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Ishii H, Kushima H, Koide Y, Kinoshita Y. Pseudomonas fluorescens pneumonia. Int J Infect Dis 2024; 140:92-94. [PMID: 38218379 DOI: 10.1016/j.ijid.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/01/2024] [Accepted: 01/10/2024] [Indexed: 01/15/2024] Open
Abstract
Pseudomonas fluorescens (P. fluorescens) is not generally considered a bacterial pathogen in humans; however, multiple culture-based and culture-independent studies have identified it in the indigenous microbiota of multiple body sites. We herein report a rare case of pneumonia caused by P. fluorescens. A man in his 80 s with chronic obstructive pulmonary disease and diabetes mellitus was diagnosed with stage II rectal cancer. He underwent laparoscopic surgery, and on the 6th postoperative day, he developed a high fever. Chest computed tomography revealed infiltration in the left lower lung. Gram staining of the sputum showed Gram-negative rods phagocytosed by neutrophils, suggesting postoperative nosocomial pneumonia. The patient was started on tazobactam/piperacillin, and his pneumonia quickly improved. Later, only P. fluorescens was detected in a sputum culture. It was susceptible to common antipseudomonal agents. Gram staining of P. fluorescens appears to show a slightly thicker and larger morphology in comparison to Pseudomonas aeruginosa. Although there have been reports of opportunistic infections caused by P. fluorescens in immunosuppressed patients, including those with advanced cancer, most have been bloodstream infections, with very few reports of pneumonia alone. Clinicians should be aware that patients, who are not necessarily immunosuppressed, may develop pneumonia caused by P. fluorescens.
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Affiliation(s)
- Hiroshi Ishii
- Department of Respiratory Medicine, Fukuoka University Chikushi Hospital, Chikushino, Fukuoka, Japan; Department of Infection Control and Prevention, Fukuoka University Chikushi Hospital, Chikushino, Fukuoka, Japan.
| | - Hisako Kushima
- Department of Respiratory Medicine, Fukuoka University Chikushi Hospital, Chikushino, Fukuoka, Japan; Department of Infection Control and Prevention, Fukuoka University Chikushi Hospital, Chikushino, Fukuoka, Japan
| | - Yohei Koide
- Department of Respiratory Medicine, Fukuoka University Chikushi Hospital, Chikushino, Fukuoka, Japan; Department of Infection Control and Prevention, Fukuoka University Chikushi Hospital, Chikushino, Fukuoka, Japan
| | - Yoshiaki Kinoshita
- Department of Respiratory Medicine, Fukuoka University Chikushi Hospital, Chikushino, Fukuoka, Japan
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2
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Doty SL, Joubert PM, Firrincieli A, Sher AW, Tournay R, Kill C, Parikh SS, Okubara P. Potential Biocontrol Activities of Populus Endophytes against Several Plant Pathogens Using Different Inhibitory Mechanisms. Pathogens 2022; 12:pathogens12010013. [PMID: 36678361 PMCID: PMC9862643 DOI: 10.3390/pathogens12010013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
The plant microbiome can be used to bolster plant defense against abiotic and biotic stresses. Some strains of endophytes, the microorganisms within plants, can directly inhibit the growth of plant fungal pathogens. A previously isolated endophyte from wild Populus (poplar), WPB of the species Burkholderia vietnamiensis, had robust in vitro antifungal activity against pathogen strains that are highly virulent and of concern to Pacific Northwest agriculture: Rhizoctonia solani AG-8, Fusarium culmorum 70110023, and Gaemannomyces graminis var. tritici (Ggt) ARS-A1, as well as activity against the oomycete, Pythium ultimum 217. A direct screening method was developed for isolation of additional anti-fungal endophytes from wild poplar extracts. By challenging pathogens directly with dilute extracts, eleven isolates were found to be inhibitory to at least two plant pathogen strains and were therefore chosen for further characterization. Genomic analysis was conducted to determine if these endophyte strains harbored genes known to be involved in antimicrobial activities. The newly isolated Bacillus strains had gene clusters for production of bacillomycin, fengicyn, and bacillibactin, while the gene cluster for the synthesis of sessilin, viscosin and tolaasin were found in the Pseudomonas strains. The biosynthesis gene cluster for occidiofungin (ocf) was present in the Burkholderia vietnamiensis WPB genome, and an ocf deletion mutant lost inhibitory activity against 3 of the 4 pathogens. The new isolates lacked the gene cluster for occidiofungin implying they employ different modes of action. Other symbiotic traits including nitrogen fixation, phosphate solubilization, and the production of auxins and siderophores were investigated. Although it will be necessary to conduct in vivo tests of the candidates with pathogen-infected agricultural crops, the wild poplar tree microbiome may be a rich source of beneficial endophyte strains with potential for biocontrol applications against a variety of pathogens and utilizing varying modes of action.
