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Weimann A, Dinan AM, Ruis C, Bernut A, Pont S, Brown K, Ryan J, Santos L, Ellison L, Ukor E, Pandurangan AP, Krokowski S, Blundell TL, Welch M, Blane B, Judge K, Bousfield R, Brown N, Bryant JM, Kukavica-Ibrulj I, Rampioni G, Leoni L, Harrison PT, Peacock SJ, Thomson NR, Gauthier J, Fothergill JL, Levesque RC, Parkhill J, Floto RA. Evolution and host-specific adaptation of Pseudomonas aeruginosa. Science 2024; 385:eadi0908. [PMID: 38963857 DOI: 10.1126/science.adi0908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/02/2024] [Indexed: 07/06/2024]
Abstract
The major human bacterial pathogen Pseudomonas aeruginosa causes multidrug-resistant infections in people with underlying immunodeficiencies or structural lung diseases such as cystic fibrosis (CF). We show that a few environmental isolates, driven by horizontal gene acquisition, have become dominant epidemic clones that have sequentially emerged and spread through global transmission networks over the past 200 years. These clones demonstrate varying intrinsic propensities for infecting CF or non-CF individuals (linked to specific transcriptional changes enabling survival within macrophages); have undergone multiple rounds of convergent, host-specific adaptation; and have eventually lost their ability to transmit between different patient groups. Our findings thus explain the pathogenic evolution of P. aeruginosa and highlight the importance of global surveillance and cross-infection prevention in averting the emergence of future epidemic clones.
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Affiliation(s)
- Aaron Weimann
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Adam M Dinan
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | - Christopher Ruis
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Audrey Bernut
- Laboratory of Pathogens and Host Immunity (LPHI), UMR5235, CNRS/Université de Montpellier, Montpellier, France
| | - Stéphane Pont
- Laboratory of Pathogens and Host Immunity (LPHI), UMR5235, CNRS/Université de Montpellier, Montpellier, France
| | - Karen Brown
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
| | - Judy Ryan
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Lúcia Santos
- Department of Physiology, Bioscience Institute, University College Cork, Cork, Ireland
| | - Louise Ellison
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Emem Ukor
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
| | - Arun P Pandurangan
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Sina Krokowski
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Tom L Blundell
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Beth Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kim Judge
- Wellcome Sanger Institute, Hinxton, UK
| | - Rachel Bousfield
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals Trust, Cambridge, UK
| | | | | | - Irena Kukavica-Ibrulj
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Québec, Canada
| | - Giordano Rampioni
- Department of Science, University Roma Tre, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Livia Leoni
- Department of Science, University Roma Tre, Rome, Italy
| | - Patrick T Harrison
- Department of Physiology, Bioscience Institute, University College Cork, Cork, Ireland
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals Trust, Cambridge, UK
| | - Nicholas R Thomson
- Wellcome Sanger Institute, Hinxton, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Jeff Gauthier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Québec, Canada
| | - Jo L Fothergill
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Roger C Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Québec, Canada
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - R Andres Floto
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals Trust, Cambridge, UK
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2
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Hibbert TM, Whiteley M, Renshaw SA, Neill DR, Fothergill JL. Emerging strategies to target virulence in Pseudomonas aeruginosa respiratory infections. Crit Rev Microbiol 2023:1-16. [PMID: 37999716 DOI: 10.1080/1040841x.2023.2285995] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that is responsible for infections in people living with chronic respiratory conditions, such as cystic fibrosis (CF) and non-CF bronchiectasis (NCFB). Traditionally, in people with chronic respiratory disorders, P. aeruginosa infection has been managed with a combination of inhaled and intravenous antibiotic therapies. However, due in part to the prolonged use of antibiotics in these people, the emergence of multi-drug resistant P. aeruginosa strains is a growing concern. The development of anti-virulence therapeutics may provide a new means of treating P. aeruginosa lung infections whilst also combatting the AMR crisis, as these agents are presumed to exert reduced pressure for the emergence of drug resistance as compared to antibiotics. However, the pipeline for developing anti-virulence therapeutics is poorly defined, and it is currently unclear as to whether in vivo and in vitro models effectively replicate the complex pulmonary environment sufficiently to enable development and testing of such therapies for future clinical use. Here, we discuss potential targets for P. aeruginosa anti-virulence therapeutics and the effectiveness of the current models used to study them. Focus is given to the difficulty of replicating the virulence gene expression patterns of P. aeruginosa in the CF and NCFB lung under laboratory conditions and to the challenges this poses for anti-virulence therapeutic development.
