**6. The open pangenome of** *P. aeruginosa* **pathogen**

As we defined in **Table 2**, an open pangenome increases when a new genome is added to the pangenome. In other words, the open pangenome is contrary to the closed pangenome, so there are changes when new genomes are added, and new strains provide new genes to the species pangenome. *P. aeruginosa was defined as an opened pangenome* [39]*. Likely, we will found continuously new strains with new genes.* As mentioned by Rouli et al. [8]: the sympatric species, present in a community, have large genomes and, thereby, an open pangenome, a high rate of HGT genes transfer, and several ribosomal operons, citing to Georgiades and Raoult [40], and Diene et al. [41]. The open pangenome of *P. aeruginosa* has a large accessory genome highly mobile with a short core genome conserved, interchanging duplication and translocations, where HGTs enter (insertions) and go out (deletions). The evolution mechanisms as

*DOI: http://dx.doi.org/10.5772/intechopen.108187 The Pangenome of* Pseudomonas aeruginosa

#### **Figure 3.**

*Open pagenome of P. aeruginosa. The bacterial genome of P. aeruginosa has a large circular chromosome. The pangenome in total strains is divided by two regions in each chromosome, one conserved in overall strains (core genome) and the other not shared by the overall strains (accessory genome). This open pangenome among those strains has a large accessory genome highly mobile with a short core genome conserved. In the pangenome inside the species, different strains interchange HGTs, which enter (insertions) and go out (deletions). Both the core and accessory genomes undergo duplications and translocations. The evolution mechanisms such as selection, genetic drift, and others play a central role inside the genome of the strain population.*

selection and genetic drift, play a central role inside the genome of the strain population (see **Figure 3**).

The *P. aeruginosa* genome has G + C content, ranging from 65 to 67%, with a size of 5.5–7 Mbp. It has a single circular chromosome and a variable number of plasmids [42]. The genome encodes a considerable repertoire of transporters, transcriptional regulators, and two-component regulatory systems, which reflects its metabolic diversity to utilize a broad range of nutrients. Additional works agree that *P. aeruginosa* has an open pangenome [39, 43]. Mosquera-Rendon et al. [4] identified distinctive positive selection in a variety of outer membrane proteins, with the data supporting the concept of genetic variation in *P. aeruginosa* proteins likely recognized as antigens. Hilker et al. [30], comparing single nucleotide polymorphism synteny indicated unrestricted gene flow between clonal complexes by recombination. Also, comparing the genomes point out that the differential genetic repertoire of clones maintains a habitat-independent gradient of virulence in the *P. aeruginosa* population.

#### **7. The size of** *P. aeruginosa* **pangenome**

There is a large variability in the size *of the P. aeruginosa* genome. For example, the RW109 strain has 7.049.347 bp and 6829 genes, and the PAO reference strain has 6.264.404 bp and 5697 genes. More than 700.000 bp and 1100 genes of difference between both strains, in other words, the core genome between both strains could be lower than 5697 genes, and the accessory genome could probably exceed more than 1100 genes, ignoring the repeated genes and excluding plasmids or other mobile elements. This simple exercise without robustness, and data processing without software, is less wise than Sharma et al. [3], using only five genomes, which shows the requirement to improve the level of comparison between two strains to reach the data support and confident results in pangenomics. It is the same exercise when we

compare two phenotypes in metabolism or antibiotic resistance. We look by a cylinder at the wide world of the genome and its interactions, looking at a pair of genes or products, sometimes ignoring that two strains can reach the same product in two different ways. Nevertheless, Hilker et al. [30] identified 5892-7187 open reading frames (with a median of 6381 ORFs) in the *P. aeruginosa* pangenome of representative 20 strains, ranging from 6.4 to 7.4 Mbp large genomes with a core genome with approximately 4000 genes. Of course, 20 genomes is a small study for a pangenome, but there are 15 most frequent clonal complexes of the *P. aeruginosa* population.

Now, thinking about again the reported pangenomes: Sharma et al. [3] 5 genomes, Fischer et al. [5] 100 genomes, Ding et al. [7] 153 genomes, Mosquera-Rendón et al. [4] 181 genomes, and Freschi et al. [6] used 1311 genomes. It is clear that Freschi et al.'s study has the maximum number of samples and likely the best pangenome results for the *P. aeruginosa* species. However, pangenomics are not one study with the highest catalogs or number of samples. Those essential five studies have interesting matches: the accessory genome in *P. aeruginosa* is bigger than core genomes, and, thereby, *the P. aeruginosa* genome is an open pangenome, as we continue to emphasize.