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Affiliation(s)
- Sharon L. Doty
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
- Correspondence:
| | - Pierre M. Joubert
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Andrea Firrincieli
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy
| | - Andrew W. Sher
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
| | - Robert Tournay
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
| | - Carina Kill
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
- Native Roots School, Taos, NM 87571, USA
| | - Shruti S. Parikh
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195, USA
- Department of Food Science and Technology, University of California, Davis, CA 95616, USA
| | - Patricia Okubara
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
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3
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Atanasov KE, Galbis DM, Cornadó D, Serpico A, Sánchez G, Bosch M, Ferrer A, Altabella T. Pseudomonas fitomaticsae sp. nov., isolated at Marimurtra Botanical Garden in Blanes, Catalonia, Spain. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In the framework of the research project called fitomatics, we have isolated and characterized a bacterial plant-endophyte from the rhizomes of Iris germanica, hereafter referred to as strain FIT81T. The bacterium is Gram negative, rod-shaped with lophotrichous flagella, and catalase- and oxidase-positive. The optimal growth temperature of strain FIT81T is 28 °C, although it can grow within a temperature range of 4–32 °C. The pH growth tolerance ranges between pH 5 and 10, and it tolerates 4% (w/v) NaCl. A 16S rRNA phylogenetic analysis positioned strain FIT81T within the genus
Pseudomonas
, and multilocus sequence analysis revealed that
Pseudomonas gozinkensis
IzPS32dT,
Pseudomonas glycinae
MS586T,
Pseudomonas allokribbensis
IzPS23T, 'Pseudomonas kribbensis' 46–2 and
Pseudomonas koreensis
PS9-14T are the top five most closely related species, which were selected for further genome-to-genome comparisons, as well as for physiological and chemotaxonomic characterization. The genome size of strain FIT81T is 6 492 796 base-pairs long, with 60.6 mol% of G+C content. Average nucleotide identity and digital DNA–DNA hybridization analyses yielded values of 93.6 and 56.1%, respectively, when the FIT81T genome was compared to that of the closest type strain
P. gozinkensis
IzPS32dT. Taken together, the obtained genomic, physiologic and chemotaxonomic data indicate that strain FIT81T is different from its closest relative species, which lead us to suggest that it is a novel species to be included in the list of type strains with the name Pseudomonas fitomaticsae sp. nov. (FIT81T=CECT 30374T=DSM 112699T).
