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Tueffers L, Batra A, Zimmermann J, Botelho J, Buchholz F, Liao J, Mendoza Mejía N, Munder A, Klockgether J, Tüemmler B, Rupp J, Schulenburg H. Variation in the response to antibiotics and life-history across the major Pseudomonas aeruginosa clone type (mPact) panel. Microbiol Spectr 2024:e0014324. [PMID: 38860784 DOI: 10.1128/spectrum.00143-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/18/2024] [Indexed: 06/12/2024] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous, opportunistic human pathogen. Since it often expresses multidrug resistance, new treatment options are urgently required. Such new treatments are usually assessed with one of the canonical laboratory strains, PAO1 or PA14. However, these two strains are unlikely representative of the strains infecting patients, because they have adapted to laboratory conditions and do not capture the enormous genomic diversity of the species. Here, we characterized the major P. aeruginosa clone type (mPact) panel. This panel consists of 20 strains, which reflect the species' genomic diversity, cover all major clone types, and have both patient and environmental origins. We found significant strain variation in distinct responses toward antibiotics and general growth characteristics. Only few of the measured traits are related, suggesting independent trait optimization across strains. High resistance levels were only identified for clinical mPact isolates and could be linked to known antimicrobial resistance (AMR) genes. One strain, H01, produced highly unstable AMR combined with reduced growth under drug-free conditions, indicating an evolutionary cost to resistance. The expression of microcolonies was common among strains, especially for strain H15, which also showed reduced growth, possibly indicating another type of evolutionary trade-off. By linking isolation source, growth, and virulence to life history traits, we further identified specific adaptive strategies for individual mPact strains toward either host processes or degradation pathways. Overall, the mPact panel provides a reasonably sized set of distinct strains, enabling in-depth analysis of new treatment designs or evolutionary dynamics in consideration of the species' genomic diversity. IMPORTANCE New treatment strategies are urgently needed for high-risk pathogens such as the opportunistic and often multidrug-resistant pathogen Pseudomonas aeruginosa. Here, we characterize the major P. aeruginosa clone type (mPact) panel. It consists of 20 strains with different origins that cover the major clone types of the species as well as its genomic diversity. This mPact panel shows significant variation in (i) resistance against distinct antibiotics, including several last resort antibiotics; (ii) related traits associated with the response to antibiotics; and (iii) general growth characteristics. We further developed a novel approach that integrates information on resistance, growth, virulence, and life-history characteristics, allowing us to demonstrate the presence of distinct adaptive strategies of the strains that focus either on host interaction or resource processing. In conclusion, the mPact panel provides a manageable number of representative strains for this important pathogen for further in-depth analyses of treatment options and evolutionary dynamics.
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Affiliation(s)
- Leif Tueffers
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Aditi Batra
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Antibiotic resistance group, Max-Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Johannes Zimmermann
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Antibiotic resistance group, Max-Planck Institute for Evolutionary Biology, Ploen, Germany
| | - João Botelho
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Antibiotic resistance group, Max-Planck Institute for Evolutionary Biology, Ploen, Germany
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Florian Buchholz
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Junqi Liao
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | | | - Antje Munder
- Department of Pediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover, Germany
| | - Jens Klockgether
- Department of Pediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Hannover, Germany
| | - Burkhard Tüemmler
- Department of Pediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Hinrich Schulenburg
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Antibiotic resistance group, Max-Planck Institute for Evolutionary Biology, Ploen, Germany
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2
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Miller WR, Arias CA. ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics. Nat Rev Microbiol 2024:10.1038/s41579-024-01054-w. [PMID: 38831030 DOI: 10.1038/s41579-024-01054-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 06/05/2024]
Abstract
The rise of antibiotic resistance and a dwindling antimicrobial pipeline have been recognized as emerging threats to public health. The ESKAPE pathogens - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. - were initially identified as critical multidrug-resistant bacteria for which effective therapies were rapidly needed. Now, entering the third decade of the twenty-first century, and despite the introduction of several new antibiotics and antibiotic adjuvants, such as novel β-lactamase inhibitors, these organisms continue to represent major therapeutic challenges. These bacteria share several key biological features, including adaptations for survival in the modern health-care setting, diverse methods for acquiring resistance determinants and the dissemination of successful high-risk clones around the world. With the advent of next-generation sequencing, novel tools to track and combat the spread of these organisms have rapidly evolved, as well as renewed interest in non-traditional antibiotic approaches. In this Review, we explore the current epidemiology and clinical impact of this important group of bacterial pathogens and discuss relevant mechanisms of resistance to recently introduced antibiotics that affect their use in clinical settings. Furthermore, we discuss emerging therapeutic strategies needed for effective patient care in the era of widespread antimicrobial resistance.
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Affiliation(s)
- William R Miller
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Cesar A Arias
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA.
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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Morales-Espinosa R, Delgado G, Espinosa-Camacho F, Flores-Alanis A, Rodriguez C, Mendez JL, Gonzalez-Pedraza A, Cravioto A. Pseudomonas aeruginosa strains isolated from animal with high virulence genes content and highly sensitive to antimicrobials. J Glob Antimicrob Resist 2024; 37:75-80. [PMID: 38452900 DOI: 10.1016/j.jgar.2024.02.023] [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: 06/19/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024] Open
Abstract
OBJECTIVES P. aeruginosa is one of the most metabolically versatile bacteria having the ability to survive in multiple environments through its accessory genome. An important hallmark of P. aeruginosa is the high level of antibiotic resistance, which often makes eradication difficult and sometimes impossible. Evolutionary forces have led to this bacterium to develop high antimicrobial resistance with a variety of elements contributing to both intrinsic and acquired resistance. The objectives were to genetically and phenotypically characterizer P. aeruginosa strains isolated from companion animals of different species. METHODS We characterized a collection of 39 P. aeruginosa strains isolated from infected animals. The genetic characterization was in relation to chromosomal profile by PFGE; content of virulence gene; presence of genomic islands (GIs); genes of the cytotoxins exported by T3SS: exoU, exoS, exoT and exoY; and type IV pili allele. The phenotypic characterization was based on patterns of susceptibility to different antimicrobials. RESULTS Each strain had a PFGE profile, a high virulence genes content, and a large accessory genome. However, most of the strains presented high sensitivity to almost all antimicrobials tested, showing no acquired resistance (no β-lactamases). The exception to this lack of resistance was seen with penicillin. CONCLUSIONS P. aeruginosa could be a naturally sensitive bacterium to standard antimicrobials but could rapidly develop intrinsic and acquired resistance when the bacterium is exposed to pressure exerted by antibiotics, as observed in hospital settings.
