Drug treatments and vaccine designs against the opportunistic human pathogen Pseudomonas aeruginosa have multiple issues, all associated with the diverse genetic traits present in this pathogen, ranging from multi-drug resistant genes to the molecular machinery for the biosynthesis of biofilms. Several candidate vaccines against P. aeruginosa have been developed, which target the outer membrane proteins; however, major issues arise when attempting to establish complete protection against this pathogen due to its presumably genotypic variation at the strain level. To shed light on this concern, we proposed this study to assess the P. aeruginosa pangenome and its molecular evolution across multiple strains. The P. aeruginosa pangenome was estimated to contain more than 16,000 non-redundant genes, and approximately 15 % of these constituted the core genome. Functional analyses of the accessory genome indicated a wide presence of genetic elements directly associated with pathogenicity. An in-depth molecular evolution analysis revealed the full landscape of selection forces acting on the P. aeruginosa pangenome, in which purifying selection drives evolution in the genome of this human pathogen. We also detected distinctive positive selection in a wide variety of outer membrane proteins, with the data supporting the concept of substantial genetic variation in proteins probably recognized as antigens. Approaching the evolutionary information of genes under extremely positive selection, we designed a new Multi-Locus Sequencing Typing assay for an informative, rapid, and cost-effective genotyping of P. aeruginosa clinical isolates. We report the unprecedented pangenome characterization of P. aeruginosa on a large scale, which included almost 200 bacterial genomes from one single species and a molecular evolutionary analysis at the pangenome scale. Evolutionary information presented here provides a clear explanation of the issues associated with the use of protein conjugates from pili, flagella, or secretion systems as antigens for vaccine design, which exhibit high genetic variation in terms of non-synonymous substitutions in P. aeruginosa strains.

Methyltransferases play a fundamental role in aminoglycoside resistance of Gram-negative bacteria, and some of its mechanisms were described in the past years, especially in Escherichia coli; however, it remains unsolved for other resistant bacteria such as Pseudomonas aeruginosa. Despite hurdles to determine resistance acquisition, high-throughput approaches (genomics, transcriptomics, and proteomics) have allowed data mining and analysis in a systemic way. Likewise, bioinformatics modelling of homologous genes or proteins has permitted to elucidate the emerging resistance in this pathogen. P. aeruginosa is a bacterial resistance treat since practically all known resistance mechanisms can be described using this model, particularly RNA methyltransferases. The RNA methyltransferases perform methylation or demethylation of ribosomal RNA to allow or restrict the antibiotic resistance development. The Kgm and Kam methyltransferases families are found in P. aeruginosa and confer resistance to several aminoglycosides. Loss of native methylations may also confer a resistant phenotype. The P. aeruginosa RsmG has high structural homology with Thermus aquaticus protein. Today, molecular data will promote a new paradigm on antibiotic therapy for treatment against P. aeruginosa. This chapter provides an overview of what role P. aeruginosa’s methyltransferases play in antibiotic resistance, induced by methylation or demethylation in the ribosome.

Antibiotics were the world’s great therapeutic hope after the Second World War, but today, unmonitored use has become one of the greatest risks for humanity. Without overestimation, one of the last scientific books on antibiotics was entitled: Antibiotics, the perfect storm. Before to environmental contamination by antibiotics, the pathogens got resistant to them. Because of the radical changes that antibiotics have brought about, they can generate new resistant bacteria in the environment that were previously harmless. These microorganisms will be exposed to concentrations of antibiotics never reached or will be exposed to unknown molecules that, for many of them, in certain environments, have never been exposed before. Initially, many of these antibiotics did not penetrate soils with high agricultural production, but in the following decades, they were even interspersed into crops. Nowadays, hundreds of tons of antibiotics are dumped into rivers and the sea. Many hospitals have water treatment facilities to prevent significant contamination, but not all companies, farms, and hospitals in developed, emerging, or poor countries apply wastewater treatment. Antibiotics are incorporated into wild microorganisms and plants, triggering a broad “unnatural” resistance, which will rapidly incorporate this information into the genome of other pathogenic microorganisms by horizontal transfer. On the other hand, antibiotics could be incorporated into drinking water and water intended for human or agricultural consumption that travels without being detected or monitored. This review covers the most important aspects of environmental pollution by antibiotics.

This review summarizes the most important reports about Pseudomonas aeruginosa pangenome. Pan-genomics has tackled some fundamental concerns in pathogenic bacteria. PATRIC and other databases, store more than 9000 P. aeruginosa genomes. This data mining is an opportunity to develop discoveries related to antibiotic resistance, virulence, pathogenicity, fitness, and evolution, among others. Observing the different pangenomes of P. aeruginosa, it is concluded that this species has an open pangenome, and its accessory genome is larger than the central genome. HGT is one important source for P. aeruginosa genome. In recent years various authors developed P. aeruginosa pangenomes, from works with five genomes to more than 1300 genomes. This last work analyzed 54,272 genes, and they found a short and tiny core genome (only 665 genes). Other research with lesser strains or genomes identified a core genome bigger, almost 20% of the pangenome. Nevertheless, the total work proves that the accessory plus unique genome is larger than the core genome in P. aeruginosa.

Background: Drug treatments and vaccine designs against the opportunistic human pathogen Pseudomonas aeruginosa have multiple issues, all associated with the diverse genetic traits present in this pathogen, ranging from multi-drug resistant genes to the molecular machinery for the biosynthesis of biofilms. Several candidate vaccines against P. aeruginosa have been developed, which target the outer membrane proteins; however, major issues arise when attempting to establish complete protection against this pathogen due to its presumably genotypic variation at the strain level. To shed light on this concern, we proposed this study to assess the P. aeruginosa pangenome and its molecular evolution across multiple strains. Results: The P. aeruginosa pangenome was estimated to contain more than 16,000 non-redundant genes, and approximately 15% of these constituted the core genome. Functional analyses of the accessory genome indicated a wide presence of genetic elements directly associated with pathogenicity. An in-depth molecular evolution analysis revealed the full landscape of selection forces acting on the P. aeruginosa pangenome, in which purifying selection drives evolution in the genome of this human pathogen. We also detected distinctive positive selection in a wide variety of outer membrane proteins, with the data supporting the concept of substantial genetic variation in proteins probably recognized as antigens. Approaching the evolutionary information of genes under extremely positive selection, we designed a new Multi-Locus Sequencing Typing assay for an informative, rapid, and cost-effective genotyping of P. aeruginosa clinical isolates. Conclusions: We report the unprecedented pangenome characterization of P. aeruginosa on a large scale, which included almost 200 bacterial genomes from one single species and a molecular evolutionary analysis at the pangenome scale. Evolutionary information presented here provides a clear explanation of the issues associated with the use of protein conjugates from pili, flagella, or secretion systems as antigens for vaccine design, which exhibit high genetic variation in terms of non-synonymous substitutions in P. aeruginosa strains.