteropathogenic *E. coli*, enteroinvasive *E. coli*, and enterotoxigenic *E. coli* (ETEC) [76]. HPI was also found in genomes of certain

It was reported that UPEC strain 536 has at least four PAIs located on the chromosome. The sizes of the first two PAI I536 and PAI II536 are 70 and 120 kb. The significant virulence-associated genes encoded on these PAIs are hemolysin and P fimbriae. PAI III536 and PAI IV536 have S fimbriae and HPI analog gene clusters [78]. It was reported that an ExPEC strain causing neonatal meningitis possessed the HPI, suggesting that HPI was associated with the development of neonatal meningitis [79]. Moreover, capsule synthesis-associated genes can be

bacterial chromosome by site-specific recombination [73].

non-O157 STEC clonal lineages [77] (**Table 4**).

antibiotic-resistant strains [71].

**74**

*Genomic islands and pathogenicity islands in* E. coli*.*

located on different PAIs in ExPEC [80]. Furthermore, it was shown that HPI in general contributes to ExPEC virulence [81]. Another novel PAI was found in an APEC strain integrated adjacent to the thrW tRNA gene encoding vacuolating autotransporter toxin. This PAI is known as Vat-encoding pathogenicity island and may contribute to APEC pathogenicity [82]. A novel function carried by a GI was reported recently—a GI located in the EHEC chromosome included the transcriptional activator GmrA that controls the motility of EHEC O157:H7 [83]. In addition, GIs have a role not only in virulence but also in the metabolic process of the bacterial cell. The *dnd* operon, which is a DNA modification system cluster encoding and catalyzing phosphorothioation of DNA in *E. coli* was found to be located on diverse GIs in *E. coli* [84]. **Table 4** shows some well-known GIs and PAIs.

#### **6. Conclusion**

*E. coli* is one of the most studied bacteria all around the world. There are various pathotypes and subclones of *E. coli* as well as commensal strains. One of the most important reasons of emerging numerous pathotypes of *E. coli* is MGEs, including transposons, plasmids, bacteriophages, and genomic islands. MGEs are significant drivers of the horizontal gene transfer. Therefore, in order to understand the genome evolution, virulence and antibiotic resistance genes acquisition among *E. coli* strains from various sources is important to study MGEs and the mobilome.

#### **Acknowledgements**

This study was supported by a fellowship from the Program (TUBITAK-2219- 2017-2nd term), and Elif Bozcal was awarded a fellowship by the Scientific and Technological Research Council of Turkey.

*The Universe of Escherichia coli*