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Affiliation(s)
- Rosario Morales-Espinosa
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México.
| | - Gabriela Delgado
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Fernando Espinosa-Camacho
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Alejandro Flores-Alanis
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Cristina Rodriguez
- Bacteriology Laboratory, Faculty of Veterinary, Universidad Nacional Autónoma de México., Coyoacán, Ciudad de México, México
| | - Jose L Mendez
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Alberto Gonzalez-Pedraza
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Alejandro Cravioto
- Bacterial Genomic Laboratory, Microbiology and Parasitology Deparment, Faculty of Medicine, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
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Kaczmarczyk A, van Vliet S, Jakob RP, Teixeira RD, Scheidat I, Reinders A, Klotz A, Maier T, Jenal U. A genetically encoded biosensor to monitor dynamic changes of c-di-GMP with high temporal resolution. Nat Commun 2024; 15:3920. [PMID: 38724508 PMCID: PMC11082216 DOI: 10.1038/s41467-024-48295-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
Monitoring changes of signaling molecules and metabolites with high temporal resolution is key to understanding dynamic biological systems. Here, we use directed evolution to develop a genetically encoded ratiometric biosensor for c-di-GMP, a ubiquitous bacterial second messenger regulating important biological processes like motility, surface attachment, virulence and persistence. The resulting biosensor, cdGreen2, faithfully tracks c-di-GMP in single cells and with high temporal resolution over extended imaging times, making it possible to resolve regulatory networks driving bimodal developmental programs in different bacterial model organisms. We further adopt cdGreen2 as a simple tool for in vitro studies, facilitating high-throughput screens for compounds interfering with c-di-GMP signaling and biofilm formation. The sensitivity and versatility of cdGreen2 could help reveal c-di-GMP dynamics in a broad range of microorganisms with high temporal resolution. Its design principles could also serve as a blueprint for the development of similar, orthogonal biosensors for other signaling molecules, metabolites and antibiotics.
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Affiliation(s)
- Andreas Kaczmarczyk
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
| | - Simon van Vliet
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Roman Peter Jakob
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | | | - Inga Scheidat
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Alberto Reinders
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Alexander Klotz
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Timm Maier
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Urs Jenal
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
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5
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Pan S, Underhill SAM, Hamm CW, Stover MA, Butler DR, Shults CA, Manjarrez JR, Cabeen MT. Glycerol metabolism impacts biofilm phenotypes and virulence in Pseudomonas aeruginosa via the Entner-Doudoroff pathway. mSphere 2024; 9:e0078623. [PMID: 38501832 PMCID: PMC11036800 DOI: 10.1128/msphere.00786-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/23/2024] [Indexed: 03/20/2024] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous bacterium and a notorious opportunistic pathogen that forms biofilm structures in response to many environmental cues. Biofilm formation includes attachment to surfaces and the production of the exopolysaccharide Pel, which is present in both the PAO1 and PA14 laboratory strains of P. aeruginosa. Biofilms help protect bacterial cells from host defenses and antibiotics and abet infection. The carbon source used by the cells also influences biofilm, but these effects have not been deeply studied. We show here that glycerol, which can be liberated from host surfactants during infection, encourages surface attachment and magnifies colony morphology differences. We find that glycerol kinase is important but not essential for glycerol utilization and relatively unimportant for biofilm behaviors. Among downstream enzymes predicted to take part in glycerol utilization, Edd stood out as being important for glycerol utilization and for enhanced biofilm phenotypes in the presence of glycerol. Thus, gluconeogenesis and catabolism of anabolically produced glucose appear to impact not only the utilization of glycerol but also glycerol-stimulated biofilm phenotypes. Finally, waxworm moth larvae and nematode infection models reveal that interruption of the Entner-Doudoroff pathway, but not abrogation of glycerol phosphorylation, unexpectedly increases P. aeruginosa lethality in both acute and chronic infections, even while stimulating a stronger immune response by Caenorhabditis elegans.IMPORTANCEPseudomonas aeruginosa, the ubiquitous environmental bacterium and human pathogen, forms multicellular communities known as biofilms in response to various stimuli. We find that glycerol, a common carbon source that bacteria can use for energy and biosynthesis, encourages biofilm behaviors such as surface attachment and colony wrinkling by P. aeruginosa. Glycerol can be derived from surfactants that are present in the human lungs, a common infection site. Glycerol-stimulated biofilm phenotypes do not depend on phosphorylation of glycerol but are surprisingly impacted by a glucose breakdown pathway, suggesting that it is glycerol utilization, and not its mere presence or cellular import, that stimulates biofilm phenotypes. Moreover, the same mutations that block glycerol-stimulated biofilm phenotypes also impact P. aeruginosa virulence in both acute and chronic animal models. Notably, a glucose-breakdown mutant (Δedd) counteracts biofilm phenotypes but shows enhanced virulence and stimulates a stronger immune response in Caenorhabditis elegans.
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Affiliation(s)
- Somalisa Pan
- Department of Microbiology, Oklahoma State University, Stillwater, Oklahoma, USA
| | | | - Christopher W. Hamm
- Department of Microbiology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Mylissa A. Stover
- Department of Biochemistry and Microbiology, OSU Center for Health Sciences, Tulsa, Oklahoma, USA
| | - Daxton R. Butler
- Department of Microbiology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Crystal A. Shults
- Department of Biochemistry and Microbiology, OSU Center for Health Sciences, Tulsa, Oklahoma, USA
| | - Jacob R. Manjarrez
- Department of Biochemistry and Microbiology, OSU Center for Health Sciences, Tulsa, Oklahoma, USA
| | - Matthew T. Cabeen
- Department of Microbiology, Oklahoma State University, Stillwater, Oklahoma, USA
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6
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Hu Y, Yuan M, Julian A, Tuz K, Juárez O. Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions. Front Microbiol 2024; 15:1347466. [PMID: 38468849 PMCID: PMC10926992 DOI: 10.3389/fmicb.2024.1347466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/08/2024] [Indexed: 03/13/2024] Open
Abstract
Pseudomonas aeruginosa is a common cause of urinary tract infections by strains that are often multidrug resistant, representing a major challenge to the world's health care system. This microorganism has a highly adaptable metabolism that allows it to colonize many environments, including the urinary tract. In this work, we have characterized the metabolic strategies used by stationary phase P. aeruginosa cells cultivated in urine-like media to understand the adaptations used by this microorganism to survive and produce disease. Our proteomics results show that cells rely on the Entner-Duodoroff pathway, pentose phosphate pathway, the Krebs cycle/ glyoxylate shunt and the aerobic oxidative phosphorylation to survive in urine-like media and other conditions. A deep characterization of the oxidative phosphorylation showed that the respiratory rate of stationary phase cells is increased 3-4 times compared to cells in the logarithmic phase of growth, indicating that the aerobic metabolism plays critical roles in the stationary phase of cells grown in urine like media. Moreover, the data show that respiratory complex III, succinate dehydrogenase and the NADH dehydrogenase NQR have important functions and could be used as targets to develop new antibiotics against this bacterium.
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Affiliation(s)
- Yuyao Hu
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, United States
| | - Ming Yuan
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, United States
| | - Alexander Julian
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, United States
| | - Karina Tuz
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, United States
| | - Oscar Juárez
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, United States
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7
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Mawla GD, Kamal SM, Cao LY, Purhonen P, Hebert H, Sauer RT, Baker TA, Römling U. The membrane-cytoplasmic linker defines activity of FtsH proteases in Pseudomonas aeruginosa clone C. J Biol Chem 2024; 300:105622. [PMID: 38176647 PMCID: PMC10850787 DOI: 10.1016/j.jbc.2023.105622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/06/2024] Open
Abstract
Pandemic Pseudomonas aeruginosa clone C strains encode two inner-membrane associated ATP-dependent FtsH proteases. PaftsH1 is located on the core genome and supports cell growth and intrinsic antibiotic resistance, whereas PaftsH2, a xenolog acquired through horizontal gene transfer from a distantly related species, is unable to functionally replace PaftsH1. We show that purified PaFtsH2 degrades fewer substrates than PaFtsH1. Replacing the 31-amino acid-extended linker region of PaFtsH2 spanning from the C-terminal end of the transmembrane helix-2 to the first seven highly divergent residues of the cytosolic AAA+ ATPase module with the corresponding region of PaFtsH1 improves hybrid-enzyme substrate processing in vitro and enables PaFtsH2 to substitute for PaFtsH1 in vivo. Electron microscopy indicates that the identity of this linker sequence influences FtsH flexibility. We find membrane-cytoplasmic (MC) linker regions of PaFtsH1 characteristically glycine-rich compared to those from FtsH2. Consequently, introducing three glycines into the membrane-proximal end of PaFtsH2's MC linker is sufficient to elevate its activity in vitro and in vivo. Our findings establish that the efficiency of substrate processing by the two PaFtsH isoforms depends on MC linker identity and suggest that greater linker flexibility and/or length allows FtsH to degrade a wider spectrum of substrates. As PaFtsH2 homologs occur across bacterial phyla, we hypothesize that FtsH2 is a latent enzyme but may recognize specific substrates or is activated in specific contexts or biological niches. The identity of such linkers might thus play a more determinative role in the functionality of and physiological impact by FtsH proteases than previously thought.