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Affiliation(s)
- Kostadin Evgeniev Atanasov
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
- Department of Biology, Healthcare and the Environment, Plant Physiology Section, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
| | - David Miñana Galbis
- Department of Biology, Healthcare and the Environment, Microbiology Section, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Deborah Cornadó
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Annabel Serpico
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Guiomar Sánchez
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Montserrat Bosch
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Albert Ferrer
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
| | - Teresa Altabella
- Department of Biology, Healthcare and the Environment, Plant Physiology Section, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
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4
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Whole-Genome Sequencing-Based Re-Identification of Pseudomonas putida/ fluorescens Clinical Isolates Identified by Biochemical Bacterial Identification Systems. Microbiol Spectr 2022; 10:e0249121. [PMID: 35389240 PMCID: PMC9045174 DOI: 10.1128/spectrum.02491-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The genus Pseudomonas, a complex Gram-negative genus, includes species isolated from various environments, plants, animals, and humans. We compared whole-genome sequencing (WGS) with clinical bacteriological methods and evaluated matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) to identify Pseudomonas species. Clinical isolates (N = 42) identified as P. putida or P. fluorescens by a bacterial identification system based on biochemical properties were reexamined by another identification system based on biochemical properties, two systems based on MALDI-TOF MS, and WGS. WGS revealed that 30 of the 42 isolates belonged to one of 14 known Pseudomonas species, respectively. The remaining 12 belonged to one of 9 proposed novel Pseudomonas species, respectively. MALDI-TOF MS analysis showed that the 9 novel species had unique major peaks. These results suggest that WGS is the optimal method to identify Pseudomonas species and that MALDI-TOF MS may complement WGS in identification. Based on their morphologic, physiologic, and biochemical properties, we propose nine novel Pseudomonas species. IMPORTANCE Most of the clinical isolates, identified as P. putida or P. fluorescens, were misidentified in clinical laboratories. Whole-genome sequencing (WGS) revealed that these isolates belonged to different Pseudomonas species, including novel species. WGS is a gold-standard method to identify Pseudomonas species, and MALDI-TOF MS analysis has the potential to complement WGS to reliably identify them.
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5
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Atanasov KE, Galbis DM, Gallego J, Serpico A, Bosch M, Altabella T, Ferrer A. Pseudomonas germanica sp. nov., isolated from Iris germanica rhizomes. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005268] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Through bacterial plant–endophyte extraction from rhizomes of Iris germanica plant, a Gram-stain-negative, aerobic, catalase- and oxidase-positive gammaproteobacterial strain, referred to as FIT28T, was isolated. FIT28T shows vigorous growth on nutrient rich media within the temperature range of 4–35 °C, with optimal growth at 28 °C, a wide pH tolerance from pH 5 to 11, and salt tolerance up to 6 % (w/v) NaCl. Colonies are white-yellow and quickly become mucoid. The results of analysis of the 16S rRNA gene sequence placed the strain within the genus
Pseudomonas
, and multilocus sequence analysis (MLSA) using 16S rRNA, rpoB, gyrB and rpoD concatenated sequences revealed that the closest relatives of FIT28T are
Pseudomonas zeae
OE48.2T, '
Pseudomonas crudilactis
' UCMA 17988,
Pseudomonas tensinigenes
ZA5.3T,
Pseudomonas helmanticensis
OHA11T,
Pseudomonas baetica
a390T,
Pseudomonas iridis
P42T,
Pseudomonas atagonensis
PS14T and
Pseudomonas koreensis
Ps 9-14T, within the
Pseudomonas koreensis
subgroup of the
Pseudomonas fluorescens
lineage. The genome size of FIT28T is about 6.7 Mb with 59.09 mol% DNA G+C content. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values calculated from the genomic sequences of FIT28T, and the closely related
P. zeae
OE48.2T are 95.23 and 63.4 %, respectively. Biochemical, metabolic and chemotaxonomic studies further support our proposal that Pseudomonas germanica sp. nov., should be considered a novel species of the genus
Pseudomonas
. Hence, the type strain FIT28T (=LMG 32353T=DSM 112698T) has been deposited in public cell-type culture centres.
