Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species

Abstract

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.

Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria

“…This extensive diversity results in variable metabolic capacity [67], potentially supplementing individual strains with additional ecological range and providing even more opportunities for genetic exchange. Direct comparison of population structures are difficult due to different sampling and analysis strategies [66]; nonetheless it is clear that the other Gram negative opportunists also have many deep branching lineages and large pan--genomes [9,[68][69][70][71]. Coding capacity and genome size are easy to compare using public genome data (Fig 2C): K. pneumoniae has a significantly larger genome than the other Enterobacteriaceae species considered here (mean 5.7 Mbp, 5455 protein coding genes, vs 5.1 Mbp/4915 genes in E. coli and 5.0 Mbp/4680 genes in E. cloacae; p<1x10 --15 using two--sided t--test), which may help equip K. pneumoniae for survival in a broader range of niches.…”

Comparative analysis of the volatile metabolomes ofPseudomonas aeruginosaclinical isolates

“…Additionally, P. aeruginosa is a broad-host range opportunistic pathogen, infecting plants, invertebrates, and animals (including humans), and is implicated in a wide range of clinical infections including otitis media, wound infections, and acute and chronic pneumonias [3, 4]. Seminal genomics analyses over the past decade attribute P. aeruginosa’s capabilities to a relatively large genome (mean size of 6.6 Mbp [5]), containing an average of 6175 genes per isolate [6], as well as its disproportionately large number of regulatory elements, comprising approximately 10 % of an isolate’s genes [5]. More recently, several medium- and large-scale P. aeruginosa genomics studies (< 20, and > 100 genomes, respectively) [6–11] have provided a more nuanced view of the genetic capacity of the species.…”

“…Seminal genomics analyses over the past decade attribute P. aeruginosa’s capabilities to a relatively large genome (mean size of 6.6 Mbp [5]), containing an average of 6175 genes per isolate [6], as well as its disproportionately large number of regulatory elements, comprising approximately 10 % of an isolate’s genes [5]. More recently, several medium- and large-scale P. aeruginosa genomics studies (< 20, and > 100 genomes, respectively) [6–11] have provided a more nuanced view of the genetic capacity of the species. In one of the largest studies to-date, Mosquera-Rendon and colleagues analyzed 181 genomes, and identified 16,820 non-redundant genes, constituting the predicted P. aeruginosa pan-genome.…”

“…In one of the largest studies to-date, Mosquera-Rendon and colleagues analyzed 181 genomes, and identified 16,820 non-redundant genes, constituting the predicted P. aeruginosa pan-genome. Only 15 % of the genes ( n = 2305) were identified as core genes, defined as being present in > 95 % of sequenced isolates [6]. More than half were accessory genes, defined as being present in 5–95% of P. aeruginosa genomes, and the remainder (31%) consisted of rare genes, harbored by less than 5% of the strains.…”

“…More than half were accessory genes, defined as being present in 5–95% of P. aeruginosa genomes, and the remainder (31%) consisted of rare genes, harbored by less than 5% of the strains. Therefore, genetic diversity across strains likely contributes to P. aeruginosa’s metabolic diversity and niche ubiquity [6, 7]. …”