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Affiliation(s)
- Gina D Mawla
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Shady M Kamal
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm; Sweden
| | - Lian-Ying Cao
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm; Sweden
| | - Pasi Purhonen
- Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology, Huddinge; Sweden
| | - Hans Hebert
- Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology, Huddinge; Sweden
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Tania A Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm; Sweden.
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8
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Blanco-Romero E, Garrido-Sanz D, Durán D, Rybtke M, Tolker-Nielsen T, Redondo-Nieto M, Rivilla R, Martín M. Role of extracellular matrix components in biofilm formation and adaptation of Pseudomonas ogarae F113 to the rhizosphere environment. Front Microbiol 2024; 15:1341728. [PMID: 38333580 PMCID: PMC10850567 DOI: 10.3389/fmicb.2024.1341728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/11/2024] [Indexed: 02/10/2024] Open
Abstract
Regulating the transition of bacteria from motile to sessile lifestyles is crucial for their ability to compete effectively in the rhizosphere environment. Pseudomonas are known to rely on extracellular matrix (ECM) components for microcolony and biofilm formation, allowing them to adapt to a sessile lifestyle. Pseudomonas ogarae F113 possesses eight gene clusters responsible for the production of ECM components. These gene clusters are tightly regulated by AmrZ, a major transcriptional regulator that influences the cellular levels of c-di-GMP. The AmrZ-mediated transcriptional regulation of ECM components is primarily mediated by the signaling molecule c-di-GMP and the flagella master regulator FleQ. To investigate the functional role of these ECM components in P. ogarae F113, we performed phenotypic analyses using mutants in genes encoding these ECM components. These analyses included assessments of colony morphology, dye-staining, static attachment to abiotic surfaces, dynamic biofilm formation on abiotic surfaces, swimming motility, and competitive colonization assays of the rhizosphere. Our results revealed that alginate and PNAG polysaccharides, along with PsmE and the fimbrial low molecular weight protein/tight adherence (Flp/Tad) pilus, are the major ECM components contributing to biofilm formation. Additionally, we found that the majority of these components and MapA are needed for a competitive colonization of the rhizosphere in P. ogarae F113.
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Affiliation(s)
- Esther Blanco-Romero
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Daniel Garrido-Sanz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - David Durán
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Morten Rybtke
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Miguel Redondo-Nieto
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Rafael Rivilla
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta Martín
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
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9
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Benigno V, Carraro N, Sarton-Lohéac G, Romano-Bertrand S, Blanc DS, van der Meer JR. Diversity and evolution of an abundant ICE clc family of integrative and conjugative elements in Pseudomonas aeruginosa. mSphere 2023; 8:e0051723. [PMID: 37902330 PMCID: PMC10732049 DOI: 10.1128/msphere.00517-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 09/24/2023] [Indexed: 10/31/2023] Open
Abstract
IMPORTANCE Microbial populations swiftly adapt to changing environments through horizontal gene transfer. While the mechanisms of gene transfer are well known, the impact of environmental conditions on the selection of transferred gene functions remains less clear. We investigated ICEs, specifically the ICEclc-type, in Pseudomonas aeruginosa clinical isolates. Our findings revealed co-evolution between ICEs and their hosts, with ICE transfers occurring within strains. Gene functions carried by ICEs are positively selected, including potential virulence factors and heavy metal resistance. Comparison to publicly available P. aeruginosa genomes unveiled widespread antibiotic-resistance determinants within ICEclc clades. Thus, the ubiquitous ICEclc family significantly contributes to P. aeruginosa's adaptation and fitness in diverse environments.
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Affiliation(s)
- Valentina Benigno
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Garance Sarton-Lohéac
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sara Romano-Bertrand
- Hydrosciences Montpellier, IRD, CNRS, University of Montpellier, Hospital Hygiene and Infection Control Team, University Hospital of Montpellier, Montpellier, France
| | - Dominique S. Blanc
- Prevention and Infection Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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10
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Olaniran OB, Donia A, Adeleke OE, Bokhari H. Prevalence of Type III Secretion System (T3SS) and Biofilm Development in Genetically Heterogeneous Clinical Isolates of Pseudomonas aeruginosa from Nigeria. Curr Microbiol 2023; 80:349. [PMID: 37733140 DOI: 10.1007/s00284-023-03467-x] [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: 10/19/2022] [Accepted: 09/01/2023] [Indexed: 09/22/2023]
Abstract
Pseudomonas aeruginosa infection in seriously ill patients is a major concern due to its ability to form biofilm and secrete effector toxins. There is little information on the prevalence of T3SS effector toxins and biofilm production in clinical isolates of P. aeruginosa from Nigeria. The goal of this study is to evaluate the prevalence of T3SS toxins and biofilm production among isolates from selected tertiary hospitals in Nigeria. This study examined 430 clinical isolates from our previous work, comprising 181 MDR (multidrug-resistant) and 249 non-MDR isolates. Biofilm production and type III secretion toxins were determined using colorimetric microtiter plate assay and polymerase chain reaction, respectively. Carbapenem-resistant isolates were typed using REP-PCR and BOX-PCR. Biofilm production was detected in 386/430 (89.8%) of the isolates. Out of 386 biofilm producers, 167 (43.3%) were multidrug-resistant isolates. PCR identified four T3SS virulence types among 430 isolates, including 78 (18.1%) exoU+/exoS- isolates, 343 (79.8%) exoU-/exoS + isolates, 5 (1.2%) exoU+/exoS + isolates, and 4 (0.9%) exoU-/exoS- isolates. Both REP- and BOX-PCR consist of eight clusters. On the REP-PCR dendrogram, ExoU+/ExoS- isolates majorly occupied cluster IV. Clusters IV, VII, and VIII consist of isolates from wounds on BOX-PCR dendrogram. There was a positive association between strong biofilm production and multidrug resistance in our P. aeruginosa isolates. This study identified multidrug-resistant, biofilm-producing P. aeruginosa strains that secrete cytotoxic effectors which are significant virulence factors in P. aeruginosa. This poses a severe risk to our healthcare system and highlights the importance of continuous surveillance to prevent infectious disease outbreaks.
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Affiliation(s)
- Oluwatoyin B Olaniran
- Department of Pharmaceutical Microbiology, Olabisi Onabanjo University, Ago-Iwoye, Nigeria
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
| | - Ahmed Donia
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
| | - Olufemi E Adeleke
- Department of Pharmaceutical Microbiology, University of Ibadan, Ibadan, Nigeria
| | - Habib Bokhari
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan.
