Abstract
The diversification of microbial populations may be driven by many factors including adaptation to distinct ecological niches and barriers to recombination. We examined the population structure of the bacterial pathogen Pseudomonas aeruginosa by analyzing whole-genome sequences of 739 isolates from diverse sources. We confirmed that the population structure of P. aeruginosa consists of two major groups (referred to as Groups A and B) and at least two minor groups (Groups C1 and C2). Evidence for frequent intragroup but limited intergroup recombination in the core genome was observed, consistent with sexual isolation of the groups. Likewise, accessory genome analysis demonstrated more gene flow within Groups A and B than between these groups, and a few accessory genomic elements were nearly specific to one or the other group. In particular, the exoS gene was highly overrepresented in Group A compared with Group B isolates (99.4% vs. 1.1%) and the exoU gene was highly overrepresented in Group B compared with Group A isolates (95.2% vs. 1.8%). The exoS and exoU genes encode effector proteins secreted by the P. aeruginosa type III secretion system. Together these results suggest that the major P. aeruginosa groups defined in part by the exoS and exoU genes are divergent from each other, and that these groups are genetically isolated and may be ecologically distinct. Although both groups were globally distributed and caused human infections, certain groups predominated in some clinical contexts.
Highlights
Pseudomonas aeruginosa is a gram-negative bacterium that is remarkable for its worldwide ubiquity and extensive environmental distribution in soil, water, and plant matter as well as its ability to cause a variety of opportunistic infections in humans
Most P. aeruginosa isolates segregate into two large phylogenetic groups Genomic sequences of 730 P. aeruginosa isolates representing all complete and draft genome sequences available as of February 3, 2015 were downloaded from the NCBI FTP server
As the exoU gene is present in the genomic island PAPI-2 (He, et al 2004; Morales-Espinosa, et al 2012), we examined the distribution of other portions of PAPI-2 in the isolates
Summary
Pseudomonas aeruginosa is a gram-negative bacterium that is remarkable for its worldwide ubiquity and extensive environmental distribution in soil, water, and plant matter as well as its ability to cause a variety of opportunistic infections in humans. As next-generation sequencing has become more affordable and widely available, P. aeruginosa population studies have started using whole-genome comparisons between increasing numbers of isolates (Freschi, et al 2015; Freschi, et al 2019; Hilker, et al 2015; Marvig, et al 2015; Stewart, et al 2011; Williams, et al 2015). In these phylogenetic analyses, isolates within the populations examined have generally clustered into two large clades and one small clade. The genetic differences underlying the observed population structure and possible mechanisms for these differences have not yet been defined
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