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Affiliation(s)
- Kostadin Evgeniev Atanasov
- Department of Biology, Healthcare and the Environment, Plant Physiology Section, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
| | - David Miñana Galbis
- Department of Biology, Healthcare and the Environment, Microbiology Section, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Julia Gallego
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Annabel Serpico
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Montserrat Bosch
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Teresa Altabella
- Department of Biology, Healthcare and the Environment, Plant Physiology Section, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
| | - Albert Ferrer
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
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6
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Pacheco-Moreno A, Stefanato FL, Ford JJ, Trippel C, Uszkoreit S, Ferrafiat L, Grenga L, Dickens R, Kelly N, Kingdon AD, Ambrosetti L, Nepogodiev SA, Findlay KC, Cheema J, Trick M, Chandra G, Tomalin G, Malone JG, Truman AW. Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition. eLife 2021; 10:71900. [PMID: 34792466 PMCID: PMC8719888 DOI: 10.7554/elife.71900] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/16/2021] [Indexed: 11/29/2022] Open
Abstract
Agricultural soil harbors a diverse microbiome that can form beneficial relationships with plants, including the inhibition of plant pathogens. Pseudomonas spp. are one of the most abundant bacterial genera in the soil and rhizosphere and play important roles in promoting plant health. However, the genetic determinants of this beneficial activity are only partially understood. Here, we genetically and phenotypically characterize the Pseudomonas fluorescens population in a commercial potato field, where we identify strong correlations between specialized metabolite biosynthesis and antagonism of the potato pathogens Streptomyces scabies and Phytophthora infestans. Genetic and chemical analyses identified hydrogen cyanide and cyclic lipopeptides as key specialized metabolites associated with S. scabies inhibition, which was supported by in planta biocontrol experiments. We show that a single potato field contains a hugely diverse and dynamic population of Pseudomonas bacteria, whose capacity to produce specialized metabolites is shaped both by plant colonization and defined environmental inputs. Potato scab and blight are two major diseases which can cause heavy crop losses. They are caused, respectively, by the bacterium Streptomyces scabies and an oomycete (a fungus-like organism) known as Phytophthora infestans. Fighting these disease-causing microorganisms can involve crop management techniques – for example, ensuring that a field is well irrigated helps to keep S. scabies at bay. Harnessing biological control agents can also offer ways to control disease while respecting the environment. Biocontrol bacteria, such as Pseudomonas, can produce compounds that keep S. scabies and P. infestans in check. However, the identity of these molecules and how irrigation can influence Pseudomonas population remains unknown. To examine these questions, Pacheco-Moreno et al. sampled and isolated hundreds of Pseudomonas strains from a commercial potato field, closely examining the genomes of 69 of these. Comparing the genetic information of strains based on whether they could control the growth of S. scabies revealed that compounds known as cyclic lipopeptides are key to controlling the growth of S. scabies and P. infestans. Whether the field was irrigated also had a large impact on the strains forming the Pseudomonas population. Working out how Pseudomonas bacteria block disease could speed up the search for biological control agents. The approach developed by Pacheco-Moreno et al. could help to predict which strains might be most effective based on their genetic features. Similar experiments could also work for other combinations of plants and diseases.
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Affiliation(s)
- Alba Pacheco-Moreno
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Jonathan J Ford
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Christine Trippel
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Simon Uszkoreit
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Laura Ferrafiat
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Lucia Grenga
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Ruth Dickens
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Nathan Kelly
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Alexander Dh Kingdon
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Liana Ambrosetti
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Sergey A Nepogodiev