- Kohsar University Murree, Murree, Pakistan.
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Büttner H, Hörl J, Krabbe J, Hertweck C. Discovery and Biosynthesis of Anthrochelin, a Growth-Promoting Metallophore of the Human Pathogen Luteibacter anthropi. Chembiochem 2023; 24:e202300322. [PMID: 37191164 DOI: 10.1002/cbic.202300322] [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: 04/24/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/17/2023]
Abstract
Various human pathogens have emerged from environmental strains by adapting to higher growth temperatures and the ability to produce virulence factors. A remarkable example of a pathoadapted bacterium is found in the genus Luteibacter, which typically comprises harmless soil microbes, yet Luteibacter anthropi was isolated from the blood of a diseased child. Up until now, nothing has been known about the specialized metabolism of this pathogen. By comparative genome analyses we found that L. anthropi has a markedly higher biosynthetic potential than other bacteria of this genus and uniquely bears an NRPS gene locus tentatively coding for the biosynthesis of a metallophore. By metabolic profiling, stable isotope labeling, and NMR investigation of a gallium complex, we identified a new family of salicylate-derived nonribosomal peptides named anthrochelins A-D. Surprisingly, anthrochelins feature a C-terminal homocysteine tag, which might be introduced during peptide termination. Mutational analyses provided insight into the anthrochelin assembly and revealed the unexpected involvement of a cytochrome P450 monooxygenase in oxazole formation. Notably, this heterocycle plays a key role in the binding of metals, especially copper(II). Bioassays showed that anthrochelin significantly promotes the growth of L. anthropi in the presence of low and high copper concentrations, which occur during infections.
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Affiliation(s)
- Hannah Büttner
- Leibniz Institute for Natural Product Research and Infection, Biology, HKI, Dept. of Biomolecular Chemistry, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Johannes Hörl
- Leibniz Institute for Natural Product Research and Infection, Biology, HKI, Dept. of Biomolecular Chemistry, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Jana Krabbe
- Leibniz Institute for Natural Product Research and Infection, Biology, HKI, Dept. of Biomolecular Chemistry, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection, Biology, HKI, Dept. of Biomolecular Chemistry, Beutenbergstrasse 11a, 07745, Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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Botelho J, Tüffers L, Fuss J, Buchholz F, Utpatel C, Klockgether J, Niemann S, Tümmler B, Schulenburg H. Phylogroup-specific variation shapes the clustering of antimicrobial resistance genes and defence systems across regions of genome plasticity in Pseudomonas aeruginosa. EBioMedicine 2023; 90:104532. [PMID: 36958270 PMCID: PMC10053402 DOI: 10.1016/j.ebiom.2023.104532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Pseudomonas aeruginosa is an opportunistic pathogen consisting of three phylogroups (hereafter named A, B, and C). Here, we assessed phylogroup-specific evolutionary dynamics across available and also new P. aeruginosa genomes. METHODS In this genomic analysis, we first generated new genome assemblies for 18 strains of the major P. aeruginosa clone type (mPact) panel, comprising a phylogenetically diverse collection of clinical and environmental isolates for this species. Thereafter, we combined these new genomes with 1991 publicly available P. aeruginosa genomes for a phylogenomic and comparative analysis. We specifically explored to what extent antimicrobial resistance (AMR) genes, defence systems, and virulence genes vary in their distribution across regions of genome plasticity (RGPs) and "masked" (RGP-free) genomes, and to what extent this variation differs among the phylogroups. FINDINGS We found that members of phylogroup B possess larger genomes, contribute a comparatively larger number of pangenome families, and show lower abundance of CRISPR-Cas systems. Furthermore, AMR and defence systems are pervasive in RGPs and integrative and conjugative/mobilizable elements (ICEs/IMEs) from phylogroups A and B, and the abundance of these cargo genes is often significantly correlated. Moreover, inter- and intra-phylogroup interactions occur at the accessory genome level, suggesting frequent recombination events. Finally, we provide here the mPact panel of diverse P. aeruginosa strains that may serve as a valuable reference for functional analyses. INTERPRETATION Altogether, our results highlight distinct pangenome characteristics of the P. aeruginosa phylogroups, which are possibly influenced by variation in the abundance of CRISPR-Cas systems and are shaped by the differential distribution of other defence systems and AMR genes. FUNDING German Science Foundation, Max-Planck Society, Leibniz ScienceCampus Evolutionary Medicine of the Lung, BMBF program Medical Infection Genomics, Kiel Life Science Postdoc Award.
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Affiliation(s)
- João Botelho
- Antibiotic Resistance Group, Max-Planck Institute for Evolutionary Biology, Plön, Germany; Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany.
| | - Leif Tüffers
- Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany; Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Janina Fuss
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Florian Buchholz
- Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Jens Klockgether
- Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Hannover, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Burkhard Tümmler
- Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Hinrich Schulenburg
- Antibiotic Resistance Group, Max-Planck Institute for Evolutionary Biology, Plön, Germany; Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany.
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Special Issue: “Antimicrobial Resistance in Pseudomonas aeruginosa”. Microorganisms 2023; 11:microorganisms11030744. [PMID: 36985317 PMCID: PMC10056382 DOI: 10.3390/microorganisms11030744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 03/15/2023] Open
Abstract
Pseudomonas aeruginosa is one of the most prevalent pathogens causing nosocomial infections, mainly in patients presenting with basal pathologies or those who are immunocompromised [...]
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Garza-Ramos U, Rodríguez-Medina N, Córdova-Fletes C, Rubio-Mendoza D, Alonso-Hernández CJ, López-Jácome LE, Morfín-Otero R, Rodríguez-Noriega E, Rojas-Larios F, Vázquez-Larios MDR, Ponce-de-Leon A, Choy-Chang EV, Franco-Cendejas R, Martinez-Guerra BA, Morales-de-La-Peña CT, Mena-Ramírez JP, López-Gutiérrez E, García-Romo R, Ballesteros-Silva B, Valadez-Quiroz A, Avilés-Benítez LK, Feliciano-Guzmán JM, Pérez-Vicelis T, Velázquez-Acosta MDC, Padilla-Ibarra C, López-Moreno LI, Corte-Rojas RE, Couoh-May CA, Quevedo-Ramos MA, López-García M, Chio-Ortiz G, Gil-Veloz M, Molina-Chavarria A, Mora-Domínguez JP, Romero-Romero D, May-Tec FJ, Garza-González E. Whole genome analysis of Gram-negative bacteria using the EPISEQ CS application and other bioinformatic platforms. J Glob Antimicrob Resist 2023; 33:61-71. [PMID: 36878463 DOI: 10.1016/j.jgar.2023.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/23/2023] [Accepted: 02/26/2023] [Indexed: 03/07/2023] Open
Abstract
OBJECTIVES To determine genomic characteristics and molecular epidemiology of carbapenem non-susceptible Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa from medical centres of Mexico using whole genome sequencing data analysed with the EPISEQⓇ CS application and other bioinformatic platforms. METHODS Clinical isolates collected from 28 centres in Mexico included carbapenem-non-susceptible K. pneumoniae (n = 22), E. coli (n = 24), A. baumannii (n = 16), and P. aeruginosa (n = 13). Isolates were subjected to whole genome sequencing using the Illumina (MiSeq) platform. FASTQ files were uploaded to the EPISEQⓇ CS application for analysis. Additionally, the tools Kleborate v2.0.4 and Pathogenwatch were used as comparators for Klebsiella genomes, and the bacterial whole genome sequence typing database was used for E. coli and A. baumannii. RESULTS For K. pneumoniae, both bioinformatic approaches detected multiple genes encoding aminoglycoside, quinolone, and phenicol resistance, and the presence of blaNDM-1 explained carbapenem non-susceptibility in 18 strains and blaKPC-3 in four strains. Regarding E. coli, both EPISEQⓇ CS and bacterial whole genome sequence typing database analyses detected multiple virulence and resistance genes: 20 of 24 (83.3%) strains carried blaNDM, 3 of 24 (12.4%) carried blaOXA-232, and 1 carried blaOXA-181. Genes that confer resistance to aminoglycosides, tetracyclines, sulfonamides, phenicols, trimethoprim, and macrolides were also detected by both platforms. Regarding A. baumannii, the most frequent carbapenemase-encoding gene detected by both platforms was blaOXA-72, followed by blaOXA-66. Both approaches detected similar genes for aminoglycosides, carbapenems, tetracyclines, phenicols, and sulfonamides. Regarding P. aeruginosa, blaVIM, blaIMP, and blaGES were the more frequently detected. Multiple virulence genes were detected in all strains. CONCLUSION Compared to the other available platforms, EPISEQⓇ CS enabled a comprehensive resistance and virulence analysis, providing a reliable method for bacterial strain typing and characterization of the virulome and resistome.