Taking together the data extracted from Ding et al. [7], shown in **Figure 2** for *P. aeruginosa,* performing the same analysis for other pangenomes species, such as *Clostridium botulinum, Escherichia coli, Yersinia pestis, and Mycobacterium tuberculosis*. And taken other data from the *Mycoplasma genitalum* from Corredor & Muñoz-Gómez [10], we can compare the pangenomes of these species with each other. It is observed that *P. aeruginosa* has a smaller core genome than *Y. pestis, M. tuberculosis*, and *M. genitalum*, although greater than *E. coli* and *C. botulinum* see **Figure 4**.

#### **Figure 4.**

*Comparing the size of P. aeruginosa with other bacterial pathogens species. The comparison of P. aeruginosa pangenome (navy blue and red) with Clostridium botulinum, Escherichia coli, Yersinia pestis, Mycobacterium tuberculosis and Mycoplasma genitalum (turquoise blue and rose). Data obtained from PanX web.*

## **8. The pangenome of MDR** *P. aeruginosa*

From 2006 multidrug-resistant (MDR*) P. aeruginosa* was listed, also pandrugresistant (PDR) [44]. The term PDR was inappropriately used in all five studies that used it and within a variety of genotypic and phenotypic characteristics. The terms MDR and PDR of *P. aeruginosa* likely cause confusion to researchers and clinicians. Falagas et al. [44] believe that at least an extended and accepted definition for the *Acinetobacter baumannii* and *P. aeruginosa* PDR should be uniformly used worldwide. Today, it is clear that MDR is a perfect term for *P. aeruginosa* antibiotic multiresistant, and probably PDR (resistance to all antibiotics) was an inconsistent term. However, the PDR acronym coins directly with pangenome, in the sense that MDR *P. aeruginosa* could be studied from pangenomics to solve the MDR problem.

The growth of MDR *P. aeruginosa* results from the extraordinary capacity of this bacterium for developing resistance through chromosomal mutations (probably in the core genome). In this species, there are increasing prevalence of transferable resistance elements as HGT genes (on the accessory and unique genome), particularly genes encoding carbapenemases or extended-spectrum β-lactamases (ESBLs) resistance. Given that *P. aeruginosa* has a nonclonal epidemic population structure and also has so much quantity of rare and unrelated genotypes that are recombining at high frequency [45].

As was mentioned previously, Freschi et al. [6], who developed the biggest pangenome of *P. aeruginosa*, initially predicted antimicrobial resistant gene profiles for 389 *P. aeruginosa* strains using the resistance gene identifier (RGI), and they found 334 unique profiles. Analysis of 1311 strains confirmed that there is, therefore, an immense variation in *P. aeruginosa* antimicrobial resistance (AMR) gene profiles, with the most frequent profile found in only 6% of the strains.

### **9. Antibiotic resistome**

The antibiotic resistome of some organisms is the set of antibiotic-resistant genes used to resist the high concentration of some antibiotics [46]. Perhaps, the *P. aeruginosa* resistome has longtime studied [47], and now even more so with the development of next generations sequencing, databases, and the increase of pangenomics. Postgenomics data has the objective of developing the decryption of antibiotic resistome. Mercy to the other chemical techniques, today, we distinguish if the antibiotic concentration is increasing in the environment. This will have one effect on both the diversity and the abundance of resistome genes in the *P. aeruginosa* MDR. Selection for cells that carry resistance determines the addition of their relative abundance, and thus increases the more additional genes that confer resistance [48]. Fortunately, there are still susceptible strains to antibiotics, which will allow comparing those with resistant strains.

The opened pangenome of *P. aeruginosa* shows wide diversity of genes, plasmids, and mobile elements, which establish the resistome. For example, in the three reference strains, PAO1, LESB58, and PA14 are treated with seven resistant drugs exhibit phenotypic variability in their response to 27% of the antibiotics tested. For instance, the resistome annotation of 672 *P. aeruginosa* strains identified 147 loci associated with antibiotic resistance. These loci are composed mainly of acquired genomic elements and intrinsic genes [49].

### **10. The HGT in** *P. aeruginosa* **pangenome**

In pangenomes of Freschi et al. [6] they study the role of HGTs in the evolution of the *P. aeruginosa* genome. They observed the flexible genes (accessory and unique genomes) and determined the proportion of these genes that were found in a single group of isolates, as well as the balance of flexible genes shared between multiple groups. Freschi et al. [6] found peculiar results because 10,515 genes (40%) of the 26,420 flexible genes were present in one group only and, on the contrary, 83 genes found in 3 groups of isolates were present in more than 90% of the isolates of a single group and, were not found in the other groups. The maximum of flexible genes was, thus, 15,905 or 60% present in isolates belonging to multiple groups; one result provides a higher estimate of the number of genes that could potentially be related to HGT episodes. They estimated the prevalence of phages because phages are often in connection with HGT events.