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Kim C Findlay
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Jitender Cheema
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Martin Trick
- Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Jacob G Malone
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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7
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The Two-Component System RstA/RstB Regulates Expression of Multiple Efflux Pumps and Influences Anaerobic Nitrate Respiration in Pseudomonas fluorescens. mSystems 2021; 6:e0091121. [PMID: 34726491 PMCID: PMC8562477 DOI: 10.1128/msystems.00911-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Multidrug resistance (MDR) efflux pumps are involved in bacterial intrinsic resistance to multiple antimicrobials. Expression of MDR efflux pumps can be either constitutive or transiently induced by various environmental signals, which are typically perceived by bacterial two-component systems (TCSs) and relayed to the bacterial nucleoid, where gene expression is modulated for niche adaptation. Here, we demonstrate that RstA/RstB, a TCS previously shown to control acid-induced and biofilm-related genes in Escherichiacoli, confers resistance to multiple antibiotics in Pseudomonas fluorescens by directly regulating the MDR efflux pumps EmhABC and MexCD-OprJ. Moreover, we show that phosphorylation of the conserved Asp52 residue in RstA greatly enhances RstA-DNA interaction, and regulation of the multidrug resistance by RstA/RstB is dependent on the phosphorylation of the RstA Asp52 residue by RstB. Proteome analysis reveals RstA/RstB also positively regulates the efflux pump MexEF-OprN and enzymes involved in anaerobic nitrate respiration and pyoverdine biosynthesis. Our results suggest that, by coupling the expression of multiple efflux pumps and anaerobic nitrate respiration, RstA/RstB could play a role in defense against nitrosative stress caused by anaerobic nitrate respiration. IMPORTANCE Microenvironmental hypoxia typically increases bacterial multidrug resistance by elevating expression of multidrug efflux pumps, but the precise mechanism is currently not well understood. Here, we showed that the two-component system RstA/RstB not only positively regulated expression of several efflux pumps involved in multidrug resistance, but also promoted expression of enzymes involved in anaerobic nitrate respiration and pyoverdine biosynthesis. These results suggested that, by upregulating expression of efflux pumps and pyoverdine biosynthesis-related enzymes, RstA/RstB could play a role in promoting bacterial tolerance to hypoxia by providing protection against nitrosative stress.
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8
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Dillon MM, Ruiz-Bedoya T, Bundalovic-Torma C, Guttman KM, Kwak H, Middleton MA, Wang PW, Horuz S, Aysan Y, Guttman DS. Comparative genomic insights into the epidemiology and virulence of plant pathogenic pseudomonads from Turkey. Microb Genom 2021; 7. [PMID: 34227931 PMCID: PMC8477409 DOI: 10.1099/mgen.0.000585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Pseudomonas is a highly diverse genus that includes species that cause disease in both plants and animals. Recently, pathogenic pseudomonads from the Pseudomonas syringae and Pseudomonas fluorescens species complexes have caused significant outbreaks in several agronomically important crops in Turkey, including tomato, citrus, artichoke and melon. We characterized 169 pathogenic Pseudomonas strains associated with recent outbreaks in Turkey via multilocus sequence analysis and whole-genome sequencing, then used comparative and evolutionary genomics to characterize putative virulence mechanisms. Most of the isolates are closely related to other plant pathogens distributed among the primary phylogroups of P. syringae, although there are significant numbers of P. fluorescens isolates, which is a species better known as a rhizosphere-inhabiting plant-growth promoter. We found that all 39 citrus blast pathogens cluster in P. syringae phylogroup 2, although strains isolated from the same host do not cluster monophyletically, with lemon, mandarin orange and sweet orange isolates all being intermixed throughout the phylogroup. In contrast, 20 tomato pith pathogens are found in two independent lineages: one in the P. syringae secondary phylogroups, and the other from the P. fluorescens species complex. These divergent pith necrosis strains lack characteristic virulence factors like the canonical tripartite type III secretion system, large effector repertoires and the ability to synthesize multiple bacterial phytotoxins, suggesting they have alternative molecular mechanisms to cause disease. These findings highlight the complex nature of host specificity among plant pathogenic pseudomonads.