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Affiliation(s)
| | | | | | - Daira Rubio-Mendoza
- Facultad de Medicina, Universidad Autónoma de Nuevo León, Nuevo León, Mexico
| | | | | | - Rao Morfín-Otero
- Hospital Civil de Guadalajara Fray Antonio Alcalde, Universidad de Guadalajara, Jalisco, Mexico
| | | | | | | | - Alfredo Ponce-de-Leon
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de Mexico, Mexico
| | | | | | | | | | - Juan Pablo Mena-Ramírez
- Hospital General de Zona No. 21, IMSS. Centro Universitario de los Altos, Universidad de Guadalajara. Jalisco, Mexico
| | | | | | | | | | | | | | - Talia Pérez-Vicelis
- Hospital Regional de alta especialidad Bicentenario de la independencia, Estado de México, Mexico
| | | | | | | | | | | | | | | | | | - Mariana Gil-Veloz
- Hospital Regional de Alta Especialidad del Bajío, Guanajuato, Mexico
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Moreau A, Mukherjee S, Yan J. Mechanical Characterization and Single‐Cell Imaging of Bacterial Biofilms. Isr J Chem 2023. [DOI: 10.1002/ijch.202200075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Alexis Moreau
- Department of Molecular, Cellular and Developmental Biology, Quantitative Biology Institute Yale University 260 Whitney Ave. New Haven CT 06511 USA
| | - Sampriti Mukherjee
- Department of Molecular Genetics & Cell Biology University of Chicago 920 E. 58th Street, Suite 1106 Chicago IL 60637
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Quantitative Biology Institute Yale University 260 Whitney Ave. New Haven CT 06511 USA
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Selection of Relevant Bacterial Strains for Novel Therapeutic Testing: a Guidance Document for Priority Cystic Fibrosis Lung Pathogens. CURRENT CLINICAL MICROBIOLOGY REPORTS 2022. [DOI: 10.1007/s40588-022-00182-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Abstract
Purpose of Review
People with cystic fibrosis (CF) suffer chronic lung infections with a range of antimicrobial-resistant bacterial pathogens. There is an urgent need for researchers to develop novel anti-infectives to treat these problematic infections, but how can we select bacterial strains which are relevant for robust testing and comparative research?
Recent Findings
Pseudomonas aeruginosa, Burkholderia cepacia complex and Burkholderia gladioli, Mycobacterium abscessus complex, Staphylococcus aureus, Haemophilus influenza, and several multidrug-resistant Gram-negative species were selected as key CF infections that urgently require new therapeutics. Reference isolates and strain panels were identified, and a summary of the known genotypic diversity of each pathogen was provided.
Summary
Here, we summarise the current strain resources available for priority CF bacterial pathogens and highlight systematic selection criteria that researchers can use to select strains for use in therapeutic testing.
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Phylogenetic analysis and characterization of arsenic (As) transforming bacterial marker proteins following isolation of As-tolerant indigenous bacteria. Arch Microbiol 2022; 204:660. [PMID: 36190579 DOI: 10.1007/s00203-022-03270-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/01/2022] [Accepted: 09/22/2022] [Indexed: 11/02/2022]
Abstract
Marker proteins play a significant role in bacterial arsenic (As) transformation. Phylogenetic analysis and three-dimensional (3D) characteristics of As transforming bacterial marker proteins guide the evolutionary origin and As transforming potential of the species. Indeed, As-tolerant bacteria also show a significant level of As transformation. Hence, characterization of As transforming bacterial marker proteins, isolation of As transforming bacteria, and proper integration of the findings may guide to elucidate how bacteria transform As. Therefore, phylogenetic analysis and 3D characterization of As transforming bacterial marker protein following isolation of potential indigenous As-tolerant indigenous bacteria were done to explore the mechanism of bacterial As transformation. Phylogenetic analysis of ten As transforming marker proteins (arsA, arsB, arsC, arsD, arsR, aioA, arrA, aioB, acr1, and acr3) in 20 potential bacterial genomes (except 19 for the acr3) were studied. Some bacterial genomes featured up to five marker proteins, and therefore, 3D characteristics of the marker proteins were analyzed in those genomes having three-to-five marker proteins. In phylogeny, species in close clades represent their phylogenetic resemblances and may have similar functions. P. aeruginosa, E. coli, and K. pneumonia were found to be more effective due to having the highest number (five) of marker proteins. In 3D protein modeling, most of the marker proteins were found to be active. Among 19 indigenous bacterial isolates, multiple isolates showed tolerance up to 50 mM As(III) and 250 mM As(V), which may potentially transform a significant quantities of As. Hence, integration of the results of phylogenetic analysis, 3D protein characteristics, and As tolerance in the bacterial isolates could guide to explore the mechanism of how bacteria transform As at cellular and molecular levels.
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Sun Y, Shao X, Zhang Y, Han L, Huang J, Xie Y, Liu J, Deng X. Maintenance of tRNA and elongation factors supports T3SS proteins translational elongations in pathogenic bacteria during nutrient starvation. Cell Biosci 2022; 12:147. [PMID: 36064743 PMCID: PMC9446538 DOI: 10.1186/s13578-022-00884-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/13/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Sufficient nutrition contributes to rapid translational elongation and protein synthesis in eukaryotic cells and prokaryotic bacteria. Fast synthesis and accumulation of type III secretion system (T3SS) proteins conduce to the invasion of pathogenic bacteria into the host cells. However, the translational elongation patterns of T3SS proteins in pathogenic bacteria under T3SS-inducing conditions remain unclear. Here, we report a mechanism of translational elongation of T3SS regulators, effectors and structural protein in four model pathogenic bacteria (Pseudomonas syringae, Pseudomonas aeruginosa, Xanthomonas oryzae and Ralstonia solanacearum) and a clinical isolate (Pseudomonas aeruginosa UCBPP-PA14) under nutrient-limiting conditions. We proposed a luminescence reporter system to quantitatively determine the translational elongation rates (ERs) of T3SS regulators, effectors and structural protein under different nutrient-limiting conditions and culture durations.
