**1. Introduction**

*Escherichia coli* (*E. coli*) are commensal organisms and are a part of human and animal micro‐ flora. Although most strains of *E. coli* are harmless, some isolates have the potential to cause severe diseases. Among the various nonpathogenic *E. coli* strains, some are able to acquire virulence determinants through the horizontal transfer of virulence genes. Based on the site of the infection and disease caused by *E. coli,* pathogenic strains are divided into major groups: extraintestinal pathogenic *E. coli* (ExPEC) and intestinal pathogenic *E. coli* (InPEC). This variability and adaptability reinforces the necessity of novel approaches to overcome pathogenic *E. coli*. Antibiotic resistance among pathogenic strains is considerable and is due to uncontrolled usage of antibiotics in human and veterinary field. Consequently, focus on modern and reverse vaccination, besides comparative genome analysis, is the most useful approach to control disease [1].

niche. Bacteria have no sexual life cycles, in contrast to higher organisms, to facilitate the exchange of alleles within a population. This function is fulfilled by horizontal gene trans‐ fer in bacteria; in this way the entire functional genomic unit can be imported from other sources that are not restricted by species. The DNA is transferred from less than 1 to more than 100 kb, in size. It can encode entire metabolic pathways or complex surface structures. These genes can be taken up as naked DNA or transferred in the form of plasmids, transpo‐

Horizontal Gene Transfer and the Diversity of *Escherichia coli*

http://dx.doi.org/10.5772/intechopen.68307

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Subgroups of genomic islands which have a pivotal role in HGT are pathogenicity islands (PAIs). The concept of PAI was founded in the late 1980s by Jörg Hacker and colleagues in

One or more virulence genes are carried by PAIs. There are also genomic or metabolic islands with genomic elements and characteristics similar to PAI, but lacking virulence genes. They are not present in the genome of a nonpathogenic species or a closely related species, but they

Large genomic regions are relatively occupied by PAIs. They often differ from the core genome and the majority of PAIs are in the range of 10–200 kb in their base compositions and they also show different codon usage. It is considered that the horizontally acquired PAI still has the base composition of the donor species. On the other hand, it is also observed that the horizontally acquired DNA base composition will tend to the base composition of the recipient's genome during evolution. Further factors such as DNA topology or specific codon usage of the virulence genes in PAI may also account for the maintenance of the divergent

PAIs are frequently adjacent to tRNA genes. tRNA genes serve as anchor points for insertion of foreign DNA that has been acquired by horizontal gene transfer through recombination process. They are frequently associated with mobile genetic elements and they are often flanked by direct repeat (DR) sequences. PAIs delete with distinct frequen‐ cies and they are often unstable. PAI virulence functions are lost with a frequency higher than the normal rate of mutation. Integrases, transposases, and insertion sequence (IS) elements have been identified as elements that contribute to the mobilization and insta‐

PAIs often represent mosaic-like structures rather than the homogeneous nature of horizon‐

sons, or phages [5].

**2. Horizontal gene transfer (HGT)**

*2.1.1. The genetic features of PAIs*

base composition [3].

bility of PAIs [2].

tally acquired DNA [2].

**2.1. Horizontal gene transfer (HGT) and pathogenicity islands**

are present in the genome of the same pathogenic bacterium [3].

Werner Goebel's group at the University of Würzburg, Germany [2, 3].

Genome evolution is the process by which the content and organization of genetic informa‐ tion of a species change over time. This process includes different forms of changes: point mutation and gene conversions, rearrangement (inversion or translocation), and deletion and insertion of foreign DNA (plasmid integration and transposition). These mechanisms seem to be the primary forces behind the genetic adaptation of bacterial organisms to novel environments and by which bacterial populations diverge and form separate, evolutionarily distinct species. Mechanisms of horizontal gene flux include the transmission of mobile genetic elements such as conjugative plasmids, bacteriophages, transposons, insertion ele‐ ments, and genomic islands, as well as the mechanism of recombination of foreign DNA into host DNA [2].

Point mutations and genetic rearrangements only lead to evolutionary development, primar‐ ily without creation of novel genetic determinants, while horizontal gene transfer (HGT) pro‐ duces extremely dynamic genomes. Thus, HGT can effectively alter the life-style of bacterial species. This is particularly true for bacterial pathogens, where virulence is linked to acquisi‐ tion of virulence determinants by HGT [3].

A major driving force of evolution and diversification in pathogenic bacteria compared with modification of the existing DNA is the acquisition of virulence determinants through succes‐ sive horizontal gene transfer [4]. The evolution of pathogenic bacteria with a strong lineage dependency often results from integration, retention, and expression of foreign DNA with a specific genomic background. In fact, parallel evolution from strains with the same genomic pathotype has occasionally emerged from multiple lineages, although the genetic mecha‐ nisms are not fully understood [4].

The modification of old functions and the development of new ones are required for bacte‐ rial evolution. The most frequent events are nucleotide exchange, insertion, and deletion. Mutation rates, per nucleotide per generation, are generally in the range of 10−6–10−9 in bac‐ teria. Moreover, gene disruption, deletions, and module exchange between different genes occur at appreciable frequency. These mechanisms are common in all living organisms. They allow modification of existing functions for optimizing in a niche or adapting to a new niche. Bacteria have no sexual life cycles, in contrast to higher organisms, to facilitate the exchange of alleles within a population. This function is fulfilled by horizontal gene trans‐ fer in bacteria; in this way the entire functional genomic unit can be imported from other sources that are not restricted by species. The DNA is transferred from less than 1 to more than 100 kb, in size. It can encode entire metabolic pathways or complex surface structures. These genes can be taken up as naked DNA or transferred in the form of plasmids, transpo‐ sons, or phages [5].
