**3. Structure of the** *H. pylori* **PZ**

*H. pylori* is considered to have a high genetic diversity due to the presence or absence of genes, which indicates the adaptation and coevolution of the pathogen within different populations worldwide [5, 6]. Recently, advances in DNA sequencing technology have enabled the comparison of hundreds of sequences from the genomes of related bacteria. These comparative genome analyses between species have led to a concept that encompasses all of the genetic content within a bacterial species. This concept is referred to as a "pan-genome", which is defined as the complete genetic repertoire of a specific species, composed of both the central

Comparative genomic studies of *H. pylori* began with the sequencing of strains J99 and 26,695. The *H. pylori* genome is approximately 1.6 million base pairs (1.6 Mb) in size, containing 1500 open reading frames (ORFs) and approximately 1500 protein-coding genes, with a G + C content of approximately 39%. Sequencing of these two strains showed that approximately 6–7% of the genes present in one strain are absent in the other. These genes are referred to as strain-specific genes, almost half of which are located in hypervariable regions within the *H. pylori* genome. Such regions are called plasticity zones (PZs), based on the variability of gene content between different isolates of *H. pylori*. These regions have a lower G + C content than the rest of the genome (34–35%), which suggests horizontal transfer [8]. The *cag* pathogenicity

Several studies have shown that *H. pylori* strains gain and lose genes during an infection, which suggests that a continuous genetic flow occurs, primarily within the PZ [4, 6, 10, 11]. The frequency of the PZ genes, notably *jhp0940*, *jhp0945*, *jhp0947* and *jhp0949*, has been studied among *H. pylori* isolates from different geographical regions, which has demonstrated that some of these genes are associated with disease. Currently, some of these PZs have roles in *H. pylori* pathogenesis and are included in one of the three categories of *H. pylori* virulence

After strains J99 and 26695 were sequenced, the first DNA microarray could be designed [13], allowing the first genotyping studies of diverse strains of *H. pylori* to be conducted*.* The first study compared 15 *H. pylori* isolates and observed that 362 genes (22%) were variable among the strains, which were called strain-specific genes. Subsequently, another study explored the genomic diversity of *H. pylori* isolates from children and adults who presented a single or a mixed infection (the presence of more than one strain). The number of variable genes in individuals with a mixed infection was found to be higher than that in individuals infected with a single strain. No difference was observed in the number of strain-specific genes between strains from children and adults [14]. However, a study of 56 strains from different geographical regions observed that 25% of the genomic content between these strains corresponded to strain-specific genes [6]. The genetic content of the strains has also been correlated with their pathogenesis in an animal model [4, 15]. Moreover, Romo-González et al. [16] identified and compared the differences in the genetic content of strains isolated from Mexican patients with non-atrophic gastritis, duodenal ulcers and gastric cancer. The authors observed that the core genome shared by these

genome and the accessory genome, also known as the dispensable genome [7].

island (PAI) is a region exhibiting this reduced G + C content [9].

78 Helicobacter Pylori - New Approaches of an Old Human Microorganism

classified by Yamaoka [12].

**2. Genotyping of** *H. pylori* **strains**

The PZ of strain J99 is the most studied and best characterised hypervariable region within the *H. pylori* genome. In the J99 *H. pylori* strain, the PZ is a continuous region from *jhp0916* to *jhp0961* [8]. Of the 48 ORFs that compose the PZ in strain J99, only six are present in strain 26695, and 10 are present in strain HPAG1. The PZs in strains J99 and 26695 are 45 and 68 kb in length, respectively. The PZ contains genes of unknown function as well as those encoding restriction-modification systems, topoisomerases, integrons, secretion systems, outer membrane proteins and transposons, the latter of which can be inserted into a genome without recombination. This insertion facilitates the propagation of transposons among bacterial species. These transposons are important because they can generate genomic deletions and rearrangements and even alter the expression of genes contiguous to their insertion site [17–19].