Results
The translational ERs of T3SS regulators, effectors and structural protein in these pathogenic bacteria were negatively regulated by the nutrient concentration and culture duration. The translational ERs in 0.5× T3SS-inducing medium were the highest of all tested media. In 1× T3SS-inducing medium, the translational ERs were highest at 0 min and then rapidly decreased. The translational ERs of T3SS regulators, effectors and structural protein were inhibited by tRNA degradation and by reduced levels of elongation factors (EFs).
Conclusions
Rapid translational ER and synthesis of T3SS protein need adequate tRNAs and EFs in nutrient-limiting conditions. Numeric presentation of T3SS translation visually indicates the invasion of bacteria and provides new insights into T3SS expression that can be applied to other pathogenic bacteria.
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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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Secondary Metabolites Produced during Aspergillus fumigatus and Pseudomonas aeruginosa Biofilm Formation. mBio 2022; 13:e0185022. [PMID: 35856657 PMCID: PMC9426470 DOI: 10.1128/mbio.01850-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In cystic fibrosis (CF), mucus plaques are formed in the patient's lungs, creating a hypoxic condition and a propitious environment for colonization and persistence of many microorganisms. There is clinical evidence showing that Aspergillus fumigatus can cocolonize CF patients with Pseudomonas aeruginosa, which has been associated with lung function decline. P. aeruginosa produces several compounds with inhibitory and antibiofilm effects against A. fumigatus in vitro; however, little is known about the fungal compounds produced in counterattack. Here, we annotated fungal and bacterial secondary metabolites (SM) produced in mixed biofilms under normoxia and hypoxia conditions. We detected nine SM produced by P. aeruginosa. Phenazines and different analogs of pyoverdin were the main compounds produced by P. aeruginosa, and their secretion levels were increased by the fungal presence. The roles of the two operons responsible for phenazine production (phzA1 and phzA2) were also investigated, and mutants lacking one of those operons were able to produce partial sets of phenazines. We detected a total of 20 SM secreted by A. fumigatus either in monoculture or in coculture with P. aeruginosa. All these compounds were secreted during biofilm formation in either normoxia or hypoxia. However, only eight compounds (demethoxyfumitremorgin C, fumitremorgin, ferrichrome, ferricrocin, triacetylfusigen, gliotoxin, gliotoxin E, and pyripyropene A) were detected during biofilm formation by the coculture of A. fumigatus and P. aeruginosa under normoxia and hypoxia conditions. Overall, we showed how diverse SM secretion is during A. fumigatus and P. aeruginosa mixed culture and how this can affect biofilm formation in normoxia and hypoxia. IMPORTANCE The interaction between Pseudomonas aeruginosa and Aspergillus fumigatus has been well characterized in vitro. In this scenario, the bacterium exerts a strong inhibitory effect against the fungus. However, little is known about the metabolites produced by the fungus to counterattack the bacteria. Our work aimed to annotate secondary metabolites (SM) secreted during coculture between P. aeruginosa and A. fumigatus during biofilm formation in both normoxia and hypoxia. The bacterium produces several different types of phenazines and pyoverdins in response to presence of the fungus. In contrast, we were able to annotate 29 metabolites produced during A. fumigatus biofilm formation, but only 8 compounds were detected during biofilm formation by the coculture of A. fumigatus and P. aeruginosa upon either normoxia or hypoxia. In conclusion, we detected many SM secreted during A. fumigatus and P. aeruginosa biofilm formation. This analysis provides several opportunities to understand the interactions between these two species.
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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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22
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Fischer S, Klockgether J, Gonzalez Sorribes M, Dorda M, Wiehlmann L, Tümmler B. Sequence diversity of the Pseudomonas aeruginosa population in loci that undergo microevolution in cystic fibrosis airways. Access Microbiol 2022; 3:000286. [PMID: 35024551 PMCID: PMC8749138 DOI: 10.1099/acmi.0.000286] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/04/2021] [Indexed: 12/23/2022] Open
Abstract
Five hundred and thirty-four unrelated Pseudomonas aeruginosa isolates from inanimate habitats, patients with cystic fibrosis (CF) and other human infections were sequenced in 19 genes that had been identified previously as the hot spots of genomic within-host evolution in serial isolates from 12 CF lungs. Amplicon sequencing confirmed a significantly higher sequence diversity of the 19 loci in P. aeruginosa isolates from CF patients compared to those from other habitats, but this overrepresentation was mainly due to the larger share of synonymous substitutions. Correspondingly, non-synonymous substitutions were either rare (gltT, lepA, ptsP) or benign (nuoL, fleR, pelF) in some loci. Other loci, however, showed an accumulation of non-neutral coding variants. Strains from the CF habitat were often mutated at evolutionarily conserved positions in the elements of stringent response (RelA, SpoT), LPS (PagL), polyamine transport (SpuE, SpuF) and alginate biosynthesis (AlgG, AlgU). The strongest skew towards the CF lung habitat was seen for amino acid sequence variants in AlgG that clustered in the carbohydrate-binding/sugar hydrolysis domain. The master regulators of quorum sensing lasR and rhlR were frequent targets for coding variants in isolates from chronic and acute human infections. Unique variants in lasR showed strong evidence of positive selection indicated by d N/d S values of ~4. The pelA gene that encodes a multidomain enzyme involved in both the formation and dispersion of Pel biofilms carried the highest number of single-nucleotide variants among the 19 genes and was the only gene with a higher frequency of missense mutations in P. aeruginosa strains from non-CF habitats than in isolates from CF airways. PelA protein variants are widely distributed in the P. aeruginosa population. In conclusion, coding variants in a subset of the examined loci are indeed characteristic for the adaptation of P. aeruginosa to the CF airways, but for other loci the elevated mutation rate is more indicative of infections in human habitats (lasR, rhlR) or global diversifying selection (pelA).
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Affiliation(s)
- Sebastian Fischer
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Department for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Jens Klockgether
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Department for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Marina Gonzalez Sorribes
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Department for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany.,Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Marie Dorda
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Department for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany.,Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Lutz Wiehlmann
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Department for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany.,Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis', Department for Paediatric 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, Germany
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23
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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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24
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Transcriptional Profiling of Pseudomonas aeruginosa Infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:303-323. [DOI: 10.1007/978-3-031-08491-1_11] [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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25
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Yi B, Dalpke AH. Revisiting the intrageneric structure of the genus Pseudomonas with complete whole genome sequence information: Insights into diversity and pathogen-related genetic determinants. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 97:105183. [PMID: 34920102 DOI: 10.1016/j.meegid.2021.105183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 08/09/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Pseudomonas spp. exhibit considerable differences in host specificity and virulence. Most Pseudomonas species were isolated exclusively from environmental sources, ranging from soil to plants, but some Pseudomonas species have been detected from versatile sources, including both human host and environmental sources. Understanding genome variations that generate the tremendous diversity in Pseudomonas biology is important in controlling the incidence of infections. With a data set of 704 Pseudomonas complete whole genome sequences representing 186 species, Pseudomonas intrageneric structure was investigated by hierarchical clustering based on average nucleotide identity, and by phylogeny analysis based on concatenated core-gene alignment. Further comparative functional analyses indicated that Pseudomonas species only living in natural habitats lack multiple functions that are important in the regulation of bacterial pathogenesis, indicating the possession of these functions might be characteristic of Pseudomonas human pathogens. Moreover, we have performed pan-genome based homogeneity analyses, and detected genes with conserved structures but diversified functions across the Pseudomonas genomes, suggesting these genes play a role in driving diversity. In summary, this study provided insights into the dynamics of genome diversity and pathogen-related genetic determinants in Pseudomonas, which might help the development of more targeted antibiotics for the treatment of Pseudomonas infections.
