**3. Mobile genetic elements of** *E. coli* **associated with antibiotic resistance genes**

Mobile genetic material (MGEs) has an important role in transferring resistance. Mutation has a key role in bringing changes in a particular DNA fragment. Similarly, HGT, transfer of plasmid or transposons have the major contribution in developing resistance to the reagent. Considering if point mutation brings changes in a promotor region, it will have an impact on the expression of genes [32]. Similarly, a point mutation in the gyrase gene has developed to fluoroquinoloneresistant phenotype [30]. Exogenic resistance genes encoded on plasmids, phage, integrons, and transposons can transfer horizontally through conjugation, transformation, or transduction and can encode all the 3-resistance mechanism (intrinsic, adopted, acquired) Details of genes, their mechanisms, and pathways are explained in the following section.

Resistant pathogens are a major source of infectious diseases worldwide. Infections due to MDR bacteria have considerably increased health care costs. Due to resistant pathogens, morbidity and mortality have been reported in different parts of the world. Molecular characterization showed that extensive multi drugresistant has commonly been accomplished by the acquisition of pre-existing causes followed by amplification in response to selection. The accumulation, retention, and transfer of resistant genes are frequently due to the activities of MGEs of *E. coli*, MGEs are known as non-core genes, and have a significant contribution to the plasticity of bacterial genomes. Transposable elements, integrons (In), Plasmids, gene cassettes, insertion sequences (IS), bacteriophages, and genomic islands (GIs), all are considered as MGEs. Though, from 20 sequenced *E. coli* genomes, almost 2000 genes were detected to be noncore genes [33]. Transposons (Tn) and IS are discrete segments of DNA that can almost randomly transfer themselves within a DNA molecule. Other mobile elements, like integrons (In), use site-specific recombination to transfer resistance genes among distinct sites. Similarly, these types of MGEs are mostly present in different locations in the form of multiple copies in the genome, they can also facilitate homologous recombination (interchange of sequences between same or different segments). Genetic exchange of Intercellular mechanisms contain transduction (facilitated by bacteriophages), conjugation/ mobilization (facilitated by plasmids and integrative conjugative elements [ICE]), and transformation (uptake of various superfluous types of MGEs) support the rapid development of various multi-resistant bacteria in the aspect of antibiotics chemotherapy [34]. Within genomic DNA the presence/absence of MGEs can lead to modification in pathotypes of *E. coli*. In fact, strains of *E. coli* have been identified as part of the normal microbiota of the human gastrointestinal tract. In addition*,*

there are also pathogenic strains, and thereby the *E. coli* strains are characterized either as (i) non-pathogenic, which are commensal (ii) intestinal pathogenic strains (IPEC), or (iii) extraintestinal pathogenic (EXPEC) strains. Integration, excision, and rearrangements of the DNA fragments can be the mechanisms behind the rapid evolution of pathogenic *E. coli* strains [35].

## **3.1 Transposons**

Transposons (Tn) can be defined as a DNA sequence that has potential to jump into different locations of the genome hence, they are called jumping genes. Transposons are divided into two-main groups: class I (Retrotransposons) and class II (DNA transposons). Retrotransposons are mostly found in eukaryotic organisms while DNA transposons can be found in both prokaryotes and eukaryotes. Prokaryotic DNA transposons harbor antibiotic resistance genes. It has the potential to move from plasmid to plasmids or from chromosomal DNA into a plasmid, as a result, it became the source of resistant genes dissemination [36, 37]. Transposon's elements have two major characteristics that differentiate them from other genetic elements. on basis of its mobile nature, it can move from one place to another and bring variation in the genetic makeup of the organism. During transpositions process, transposons can transmit resistance genes and can multiply intracellularly. Despite its large number, only few copies get access into an integral part of the genome. Transposons have stability and are maintained by their capability to replicate and maintain their existence [38]. Transposable elements have an important role in genome evolution and organization [39]. *E. coli* transposable elements are divided into three different types: (a) composite transposons, (b) non-composite transposons, (c) insertion sequence elements (ISE). Composite and non-composite transposons have extra genetic material not related to transposition, for example, antibiotic resistance genes. Composite transposons are lined by the IS. IS elements are the simplest type of transposable elements and do not carry extra genetic information apart from those needed for their mobility [40].