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Affiliation(s)
- Tegan M Hibbert
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Marvin Whiteley
- School of Biological Sciences, Georgia Institute of Technology, Centre for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Stephen A Renshaw
- The Bateson Centre and Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK
| | - Daniel R Neill
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Joanne L Fothergill
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
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3
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Cramer N, Nawrot ML, Wege L, Dorda M, Sommer C, Danov O, Wronski S, Braun A, Jonigk D, Fischer S, Munder A, Tümmler B. Competitive fitness of Pseudomonas aeruginosa isolates in human and murine precision-cut lung slices. Front Cell Infect Microbiol 2022; 12:992214. [PMID: 36081773 PMCID: PMC9446154 DOI: 10.3389/fcimb.2022.992214] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic respiratory infections with the gram-negative bacterium Pseudomonas aeruginosa are an important co-morbidity for the quality of life and prognosis of people with cystic fibrosis (CF). Such long-term colonization, sometimes lasting up to several decades, represents a unique opportunity to investigate pathogen adaptation processes to the host. Our studies aimed to resolve if and to what extent the bacterial adaptation to the CF airways influences the fitness of the pathogen to grow and to persist in the lungs. Marker-free competitive fitness experiments of serial P. aeruginosa isolates differentiated by strain-specific SNPs, were performed with murine and human precision cut lung slices (PCLS). Serial P. aeruginosa isolates were selected from six mild and six severe CF patient courses, respectively. MPCLS or hPCLS were inoculated with a mixture of equal numbers of the serial isolates of one course. The temporal change of the composition of the bacterial community during competitive growth was quantified by multi-marker amplicon sequencing. Both ex vivo models displayed a strong separation of fitness traits between mild and severe courses. Whereas the earlier isolates dominated the competition in the severe courses, intermediate and late isolates commonly won the competition in the mild courses. The status of the CF lung disease rather than the bacterial genotype drives the adaptation of P. aeruginosa during chronic CF lung infection. This implies that the disease status of the lung habitat governed the adaptation of P. aeruginosa more strongly than the underlying bacterial clone-type and its genetic repertoire.
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Affiliation(s)
- Nina Cramer
- Clinical Research Group ‘Pseudomonas Genomics’, Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
- *Correspondence: Nina Cramer,
| | - Marie Luise Nawrot
- Clinical Research Group ‘Pseudomonas Genomics’, Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Lion Wege
- Clinical Research Group ‘Pseudomonas Genomics’, Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research, Hannover Medical School, Hannover, Germany
| | - Marie Dorda
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Charline Sommer
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Member of Fraunhofer International Consortium for Anti-Infective Research (iCAIR), Hannover, Germany
| | - Olga Danov
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Member of Fraunhofer International Consortium for Anti-Infective Research (iCAIR), Hannover, Germany
| | - Sabine Wronski
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Member of Fraunhofer International Consortium for Anti-Infective Research (iCAIR), Hannover, Germany
| | - Armin Braun
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Member of Fraunhofer International Consortium for Anti-Infective Research (iCAIR), Hannover, Germany
| | - Danny Jonigk
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Sebastian Fischer
- Clinical Research Group ‘Pseudomonas Genomics’, Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Antje Munder
- Clinical Research Group ‘Pseudomonas Genomics’, Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Clinical Research Group ‘Pseudomonas Genomics’, Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
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Caliskan AB, Horani A, Manion M, Brody SL. Variations in infection control practices suggest a need for guidelines in primary ciliary dyskinesia patient care. Pediatr Pulmonol 2022; 57:1072-1075. [PMID: 35043594 DOI: 10.1002/ppul.25836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/24/2021] [Accepted: 01/17/2022] [Indexed: 11/10/2022]
Abstract
Primary ciliary dyskinesis (PCD) is an autosomal recessive disorder associated with impaired mucociliary clearance caused by defects in ciliary structure and function. The major clinical feature of PCD is recurring or persistent respiratory tract infection. Respiratory tract colonization with drug-resistant organisms impacts the frequency of infections and lung function decline. Protective gear has been employed by caregivers in an attempt to control respiratory tract bacterial spread between patients with cystic fibrosis, but use in PCD is not known. We conducted a web-based survey to investigate infection control and prevention practices of PCD centers in North America, and how practices have been influenced by the COVID-19 pandemic. The response rate was 87.0%. Before the COVID-19 pandemic, glove, gown, and mask use were variable, and only 3.7% of centers used masks during encounters with PCD outpatients. After COVID-19 mandates are lifted, 48.1% of centers plan to continue to use masks during outpatient care, while the practice regarding the use of gloves and gowns was not influenced by the current pandemic. There is no uniform practice for infection control in PCD care indicating the need for practice guidelines. Mitigation of respiratory virus transmission learned during the COVID-19 pandemic may impact future infection control approaches used for patients with PCD and other lung diseases.