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Affiliation(s)
- Buqing Yi
- Institute of Medical Microbiology and Virology, Medical Faculty, Technische Universität Dresden, Dresden, Germany.
| | - Alexander H Dalpke
- Institute of Medical Microbiology and Virology, Medical Faculty, Technische Universität Dresden, Dresden, Germany.
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26
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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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27
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Laborda P, Sanz-García F, Hernando-Amado S, Martínez JL. Pseudomonas aeruginosa: an antibiotic resilient pathogen with environmental origin. Curr Opin Microbiol 2021; 64:125-132. [PMID: 34710741 DOI: 10.1016/j.mib.2021.09.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/31/2021] [Accepted: 09/23/2021] [Indexed: 12/24/2022]
Abstract
Pseudomonas aeruginosa, a bacterium characterized for its low antibiotics' susceptibility, is one of the most relevant opportunistic pathogens, causing infections at hospitals and in cystic fibrosis patients. Besides its relevance for human health, P. aeruginosa colonizes environmental ecosystems; therefore the elements driving its infectivity and antibiotic resistance must be analyzed from a One-Health perspective. Although some epidemic clones have been described, there are not specific lineages linked to infections, suggesting that P. aeruginosa virulence and antibiotic resistance determinants evolved in nature to play functions other than infecting the human host and avoiding antimicrobial treatment. Herein, we review current information on the population structure of P. aeruginosa and on the functional role that its resistance and virulence determinants have in non-clinical ecosystems.
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Affiliation(s)
- Pablo Laborda
- Centro Nacional de Biotecnología, CSIC, 28049, Madrid, Spain
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28
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Fraser-Pitt DJ, Dolan SK, Toledo-Aparicio D, Hunt JG, Smith DW, Lacy-Roberts N, Nupe Hewage PS, Stoyanova TN, Manson E, McClean K, Inglis NF, Mercer DK, O'Neil DA. Cysteamine Inhibits Glycine Utilisation and Disrupts Virulence in Pseudomonas aeruginosa. Front Cell Infect Microbiol 2021; 11:718213. [PMID: 34631600 PMCID: PMC8494450 DOI: 10.3389/fcimb.2021.718213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa is a major opportunistic human pathogen which employs a myriad of virulence factors. In people with cystic fibrosis (CF) P. aeruginosa frequently colonises the lungs and becomes a chronic infection that evolves to become less virulent over time, but often adapts to favour persistence in the host with alginate-producing mucoid, slow-growing, and antibiotic resistant phenotypes emerging. Cysteamine is an endogenous aminothiol which has been shown to prevent biofilm formation, reduce phenazine production, and potentiate antibiotic activity against P. aeruginosa, and has been investigated in clinical trials as an adjunct therapy for pulmonary exacerbations of CF. Here we demonstrate (for the first time in a prokaryote) that cysteamine prevents glycine utilisation by P. aeruginosa in common with previously reported activity blocking the glycine cleavage system in human cells. Despite the clear inhibition of glycine metabolism, cysteamine also inhibits hydrogen cyanide (HCN) production by P. aeruginosa, suggesting a direct interference in the regulation of virulence factor synthesis. Cysteamine impaired chemotaxis, lowered pyocyanin, pyoverdine and exopolysaccharide production, and reduced the toxicity of P. aeruginosa secreted factors in a Galleria mellonella infection model. Thus, cysteamine has additional potent anti-virulence properties targeting P. aeruginosa, further supporting its therapeutic potential in CF and other infections.
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Affiliation(s)
| | - Stephen K Dolan
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | | | | | | | | | - Piumi Sara Nupe Hewage
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, United Kingdom
| | - Teodora N Stoyanova
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, United Kingdom
| | - Erin Manson
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Kevin McClean
- Proteomics Facility Services, Moredun Research Institute, Penicuik, United Kingdom
| | - Neil F Inglis
- Proteomics Facility Services, Moredun Research Institute, Penicuik, United Kingdom
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29
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Muthukumarasamy U, Preusse M, Kordes A, Koska M, Schniederjans M, Khaledi A, Häussler S. Single-Nucleotide Polymorphism-Based Genetic Diversity Analysis of Clinical Pseudomonas aeruginosa Isolates. Genome Biol Evol 2021; 12:396-406. [PMID: 32196089 PMCID: PMC7197496 DOI: 10.1093/gbe/evaa059] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2020] [Indexed: 01/26/2023] Open
Abstract
Extensive use of next-generation sequencing has the potential to transform our knowledge on how genomic variation within bacterial species impacts phenotypic versatility. Because different environments have unique selection pressures, they drive divergent evolution. However, there is also parallel or convergent evolution of traits in independent bacterial isolates inhabiting similar environments. The application of tools to describe population-wide genomic diversity provides an opportunity to measure the predictability of genetic changes underlying adaptation. Here, we describe patterns of sequence variations in the core genome among 99 individual Pseudomonas aeruginosa clinical isolates and identified single-nucleotide polymorphisms that are the basis for branching of the phylogenetic tree. We also identified single-nucleotide polymorphisms that were acquired independently, in separate lineages, and not through inheritance from a common ancestor. Although our results demonstrate that the Pseudomonas aeruginosa core genome is highly conserved and in general, not subject to adaptive evolution, instances of parallel evolution will provide an opportunity to uncover genetic changes that underlie phenotypic diversity.
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Affiliation(s)
- Uthayakumar Muthukumarasamy
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, Hannover, Germany
| | - Matthias Preusse
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, Hannover, Germany
| | - Adrian Kordes
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, Hannover, Germany
| | - Michal Koska
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, Hannover, Germany
| | - Monika Schniederjans
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, Hannover, Germany
| | - Ariane Khaledi
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, Hannover, Germany
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, Hannover, Germany
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30
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Reales-Calderón JA, Sun Z, Mascaraque V, Pérez-Navarro E, Vialás V, Deutsch EW, Moritz RL, Gil C, Martínez JL, Molero G. A wide-ranging Pseudomonas aeruginosa PeptideAtlas build: A useful proteomic resource for a versatile pathogen. J Proteomics 2021; 239:104192. [PMID: 33757883 PMCID: PMC8668395 DOI: 10.1016/j.jprot.2021.104192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/17/2021] [Accepted: 03/10/2021] [Indexed: 01/05/2023]
Abstract
Pseudomonas aeruginosa is an important opportunistic human pathogen with high prevalence in nosocomial infections. This microorganism is a good model for understanding biological processes such as the quorum-sensing response, the metabolic integration of virulence, the mechanisms of global regulation of bacterial physiology, and the evolution of antibiotic resistance. Till now, P. aeruginosa proteomic data, although available in several on-line repositories, were dispersed and difficult to access. In the present work, proteomes of the PAO1 strain grown under different conditions and from diverse cellular compartments have been joined to build the Pseudomonas PeptideAtlas. This resource is a comprehensive mass spectrometry-derived peptide and inferred protein database with 71.3% coverage of the total predicted proteome of P. aeruginosa PAO1, the highest coverage among bacterial PeptideAtlas datasets. The proteins included cover 89% of metabolic proteins, 72% of proteins involved in genetic information processing, 83% of proteins responsible for environmental information processing, more than 88% of the ones related to quorum sensing and biofilm formation, and 89% of proteins responsible for antimicrobial resistance. It exemplifies a necessary tool for targeted proteomics studies, system-wide observations, and cross-species observational studies. The manuscript describes the building of the PeptideAtlas and the contribution of the different proteomic data used. SIGNIFICANCE: Pseudomonas aeruginosa is among the most versatile human bacterial pathogens. Studies of its proteome are very important as they can reveal virulence factors and mechanisms of antibiotic resistance. The construction of a proteomic resource such as the PeptideAtlas enables targeted proteomics studies, system-wide observations, and cross-species observational studies.
