Insight into the mobilome of *Escherichia coli*

*Elif Bozcal*

### **Abstract**

Mobilomes are all mobile genetic elements (plasmids, transposable elements, insertion sequences, gene cassettes, integrons, genomic islands, and bacteriophages) in a genome. Mobilome is one of the responsible agents for the bacterial evolution, virulence, and increasing antibiotic resistance. The mobile genetic elements in the *Escherichia coli* genome can carry antibiotic resistance genes and/or virulence genes. The acquisition of new mobile genetic elements can lead to the emergence of new pathotypes. The aim of this chapter is to gather knowledge about mobile genetic elements in *E. coli* strains. The method in this chapter depends on a literature survey, which scans reviews, research articles, and theses published about transposable elements, plasmids, bacteriophages, and genomic islands in *E. coli* strains.

**Keywords:** *Escherichia coli*, mobilome, genomic island, plasmid, transposon, bacteriophage

#### **1. Introduction to mobilome and mobile genetic elements**

Mobilome encompasses all mobile genetic elements (MGEs) in a genome [1]. Mobile genetic elements are moveable DNA segments, transferring among bacterial genomes. MGEs carry the so-called noncore genes and they have an important contribution to the plasticity of bacterial genomes. Plasmids, transposable elements, insertion sequences, gene cassettes, integrons, genomic islands, and bacteriophages are MGEs. Approximately, 2000 genes from 20 sequenced *E. coli* genomes were found to be noncore genes [2].

The presence and/or absence of MGEs within genomic DNA can lead to variance in *E. coli* pathotypes. Despite the fact that *E. coli* strains have been known as part of the normal microbiota of human gastrointestinal tract among *E. coli,* there are also pathogenic strains, and hence, the strains of *E. coli* are grouped either as (i) commensal, which are nonpathogenic, (ii) intestinal pathogenic strains (IPEC), or (iii) extraintestinal pathogenic (ExPEC) strains [3]. Rearrangements, excision, and integration of the DNA fragments can be the mechanisms behind the rapid evolution of *E. coli* strains and also the emerging pathogenic *E. coli* strains [4].

The most studied MGEs are transposable elements, plasmids, bacteriophages, and genomic islands in *E. coli* strains. Transposable elements are known as DNA sequences that can transfer among different locations in the bacterial genome [5]. Resistance genes can be harbored by a transposon in a genome. Transposons can be integrated and excised from the chromosome by enzymes, called transposases. The simplest version of the transposon is the insertion sequence [6]. Plasmids are self-replicating genetic elements. Different groups of plasmids exist according to

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].