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Affiliation(s)
- Ayse B Caliskan
- Department of Pediatrics, Division of Allergy and Pulmonary Medicine, School of Medicine, Washington University in Saint Louis, St. Louis, Missouri, USA
| | - Amjad Horani
- Department of Pediatrics, Division of Allergy and Pulmonary Medicine, School of Medicine, Washington University in Saint Louis, St. Louis, Missouri, USA
- Department of Cell Biology and Physiology, School of Medicine, Washington University in Saint Louis, St. Louis, Missouri, USA
| | - Michele Manion
- Primary Ciliary Dyskinesia Foundation, Minneapolis, MN, USA
| | - Steven L Brody
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, School of Medicine, Washington University in Saint Louis, St. Louis, Missouri, USA
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5
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Namonyo S, Carvalho G, Guo J, Weynberg KD. Novel Bacteriophages Show Activity against Selected Australian Clinical Strains of Pseudomonas aeruginosa. Microorganisms 2022; 10:microorganisms10020210. [PMID: 35208664 PMCID: PMC8875357 DOI: 10.3390/microorganisms10020210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
Multi-drug resistant (MDR) clinical strains of Pseudomonas aeruginosa are the most prevalent bacteria in the lungs of patients with cystic fibrosis (CF) and burn wounds and among the most common in immunocompromised hospital patients in Australia. There are currently no promising antibiotics in the pipeline being developed against these strains. Phage therapy, which uses viruses known as bacteriophages to infect and kill pathogenic bacteria, could be a possible alternative treatment. To this end, we isolated and characterised four novel phages against Australian clinical strains of P. aeruginosa isolated from patients with cystic fibrosis, from infected blood and joint aspirate in Southeast Queensland, Australia. Activated sludge was enriched for phages using the clinical strains, and four bacteriophages were isolated. The phages were able to cause lysis in a further three identified clinical isolates. Morphology showed that they were all tailed phages (of the order Caudovirales), two belonging to the family Myoviridae and the others assigned to the Podoviridae and Siphoviridae. Their genomes were sequenced to reveal a doubled stranded DNA topology with genome sizes ranging from 42 kb to 65 kb. In isolating and characterising these novel phages, we directed our efforts toward the development and use of these phages as candidates for phage therapy as an alternative strategy for the management or elimination of these pathogenic strains. Here we describe novel phage candidates for potential therapeutic treatment of MDR Australian clinical isolates of P. aeruginosa.
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Affiliation(s)
- Samuel Namonyo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, QLD 4072, Australia; (S.N.); (J.G.)
- Queensland Alliance for Environmental Health Services, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Gilda Carvalho
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, QLD 4072, Australia; (S.N.); (J.G.)
- Correspondence: (G.C.); (K.D.W.)
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, QLD 4072, Australia; (S.N.); (J.G.)
| | - Karen D. Weynberg
- Australian Centre for Ecogenomics, School of Chemistry & Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
- Correspondence: (G.C.); (K.D.W.)
