**3. Diversity of** *E. coli* **strains**

gene transfer [17]. *cdt*-I and *cdt*-IV genes might have been acquired by phage transduction from a common ancestor and evolution of the CDT-encoding phages in different bacterial

The presence of CDT-V in Shiga-toxigenic *E. coli* (STEC) strains of various serotypes has been reported with clinical and nonclinical origin. CDT-V has also been associated with other strains in different serotypes and pathotypes associated with human diarrhea. The P2-like prophage sequences seem to be characteristic for the CDT-V-positive strains, with few differ‐ ences that can be attributed to the adaptation processes in various hosts. The common acqui‐ sition of the *cdt*-V operon in O157: NM EHEC strains has been proposed by the presence of P2-like phage sequences after lineage divergence from the O157:H7 strains. However, there is

These findings indicate that during evolution, while the *cdt‐V* genes are rather conserved and the carrier P2-like phages became diverse, in most cases it may have resulted in loss of their mobility. Therefore, the evolutionary history of the *cdt‐V* operon and its P2-like carrying pro‐ phages is proposed. Within more variable and potentially inactivated bacteriophage genomes, the highly conserved *cdt‐V* operon may cause selective pressure to maintain a functional *cdt* gene cluster. Stabilization of this cargo determinant was done by inactivation of this bacterio‐ phage genome. It is clear that further investigations of flanking regions and P2-like prophage sequences in CDT-V-positive strains will help to clarify the evolutionary background of the

The presence of *cdt* genes in different bacterial species and the analysis of DNA in the vicinity of the *cdt* genes suggest that the toxin has been acquired from heterogenic species by horizon‐ tal gene transfer. However, the probable phylogenetic origin (or ancestor) has still remained elusive. Interestingly, the phage and the corresponding insertion sequence remnants were found nearby the *E. coli cdt* genes. All these data suggest that *cdt* genes were acquired by hori‐ zontal transfer events and evolved separately since then. *stx* gene, and some types of *cdt* genes are the examples of horizontally acquired genes by phages in *E. coli*. CDT production which has been associated with some pathogenic *E. coli*, isolated from clinical diarrheal patients, suggests that the *cdt* genes are acquired independently in a number of *E. coli* lineages, pos‐

It is now evident that some virulent genes are located on a large plasmid (pO157) in patho‐ genic *E. coli*. Some of these genes are the extracellular serine protease gene (*espP*), catalaseperoxidase gene (*katP*), and type II secretion pathway protein D (*etpD*). Different sizes of this plasmid were reported that may contain some of these three genes. pO157 plasmid is mainly associated with EHEC and ETEC strains. In fact, pO157 plasmid was detected in clinical EHEC O157 isolates in 1983 for the first time. This plasmid could be detected in other atypical human EPEC. Atypical EPEC strain lacks EAF plasmid and *bfp* gene. In addition, the genome content of this plasmid in Shiga toxin-producing strains is quite divergent. However, viru‐

host-generated differences in the *cdt* genes and their flanking DNA contents [16].

326 *Escherichia coli* Escherichia coli - Recent Advances on Physiology, Pathogenesis and Biotechnological Applications - Recent Advances on Physiology, Pathogenesis and Biotechnological Applications

a strong association between the presence of CDT-V and O157: NM strains [14].

*2.3.3. HGT and plasmids harboring virulence genes in pathogenic E. coli*

lence-associated genes' profile is serotype dependent [18].

distribution of these variants [14–17].

sibly as a result of HGT.

The coevolution of bacterial pathogens related to genetic elements, including pathogenicity islands and phages encoding virulence factors, has been observed in several species. *E. coli* is a member of the normal intestinal microflora of humans and animals. However, certain *E. coli* strains have acquired virulence-associated factors via horizontal gene transfer, enabling the bacteria to colonize its host and cause disease. Pathogenic *E. coli* utilize particular strategies to penetrate into host cells and tissues. Special enzymes and pathogenic factors are known as unique virulence determinants of each bacterium. However, each bacterium has a unique genomic background of its own chromosome, such as *fliC* and *fimH* genes that encode the main subunit of flagella and fimbriae type I, respectively. Both of them are known as viru‐ lence-associated factors and interfere in pathogenicity of *E. coli* [19].

Investigations have revealed, *hly* gene which is located on a PAI and encodes alpha-hemolysin, is frequently detected in *cdt*-III- and *cdt*-IV-producing human and animal pathogenic *E. coli* strains. The prevalence of *hly* gene in *cdt*-type III, IV, and V was more than other isolates. These results demonstrate that, possibly, there could be a relationship between the existence of *hly* gene and the type of *cdt* gene in clinical *E. coli* isolates. *fliC* and *fim* are two chromosomally located genes that can be defined as the genomic background of *E. coli* strains. The *fliC* gene encodes the flagel‐ lin subunit; type 1 fimbriae are also encoded by the chromosomally located *fim* gene cluster. The presence of *fim* DNA sequences is common among *E. coli* strains. In fact, the majority of clinical isolates, both virulent and non-virulent, could be induced to express type 1 fimbriae [19].

