Draft genomes of 12 host-adapted and environmental isolates ofPseudomonas aeruginosaand their positions in the core genome phylogeny

Abstract

Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen particularly associated with the inherited disease cystic fibrosis (CF). Pseudomonas aeruginosa is well known to have a large and adaptable genome that enables it to colonise a wide range of ecological niches. Here, we have used a comparative genomics approach to identify changes that occur during infection of the CF lung. We used the mucoid phenotype as an obvious marker of host adaptation and compared these genomes to analyse SNPs, indels and islands within near-isogenic pairs. To commence the correction of the natural bias towards clinical isolates in genomics studies and to widen our understanding of the genomic diversity of P. aeruginosa, we included four environmental isolates in our analysis. Our data suggest that genome plasticity plays an important role in chronic infection and that the strains sequenced in this study are representative of the two major phylogenetic groups as determined by core genome SNP analysis.

Diversity of environmental and clinical Pseudomonas aeruginosa isolates

“…However, for those studies which do comment, isolates with unique sequence types comprise the majority of strains (Head and Yu 2004;Manos et al 2013). Rather than demonstrating a loss of motility based on infection status, I have shown that isolates from chronically infected patients, with a unique sequence type more closely resembled isolates from other clinical settings with moderate to high levels of positive motility reported.Similar to this study, a number of published studies have included non-CF and/or environmental isolates for comparison (Cullen et al 2015;Head and Yu 2004;Jeukens et al 2014; 119 Mahenthiralingam et al 1994;O'May et al 2006). Results from the current work are concordant with these earlier studies; both demonstrating enhanced motility among isolates arising from ecological niches outside of CF.…”

“…Typically, most studies have relied on using the PAO1 strain or knockout mutants as comparators (Carter et al 2010;Jeukens et al 2014; Jiricny et al 2014; Kukavica-Ibrulj et al 2008;Manos et al 2008;Manos et al 2013;O'May et al 2006;Yang et al 2011). While a standard needs to be included to account for inter-run variation and to set a baseline for isolate comparison, the expression and capabilities of this strain needs to be known in the context of the broader population so that degrees of change from this 37 baseline can be interpreted correctly.…”

“…In 18 addition, deletions, mutations and rearrangements also occur within the accessory genes. It has been noted that the accessory genome encodes various genes that enable increased survival and niche adaptation within specific strains (Dettman et al 2013; Kung et al 2010;Stewart et al 2014). …”

“…Overall, these studies demonstrate that during chronic infection, P. aeruginosa adopts a biofilm mode of growth, but there appears to be some variability in each strain's biofilm forming capacity. Likewise, there seems to be some inter-strain variation with respect to motility (Jeukens et al 2014; Winstanley et al 2009).However, it must be noted that in most of these studies the overall number of isolates (in particular,those of environmental origin) tested and the diversity of the strains used was limited. Typically, most studies have relied on using the PAO1 strain or knockout mutants as comparators (Carter et al 2010;Jeukens et al 2014; Jiricny et al 2014; Kukavica-Ibrulj et al 2008;Manos et al 2008;Manos et al 2013;O'May et al 2006;Yang et al 2011).…”

“…Likewise, there seems to be some inter-strain variation with respect to motility (Jeukens et al 2014; Winstanley et al 2009).…”