Microbiology, genomics, and clinical significance of the Pseudomonas fluorescens species complex, an unappreciated colonizer of humans

Abstract

Pseudomonas fluorescens is not generally considered a bacterial pathogen in humans; however, multiple culture-based and culture-independent studies have identified it at low levels in the indigenous microbiota of various body sites. With recent advances in comparative genomics, many isolates originally identified as the "species" P. fluorescens are now being reclassified as novel Pseudomonas species within the P. fluorescens "species complex." Although most widely studied for its role in the soil and the rhizosphere, P. fluorescens possesses a number of functional traits that provide it with the capability to grow and thrive in mammalian hosts. While significantly less virulent than P. aeruginosa, P. fluorescens can cause bacteremia in humans, with most reported cases being attributable either to transfusion of contaminated blood products or to use of contaminated equipment associated with intravenous infusions. Although not suspected of being an etiologic agent of pulmonary disease, there are a number of reports identifying it in respiratory samples. There is also an intriguing association between P. fluorescens and human disease, in that approximately 50% of Crohn's disease patients develop serum antibodies to P. fluorescens. Altogether, these reports are beginning to highlight a far more common, intriguing, and potentially complex association between humans and P. fluorescens during health and disease.

Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Figures

FIG 1

Functional range and environmental niches of the Pseudomonas genus, highlighting the broad distribution of the P. fluorescens species complex. Members of the P. fluorescens species complex are successful colonizers in a wide range of environments and habitats due to diverse functional abilities. (Reprinted from reference with permission of John Wiley and Sons [copyright 2011 Federation of European Microbiological Societies].)

FIG 2

Species diversity within the P. fluorescens species complex. Mulet et al. generated a phylogenetic tree from 107 Pseudomonas type strains, based on concatenated analysis of the 16S rRNA, gyrB, rpoB, and rpoD genes, with Cellvibrio japonicum Ueda107 included as the outgroup (74). The bar indicates sequence divergence. (Reproduced from reference with permission of John Wiley and Sons [copyright 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.]. The names of the Pseudomonas species that have been included in the P. fluorescens species complex were added to the original figure.)

FIG 3

Scanning electron micrograph of P. fluorescens. (Photo reprinted with permission of Science Source.)

FIG 4

Phylogenetic tree of 38 Pseudomonas type strains, based on a concatenated nine-gene MLST analysis. The strains selected have full-genome sequences available through public databases. The MLST analysis was performed using nine housekeeping genes (encoding DnaE, PpsA, RecA, RpoB, GyrB, GuaA, MutL, PyrC, and AcsA), with E. coli strain K-12 used as the outgroup. A maximum likelihood tree was calculated in the online version of MAFFT (209, 210) and visualized with the software program Archaeopteryx (211). The confidence intervals after 1,000 bootstrap resamplings are indicated in red, and the branch distances are indicated in black. The bar indicates sequence divergence. P. fluorescens clade destinations are based on those proposed previously (49).

FIG 5

Phylogenetic tree of 38 Pseudomonas type strains, based on the V3-V5 region sequence of the 16S rRNA gene (V3 primer, positions 442 to 492; and V5 primer, positions 822 to 879 [numbered according to the E. coli 16S rRNA gene map]). The strains selected have full-genome sequences available through public databases. The V3-V5 sequence primers (212) were aligned to each genome by using DNAstar SeqBuilder software. A maximum likelihood tree was calculated in the online version of MAFFT (209, 210) and visualized with the software program Archaeopteryx (211). The confidence intervals after 1,000 bootstrap resamplings are indicated in red, and the branch distances are indicated in black. The bar indicates sequence divergence.

FIG 6

Scanning electron micrographs of P. fluorescens biofilms. For these photomicrographs, Baum et al. prepared and cryopreserved 14-day biofilms from P. fluorescens EvS4-B1 monocultures (56). (A) Fibrillary structures made up of twisted fibers (arrow). Bar = 1 μm. (B) Flat sheets of material (arrowheads), with some of the sheets wrapped around other structures (arrow). Bar = 20 μm. (C) The inside core of the “wrapped” structures, consisting of bacteria (B) embedded in an extracellular matrix of particulate matter, and a thin sheet of material (arrow). Bar = 1 μm. (D) The outer sheet (arrowheads), which envelops an inner core consisting of fibers forming irregular network-like structures (arrows). Bar = 10 μm. (E) Network consisting of fibers arranged in a periodic pattern, with bacteria (arrows) dispersed throughout the network. Bar = 2 μm. (F) A sheet of material (S), consisting of extracellular material and dead cells, covering and attaching to the fiber network and including associated bacteria (B) and particulate matter (P). Bar = 2 μm. (Reprinted from BMC Microbiology [56] under a Creative Commons license [http://creativecommons.org/licenses/by/2.0/].)

FIG 7

Type III secretion systems in P. fluorescens. The components and structures of the SPI-I and Hrp1 systems are shown, with lists of the corresponding strains in which these systems have been identified.