In the recent years, whole-genome sequences for many bacteria have become accessible. It improves our understanding about virulence-associated genes and horizontal gene transfer from the emergence of new pathogens aspects. Some pathogens like *E. coli* could acquire virulence genes via HGT. On the other hand, from the diagnostic point of view, virulent gene examination could improve our knowledge about different pathotypes' detection and

Horizontal Gene Transfer and the Diversity of *Escherichia coli*

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

329

Phage-related and virulence-associated factors transferred by phages were found to be preva‐ lent signature proteins. The signature proteins identified include several individual phage proteins (holins, nucleases, terminases, and transferases) and multiple members of different protein families (the lambda family, phage-integrase family, phage-tail tape protein family, putative membrane proteins, regulatory proteins, restriction-modification system proteins, tail fiber-assembly proteins, base plate-assembly proteins, and other prophage tail-related

The heterogeneous nature of strains could be because of the HGT through mobile genetic elements. The genetic exchanges that occur in bacteria provide genetic diversity and versatil‐ ity. Plasmids, bacteriophages, and genomic islands belong to the flexible *E. coli* genome and their genetic information can be horizontally acquired. The rapid evolution of *E. coli* vari‐ ants contributes to these genomic regions as they are subject to rearrangements, excision, and transfer frequently. The creation of new pathogenic variants is the result of further acquisition

The accumulating amount of sequence information generated in the era of "genomics" helps to increase our understanding of factors and mechanisms that are involved in diversifica‐ tion of this new bacterial species, as well as in those that may direct host-specificity. From a comparative genomic aspect, a significant challenge is to utilize bulky amount of datasets to distinguish and conceptualize specific sequence signatures that scientifically or diagnostically are applicable traits. By comparing more sequence data from different strains, new signature biomarkers will be recognized for use as vaccines or as diagnostic factors in future. Signature conserved proteins in a wide range of pathogenic bacterial strains can potentially be used in

classification.

proteins).

of additional genome.

**Author details**

modern vaccine-design strategies.

Maryam Javadi, Saeid Bouzari and Mana Oloomi\*

\*Address all correspondence to: manaoloomi@yahoo.com

Molecular Biology Department, Pasteur Institute of Iran, Tehran, Iran

**4. Conclusions and the way forward**

Among pathogenic *E. coli*, the existence of a large virulent plasmid (pO157) has also been observed. The *etpD*, *katP*, and *espP* genes are located on this plasmid. The pO157 plasmid is mainly associated with EHEC and ETEC strains. There is a relation between the occurrence of *stx* genes and these virulent plasmid-associated genes. Moreover, PCR analysis revealed a close relationship between the occurrence of plasmid-born *katP* gene and *stx* gene in patho‐ genic *E. coli.* Most of the *katP*+ strains belong to Shiga toxin-producing *E. coli.* The *katP* gene is mostly present in CDT-I- and CDT-II-producing strains. EspP, which possesses human coagulation factor V and pepsin A proteolytic activity, is a significant marker of virulence in Shiga toxin-producing strains. In CDT-III-producing isolates, high frequency of *espP gene* is considerable. Alpha-hemolysin is frequently associated with human uropathogenic *E. coli* (UPEC); furthermore, related encoding PAI is also unstable and the operon could be located on either a plasmid or the chromosome. Besides, urinary tract infection (UTI) is caused pre‐ dominantly by type 1fimbriated UPEC and initial binding is mediated by the FimH adhesin of the mentioned fimbriae. Investigation showed that most of the *hly*<sup>+</sup> strains harbor *fimH* gene. In addition, all *hly*<sup>+</sup> strains possess one or more of plasmid pO157 genes, including *etpD*, *katP*, and *espP.* These genes plus the *stx* gene are among the EHEC and STEC characteristics, although the *espP* gene is common in EPEC and EHEC. Simultaneous presence of these genes indicates that clinical isolates obtain *hly* operon and relevant PAI. In addition, in evolutionary pathways, isolates improve their pathogenicity by achieving the *cdt* genes. Studies demon‐ strate that virulence genes from CDT-producing strains belong to the heterogeneous group. Strains which are clustered as particular groups have similar characteristics, while possessing their own unique genotype and genomic content. For instance, each distinct *cdt*-type group, by possessing a particular *cdt* gene as genomic backbone, has an approximately similar pat‐ tern based on other virulence genes [19].

This evidence further confirms that horizontal gene transfer could occur among pathogenic strains. Moreover, findings indicate that CDT-producing strains may have originated from a common ancestor during their evolution by HGT, and they departed from each other [17].

CDT-producer strains did not show particular phylogenomic relation and pattern. Indeed, they might carry the same or similar virulence gene sets, but remarkably possess their own divergent genomic structure. This is probably because of their complex and distinct evolu‐ tionary pathways, indicating independent acquisition of mobile genetic elements that have driven from their evolution [19]. Furthermore, it was shown that there are different types of CDTs that are encoded by prophages, plasmids, and/or pathogenicity islands that result in different types of CDTs through HGT in different origins [7, 17, 19, 22].

In the recent years, whole-genome sequences for many bacteria have become accessible. It improves our understanding about virulence-associated genes and horizontal gene transfer from the emergence of new pathogens aspects. Some pathogens like *E. coli* could acquire virulence genes via HGT. On the other hand, from the diagnostic point of view, virulent gene examination could improve our knowledge about different pathotypes' detection and classification.

Phage-related and virulence-associated factors transferred by phages were found to be preva‐ lent signature proteins. The signature proteins identified include several individual phage proteins (holins, nucleases, terminases, and transferases) and multiple members of different protein families (the lambda family, phage-integrase family, phage-tail tape protein family, putative membrane proteins, regulatory proteins, restriction-modification system proteins, tail fiber-assembly proteins, base plate-assembly proteins, and other prophage tail-related proteins).