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Pseudomonas aeruginosa Pangenome: Core and Accessory Genes of a Highly Resourceful Opportunistic Pathogen. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:3-28. [DOI: 10.1007/978-3-031-08491-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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7
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Pseudomonas aeruginosa in the Cystic Fibrosis Lung. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:347-369. [DOI: 10.1007/978-3-031-08491-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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8
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Tümmler B. What Makes Pseudomonas aeruginosa a Pathogen? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:283-301. [DOI: 10.1007/978-3-031-08491-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Wardell SJT, Gauthier J, Martin LW, Potvin M, Brockway B, Levesque RC, Lamont IL. Genome evolution drives transcriptomic and phenotypic adaptation in Pseudomonas aeruginosa during 20 years of infection. Microb Genom 2021; 7. [PMID: 34826267 PMCID: PMC8743555 DOI: 10.1099/mgen.0.000681] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa chronically infects the lungs of patients with cystic fibrosis (CF). During infection the bacteria evolve and adapt to the lung environment. Here we use genomic, transcriptomic and phenotypic approaches to compare multiple isolates of P. aeruginosa collected more than 20 years apart during a chronic infection in a CF patient. Complete genome sequencing of the isolates, using short- and long-read technologies, showed that a genetic bottleneck occurred during infection and was followed by diversification of the bacteria. A 125 kb deletion, an 0.9 Mb inversion and hundreds of smaller mutations occurred during evolution of the bacteria in the lung, with an average rate of 17 mutations per year. Many of the mutated genes are associated with infection or antibiotic resistance. RNA sequencing was used to compare the transcriptomes of an earlier and a later isolate. Substantial reprogramming of the transcriptional network had occurred, affecting multiple genes that contribute to continuing infection. Changes included greatly reduced expression of flagellar machinery and increased expression of genes for nutrient acquisition and biofilm formation, as well as altered expression of a large number of genes of unknown function. Phenotypic studies showed that most later isolates had increased cell adherence and antibiotic resistance, reduced motility, and reduced production of pyoverdine (an iron-scavenging siderophore), consistent with genomic and transcriptomic data. The approach of integrating genomic, transcriptomic and phenotypic analyses reveals, and helps to explain, the plethora of changes that P. aeruginosa undergoes to enable it to adapt to the environment of the CF lung during a chronic infection.
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Affiliation(s)
| | - Jeff Gauthier
- Institut de biologie intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Lois W Martin
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Marianne Potvin
- Institut de biologie intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Ben Brockway
- Department of Medicine, University of Otago, Dunedin, New Zealand
| | - Roger C Levesque
- Institut de biologie intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Iain L Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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Goodyear MC, Garnier N, Krieger JR, Geddes-McAlister J, Khursigara CM. Label-free quantitative proteomics identifies unique proteomes of clinical isolates of the Liverpool Epidemic Strain of Pseudomonas aeruginosa and laboratory strain PAO1. Proteomics Clin Appl 2021; 15:e2100062. [PMID: 34510773 DOI: 10.1002/prca.202100062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/09/2021] [Indexed: 11/11/2022]
Abstract
PURPOSE Comparative genomics and phenotypic assays have shown that antibiotic resistance profiles differ among clinical isolates of Pseudomonas aeruginosa and that genotype-phenotype associations are difficult to establish for resistance phenotypes based on these comparisons alone. EXPERIMENTAL DESIGN Here, we used label-free quantitative proteomics to compare two isolates of the Liverpool Epidemic Strain (LES) of P. aeruginosa, LESlike1 and LESB58, and the common laboratory strain P. aeruginosa PAO1 to more accurately predict functional differences between strains. RESULTS Our results show that the proteomes of the LES isolates are more similar to each other than to PAO1; however, a number of differences were observed in the abundance of proteins involved in quorum sensing, virulence, and antibiotic resistance, including in the comparison of LESlike1 and LESB58. Additionally, the proteomic data revealed a higher abundance of proteins involved in polymyxin and aminoglycoside resistance in LESlike1. Minimum inhibitory concentration assays showed that LESlike1 had up to 128-fold higher resistance to antibiotics from these classes. CONCLUSIONS These findings provide an example of the ability of proteomic data to complement genotypic and phenotypic studies to understand resistance in clinical isolates. CLINICAL RELEVANCE P. aeruginosa is a predominant pathogen in chronic lung infections in individuals with cystic fibrosis (CF). LES isolates are capable of transferring between CF patients and have been associated with increased hospital visits and antibiotic treatments.
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Affiliation(s)
- Mara C Goodyear
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Nicole Garnier
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | | | | | - Cezar M Khursigara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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