Environmental reservoirs for exoS+ and exoU+ strains of Pseudomonas aeruginosa

Abstract

Pseudomonas aeruginosa uses its type III secretion system to inject the effector proteins ExoS and ExoU into eukaryotic cells, which subverts these cells to the bacterium's advantage and contributes to severe infections. We studied the environmental reservoirs of exoS+ and exoU+ strains of P. aeruginosa by collecting water, soil, moist substrates and plant samples from environments in the Chicago region and neighbouring states. Whole-genome sequencing was used to determine the phylogeny and type III secretion system genotypes of 120 environmental isolates. No correlation existed between geographic separation of isolates and their genetic relatedness, which confirmed previous findings of both high genetic diversity within a single site and the widespread distribution of P. aeruginosa clonal complexes. After excluding clonal isolates cultured from the same samples, 74 exoS+ isolates and 16 exoU+ isolates remained. Of the exoS+ isolates, 41 (55%) were from natural environmental sites and 33 (45%) were from man-made sites. Of the exoU+ isolates, only 3 (19%) were from natural environmental sites and 13 (81%) were from man-made sites (p < 0.05). These findings suggest that man-made water systems may be a reservoir from which patients acquire exoU+ P. aeruginosa strains.

Figure 1

The phylogeny of environmental P. aeruginosa isolates. A maximum likelihood tree was generated from core genome alignments following removal of sequences under the influence of recombination. Isolates in red are exoU+, those in blue are exoS+, and the isolate in green is exoS−/exoU−. Reference strains PA14 (exoU+) and C-NN2 (clone c, exoS+) and three previously sequenced environmental isolates, M18 (Wu et al., 2011b), F9676 (Shi et al., 2015), and USDA-ARS-USMARC-41639 (Winsor et al., 2016), are shown in black.