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Affiliation(s)
- Marcus M Dillon
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.,Present address: Department of Biology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Tatiana Ruiz-Bedoya
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | | | - Kevin M Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Haejin Kwak
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Maggie A Middleton
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Pauline W Wang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Sumer Horuz
- Department of Plant Protection, Erciyes University, Kayseri, Turkey
| | - Yesim Aysan
- Department of Plant Protection, University of Çukurova, Adana, Turkey
| | - David S Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
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9
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Liu X, Xiang L, Yin Y, Li H, Ma D, Qu Y. Pneumonia caused by Pseudomonas fluorescens: a case report. BMC Pulm Med 2021; 21:212. [PMID: 34225696 PMCID: PMC8259381 DOI: 10.1186/s12890-021-01573-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pseudomonas fluorescens (P. fluorescens) has been detected in respiratory samples from patients. However, no previous reports have been published about these P. fluorescens cultures from lung tissues. CASE PRESENTATION Here, we report a case of pneumonia caused by P. fluorescens. P. fluorescens was identified from lung biopsy specimens for the first time in this case. According to the antibiotic susceptibility testing (AST) of P. fluorescens, the patient was given ciprofloxacin treatment. The temperature of the patient then returned to normal. Chest CT examination revealed improvements in pulmonary inflammation. CONCLUSIONS These findings suggest that the patients with pneumonia caused by P. fluorescens should be treated in a timely manner according to the AST results.
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Affiliation(s)
- Xiao Liu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Lei Xiang
- Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Yunhong Yin
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Wenhuaxi Road 107#, Jinan, 250012, China
| | - Hao Li
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Wenhuaxi Road 107#, Jinan, 250012, China
| | - Dedong Ma
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Wenhuaxi Road 107#, Jinan, 250012, China
| | - Yiqing Qu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Wenhuaxi Road 107#, Jinan, 250012, China.
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10
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Lei L, Chen J, Liao W, Liu P. Determining the Different Mechanisms Used by Pseudomonas Species to Cope With Minimal Inhibitory Concentrations of Zinc via Comparative Transcriptomic Analyses. Front Microbiol 2020; 11:573857. [PMID: 33343517 PMCID: PMC7744410 DOI: 10.3389/fmicb.2020.573857] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas is one of the most diverse bacterial genera identified in the environment. Genome sequence analysis has indicated that this genus can be clustered into three lineages and ten groups. Each group can adopt different mechanisms to thrive under zinc-depleted or high-zinc conditions, two environments that are frequently encountered during their environmental propagation. The response of three prominent Pseudomonas strains (Pseudomonas aeruginosa PAO1, Pseudomonas putida KT2440, and Pseudomonas fluorescens ATCC 13525T) to minimal inhibitory concentrations of zinc were compared using RNA-seq and ultra-performance liquid chromatography-tandem mass spectrometry analysis. Results demonstrated that the three strains shared only minimal similarity at the transcriptional level. Only four genes responsible for zinc efflux were commonly upregulated. P. aeruginosa PAO1 specifically downregulated the operons involved in siderophore synthesis and the genes that encode ribosomal protein, while upregulated the genes associated with antibiotic efflux and cell envelope biosynthesis. The membrane transporters in P. putida KT2440 were globally downregulated, indicating changes in cell permeability. Compared with P. aeruginosa PAO1 and P. putida KT2440, the most remarkable transcriptional variation in P. fluorescens ATCC 13525T is the significant downregulation of the type VI secretion system. Metabolite quantitative analysis showed that low concentrations of the metabolites involved in central carbon metabolism and amino acid synthesis were detected in the three strains. In summary, the cellular responses of the three strains under high-zinc condition is quite divergent. Although similar metal efflux systems were upregulated, the three strains employed different pathways to reduce zinc intrusion. In addition, zinc treatment can increase the difficulties of scavenging P. aeruginosa from its colonization area, and reduce the competitiveness of P. fluorescens in microbiota.
