Pseudomonas aeruginosa exhibits frequent recombination, but only a limited association between genotype and ecological setting

Abstract

Pseudomonas aeruginosa is an opportunistic pathogen and an important cause of infection, particularly amongst cystic fibrosis (CF) patients. While specific strains capable of patient-to-patient transmission are known, many infections appear to be caused by unique and unrelated strains. There is a need to understand the relationship between strains capable of colonising the CF lung and the broader set of P. aeruginosa isolates found in natural environments. Here we report the results of a multilocus sequence typing (MLST)-based study designed to understand the genetic diversity and population structure of an extensive regional sample of P. aeruginosa isolates from South East Queensland, Australia. The analysis is based on 501 P. aeruginosa isolates obtained from environmental, animal and human (CF and non-CF) sources with particular emphasis on isolates from the Lower Brisbane River and isolates from CF patients obtained from the same geographical region. Overall, MLST identified 274 different sequence types, of which 53 were shared between one or more ecological settings. Our analysis revealed a limited association between genotype and environment and evidence of frequent recombination. We also found that genetic diversity of P. aeruginosa in Queensland, Australia was indistinguishable from that of the global P. aeruginosa population. Several CF strains were encountered frequently in multiple ecological settings; however, the most frequently encountered CF strains were confined to CF patients. Overall, our data confirm a non-clonal epidemic structure and indicate that most CF strains are a random sample of the broader P. aeruginosa population. The increased abundance of some CF strains in different geographical regions is a likely product of chance colonisation events followed by adaptation to the CF lung and horizontal transmission among patients.

Figure 1. Map (1∶136,268) of the Lower Brisbane River showing land use categories.

Figure 2. Rarefaction curves showing diversity by unique sequence type (ST) and Operational Taxonomical Unit (OTU).

OTUs contained closely related STs, which were separated by the mean pairwise distance of the population, 0.008 (23/2874 nucleotides).

Figure 3. Venn diagram showing the number of individual sequence types (STs) detected in each of the ecological niches.

C: STs detected in cystic fibrosis patients; Human non-CF: STs detected in non-cystic fibrosis patients; Animal: STs detected in animals; Environment: STs detected in environmental samples.

Figure 4. goeBURST Minimal Spanning Tree of the 499 typeable Pseudomonas aeruginosa isolates (n = 272 sequence types).

All sequence types (STs) were grouped up to the triple-locus variant level. Each circle corresponds to an individual ST and the dimensions of each circle are relative to the number of isolates belonging to that ST. Red, green, brown and blue circles represent isolates collected from patients with cystic fibrosis (CF), non-CF patients, animals and environmental samples, respectively. Whenever isolates of the same ST have a different ecological source, the number of isolates derived from the same source is proportional to the respective colour. Yellow coloured zones (labelled BG01 to BG05) represent the five predominant BURST groups that each consisted of three or more STs.

Figure 5. Phylogenetic tree constructed from 48 concatenated guaA, mutL, and nuoD sequences indicating a star-like phylogeny.

Figure 6. Population snapshot of the 1070 sequence types listed on the Pseudomonas aeruginosa PubMLST database (October 2011).

Dots represent sequence types (STs), and lines connect single-locus variants. The snapshot shows all BURST groups (connected STs), singleton STs, ancestral founders (blue STs), and subgroup founders (yellow STs). STs with green halos were detected in the current study only; STs showing pink halos were detected in the current study and elsewhere; STs with no halo were not detected in the current study. Line length and singleton ST placement is arbitrary.

Figure 7. eBURST diagram showing BURST Group 01 when all 1070 sequence types listed on the Pseudomonas aeruginosa PubMLST database (October 2011) were analysed.

Dots represent sequence types (STs), and lines connect single-locus variants. The diagram shows all ancestral founders (blue STs) and subgroup founders (yellow STs). STs with green halos were detected in the current study only; STs showing pink halos were detected in the current study and elsewhere; STs with no halo were not detected in the current study. Line length is arbitrary.