Kersulyte et al. [20] studied the nature of the PZ in the *H. pylori* genome by sequencing this locus in other strains and locating this area in strains that had been recently deposited in GenBank. The authors observed that the PZ is composed of inserted transposable elements

**Figure 1.** Plasticity zone of reference strain *Helicobacter pylori* J99 (*jhp0917-jhp0951*), figure adapted from [20]. This PZ is located between the *ftsZ* (*jhp0913*) gene and the 5S, 23S rRNA gene pair and is composed of TnPZ fragments: type 1 (*jhp0917-jhp0924*), type 1b (*jhp0944-jhp0951*; *jhp0925*, *jhp0926,* potentially part of *jhp0927-jhp0929* (*orfQ*) as well), and type 2 (*jhp0943-jhp0930,* potentially part of *orfQ* as well). Blue and green boxes indicate ORFs exclusive to J99 but not 26695 (another reference strain); black boxes indicate ORFs found in both strains; grey boxes indicate ORFs located between the *ftsZ* gene and the 5S, 23S rRNA gene pair that do not belong to the TnPZ.

that are flanked by discrete sequences of 5′AAGAATG and are each referred to as a TnPZ or "transposon, plasticity zone". Each TnPZ generally contains genes encoding type IV secretion proteins (tfs3), *xerT*, an ORF coding for a protein with helicase and DNA methylase domains and additional ORFs. Among the studied strains, several types of TnPZs with different gene arrangements or DNA sequence variations were observed and classified as type 1, type 1b and type 2 TnPZs. The genes *jhp0945*, *jhp0947* and *jhp0949* are located on a type 1b TnPZ, and *jhp0940* is located on a type 2 TnPZ in strain J99 (see **Figure 1**).

the gene [23]. In addition, no association was found between this gene and disease in isolates from Chinese patients with chronic active gastritis, duodenal ulcers or gastric cancer [24].

*Helicobacter pylori* Genes *jhp0940*, *jhp0945*, *jhp0947* and *jhp0949* are Associated with Gastroduodenal Disease

http://dx.doi.org/10.5772/intechopen.81290

A study in India observed less than a 20% prevalence of the *jhp0940* gene among *H. pylori* isolates [22]. However, in other isolates from India, the reported *jhp0940* prevalence was higher than 80% [25]. In Argentina, the frequency of the *jhp0940* gene was reported as 74.6%, and the frequency in isolates from individuals with chronic gastritis and peptic ulcer disease was similar, indicating no association with a specific disease [26]. However, Rizwan et al. [25] found no relationship between clinical results and the prevalence of *jhp0940* or the cag PAI in isolates from seven countries (India, South Africa, Japan, Costa Rica, Peru, France and Spain). The highest prevalence of this gene was observed in isolates from India, South Africa and

However, Yakoob et al. [27] and Gholizade Tobnagh et al. [28] reported an association between *jhp0940* and gastric ulcers and gastric cancer, respectively. In general, the prevalence of this gene is lower than that of *jhp0945*, *jhp0947* and *jhp0949* in isolates from the different geographical regions that have been studied. There appears to be a difference between the presence of PZ genes between isolates from children and adults. Romo-González et al. [29] observed that the prevalence of *jhp0940* in *H. pylori* isolates from children is higher than that in adults and that the presence of the specific gene patterns (including *jhp0940-jhp0945-jhp0947*-*jhp0949* and *jhp0940*-*jhp0947*-*jhp0949*) is more common in isolates from children than in adults. Therefore, these authors suggest that this locus is more integrated in the early stages of infection, which could contribute to the bacterial virulence and evolution of the infection. These authors found no association between the presence of these four PZ-associated genes and the presence of

Romo-González et al. evaluated the *in vitro* expression of four PZ-associated genes in isolates from children and adults and observed the expression of only *jhp0945*, *jhp0947* and *jhp0949*, without significant differences among the expression of these three genes between the isolates obtained from children and adults. However, a correlation was observed among the expres-

A possible explanation for the discordant results regarding the prevalence of *jhp0940* in different geographical regions is that geographical diversity exists in the sequence of this gene that does not allow for its identification with a single pair of primers. Another potential reason is that the absence of this gene in adult isolates is due to the loss of this gene during infection.

Studies on the prevalence of *jhp0945*, *jhp0947* and *jhp0949* among *H. pylori* isolates of different geographical origins have proposed that these genes are disease markers, suggesting that they could play a role in the pathogenesis of *H. pylori* [12]. This relationship was discovered in Costa Rica, where the prevalence of 21 ORFs present in the PZ of the J99 strain (*jhp0914-jhp0961*)

**5. The PZ-associated genes** *jhp0945***,** *jhp0947* **and** *jhp0949* **and their** 

France, in contrast to isolates from Spain, where less than 10% contained this gene.

*cagA*, cag PAI or *dupA*.

sion of these three genes (unpublished data).

**relationship with gastroduodenal disease**