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Affiliation(s)
| | | | | | - Pulin Liu
- College of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
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High Level of Resistance to Antimicrobials and Heavy Metals in Multidrug-Resistant Pseudomonas sp. Isolated from Water Sources. Curr Microbiol 2020; 77:2694-2701. [DOI: 10.1007/s00284-020-02052-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/23/2020] [Indexed: 01/11/2023]
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Jia G, Zhi A, Lai PFH, Wang G, Xia Y, Xiong Z, Zhang H, Che N, Ai L. The oral microbiota - a mechanistic role for systemic diseases. Br Dent J 2019; 224:447-455. [PMID: 29569607 DOI: 10.1038/sj.bdj.2018.217] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2017] [Indexed: 12/20/2022]
Abstract
Human oral microbiota is the ecological community of commensal, symbiotic, and pathogenic microorganisms found in the oral cavity. Oral microbiota generally exists in the form of a biofilm and plays a crucial role in maintaining oral homeostasis, protecting the oral cavity and preventing disease development. Human oral microbiota has recently become a new focus research for promoting the progress of disease diagnosis, assisting disease treatment, and developing personalised medicines. In this review, the scientific evidence supporting the association that endogenous and exogenous factors (diet, smoking, drinking, socioeconomic status, antibiotics use and pregnancy) modulate oral microbiota. It provides insights into the mechanistic role in which oral microbiota may influence systemic diseases, and summarises the challenges of clinical diagnosis and treatment based on the microbial community information. It provides information for noninvasive diagnosis and helps develop a new paradigm of personalised medicine. All these benefit human health in the post-metagenomics era.
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Affiliation(s)
- G Jia
- Shanghai Engineering Research Centre of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
| | - A Zhi
- Chemical Technology and Food Science College, Zhengzhou Institute of Engineering and Technology, Zhengzhou 450044, People's Republic of China
| | - P F H Lai
- Shanghai Engineering Research Centre of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
| | - G Wang
- Shanghai Engineering Research Centre of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
| | - Y Xia
- Shanghai Engineering Research Centre of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
| | - Z Xiong
- Shanghai Engineering Research Centre of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
| | - H Zhang
- Shanghai Engineering Research Centre of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
| | - N Che
- Department of Otolaryngology, Tongji Hospital, Tongji University, Shanghai 200065, PR China
| | - L Ai
- Shanghai Engineering Research Centre of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
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Draft Genome Sequence of Pseudomonas fluorescens Strain TR3, a Potential Biocontrol Agent against the Rice Blast Fungus Magnaporthe oryzae. GENOME ANNOUNCEMENTS 2017; 5:5/47/e01332-17. [PMID: 29167257 PMCID: PMC5701482 DOI: 10.1128/genomea.01332-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We present the draft genome sequence of the potential biocontrol agent Pseudomonas fluorescens TR3, which was isolated from rice leaves infected with Magnaporthe oryzae in a greenhouse. The genome of TR3 was assembled into 26 scaffolds (~6 Mbp) and includes genes potentially involved in bacterial interactions with fungi.
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Lugli GA, Milani C, Mancabelli L, Turroni F, Ferrario C, Duranti S, van Sinderen D, Ventura M. Ancient bacteria of the Ötzi's microbiome: a genomic tale from the Copper Age. MICROBIOME 2017; 5:5. [PMID: 28095919 PMCID: PMC5240250 DOI: 10.1186/s40168-016-0221-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/13/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Ancient microbiota information represents an important resource to evaluate bacterial evolution and to explore the biological spread of infectious diseases in history. The soft tissue of frozen mummified humans, such as the Tyrolean Iceman, has been shown to contain bacterial DNA that is suitable for population profiling of the prehistoric bacteria that colonized such ancient human hosts. RESULTS Here, we performed a microbial cataloging of the distal gut microbiota of the Tyrolean Iceman, which highlights a predominant abundance of Clostridium and Pseudomonas species. Furthermore, in silico analyses allowed the reconstruction of the genome sequences of five ancient bacterial genomes, including apparent pathogenic ancestor strains of Clostridium perfringens and Pseudomonas veronii species present in the gut of the Tyrolean Iceman. CONCLUSIONS Genomic analyses of the reconstructed C. perfringens chromosome clearly support the occurrence of a pathogenic profile consisting of virulence genes already existing in the ancient strain, thereby reinforcing the notion of a very early speciation of this taxon towards a pathogenic phenotype. In contrast, the evolutionary development of P. veronii appears to be characterized by the acquisition of antibiotic resistance genes in more recent times as well as an evolution towards an ecological niche outside of the (human) gastrointestinal tract.
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Affiliation(s)
- Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
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