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Affiliation(s)
- J A Reales-Calderón
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, Spain
| | - Z Sun
- Institute for Systems Biology, Seattle, WA, USA
| | - V Mascaraque
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, Spain
| | - E Pérez-Navarro
- Unidad de Proteómica de la Universidad Complutense de Madrid, Spain
| | - V Vialás
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, Spain
| | - E W Deutsch
- Institute for Systems Biology, Seattle, WA, USA
| | - R L Moritz
- Institute for Systems Biology, Seattle, WA, USA
| | - C Gil
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, Spain; Unidad de Proteómica de la Universidad Complutense de Madrid, Spain
| | - J L Martínez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - G Molero
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, Spain.
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31
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Pseudomonas aeruginosa: An Audacious Pathogen with an Adaptable Arsenal of Virulence Factors. Int J Mol Sci 2021; 22:ijms22063128. [PMID: 33803907 PMCID: PMC8003266 DOI: 10.3390/ijms22063128] [Citation(s) in RCA: 205] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa is a dominant pathogen in people with cystic fibrosis (CF) contributing to morbidity and mortality. Its tremendous ability to adapt greatly facilitates its capacity to cause chronic infections. The adaptability and flexibility of the pathogen are afforded by the extensive number of virulence factors it has at its disposal, providing P. aeruginosa with the facility to tailor its response against the different stressors in the environment. A deep understanding of these virulence mechanisms is crucial for the design of therapeutic strategies and vaccines against this multi-resistant pathogen. Therefore, this review describes the main virulence factors of P. aeruginosa and the adaptations it undergoes to persist in hostile environments such as the CF respiratory tract. The very large P. aeruginosa genome (5 to 7 MB) contributes considerably to its adaptive capacity; consequently, genomic studies have provided significant insights into elucidating P. aeruginosa evolution and its interactions with the host throughout the course of infection.
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32
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Lee C, Klockgether J, Fischer S, Trcek J, Tümmler B, Römling U. Why? - Successful Pseudomonas aeruginosa clones with a focus on clone C. FEMS Microbiol Rev 2021; 44:740-762. [PMID: 32990729 PMCID: PMC7685784 DOI: 10.1093/femsre/fuaa029] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/12/2020] [Indexed: 12/20/2022] Open
Abstract
The environmental species Pseudomonas aeruginosa thrives in a variety of habitats. Within the epidemic population structure of P. aeruginosa, occassionally highly successful clones that are equally capable to succeed in the environment and the human host arise. Framed by a highly conserved core genome, individual members of successful clones are characterized by a high variability in their accessory genome. The abundance of successful clones might be funded in specific features of the core genome or, although not mutually exclusive, in the variability of the accessory genome. In clone C, one of the most predominant clones, the plasmid pKLC102 and the PACGI-1 genomic island are two ubiquitous accessory genetic elements. The conserved transmissible locus of protein quality control (TLPQC) at the border of PACGI-1 is a unique horizontally transferred compository element, which codes predominantly for stress-related cargo gene products such as involved in protein homeostasis. As a hallmark, most TLPQC xenologues possess a core genome equivalent. With elevated temperature tolerance as a characteristic of clone C strains, the unique P. aeruginosa and clone C specific disaggregase ClpG is a major contributor to tolerance. As other successful clones, such as PA14, do not encode the TLPQC locus, ubiquitous denominators of success, if existing, need to be identified.
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Affiliation(s)
- Changhan Lee
- Department of Microbiology, Tumor and Cell Biology, Biomedicum C8, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Jens Klockgether
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover Medical School, D-30625 Hannover, Germany
| | - Sebastian Fischer
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover Medical School, D-30625 Hannover, Germany
| | - Janja Trcek
- Faculty of Natural Sciences and Mathematics, Department of Biology, University of Maribor, Maribor, 2000, Slovenia
| | - Burkhard Tümmler
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover Medical School, D-30625 Hannover, Germany
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Biomedicum C8, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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33
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Camus L, Vandenesch F, Moreau K. From genotype to phenotype: adaptations of Pseudomonas aeruginosa to the cystic fibrosis environment. Microb Genom 2021; 7:mgen000513. [PMID: 33529147 PMCID: PMC8190622 DOI: 10.1099/mgen.0.000513] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa is one of the main microbial species colonizing the lungs of cystic fibrosis patients and is responsible for the decline in respiratory function. Despite the hostile pulmonary environment, P. aeruginosa is able to establish chronic infections thanks to its strong adaptive capacity. Various longitudinal studies have attempted to compare the strains of early infection with the adapted strains of chronic infection. Thanks to new '-omics' techniques, convergent genetic mutations, as well as transcriptomic and proteomic dysregulations have been identified. As a consequence of this evolution, the adapted strains of P. aeruginosa have particular phenotypes that promote persistent infection.
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Affiliation(s)
- Laura Camus
- CIRI – Centre International de Recherche en Infectiologie, Université de Lyon/Inserm U1111/Université Claude Bernard Lyon 1/CNRS UMR5308/ENS de Lyon, Lyon, France
| | - François Vandenesch
- CIRI – Centre International de Recherche en Infectiologie, Université de Lyon/Inserm U1111/Université Claude Bernard Lyon 1/CNRS UMR5308/ENS de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Karen Moreau
- CIRI – Centre International de Recherche en Infectiologie, Université de Lyon/Inserm U1111/Université Claude Bernard Lyon 1/CNRS UMR5308/ENS de Lyon, Lyon, France
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34
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Xu M, Wang F, Sheng H, Stedtfeld RD, Li Z, Hashsham SA, Jiang X, Tiedje JM. Does anaerobic condition play a more positive role in dissipation of antibiotic resistance genes in soil? THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143737. [PMID: 33243511 DOI: 10.1016/j.scitotenv.2020.143737] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 06/11/2023]
Abstract
The persistence of antibiotic resistance genes (ARGs) under the aerobic vs. anaerobic conditions is unknown, especially under different fertilization. Towards this goal, a microcosm experiment was carried out with chemical fertilized and manured soil under aerobic and anaerobic conditions. High throughput qPCR was used to analyze ARGs with 144 primer sets and sequencing for microorganisms. Completely different dynamics of ARGs were observed in soil under aerobic and anaerobic conditions, regardless of the fertilization type. ARGs had different half-lives, even though they confer resistance to the same type of antibiotics. Aminoglycoside, chloramphenicol, macrolide - lincosamide - streptogramin B (MLSB) and tetracycline resistance genes were significantly accumulated in the aerobic soils. Anaerobic soil possessed a higher harboring capacity for exogenous microorganisms and ARGs than aerobic soil. The interaction between ARGs and mobile genetic elements (MGEs) in manured soil under aerobic condition was more pronounced than the anaerobic condition. These findings unveil that anaerobic soil could play a more positive role in reducing potential risk of ARGs in the farmland environment.
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Affiliation(s)
- Min Xu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA.
| | - Hongjie Sheng
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA
| | - Zhongpei Li
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA
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35
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Shmidov E, Zander I, Lebenthal-Loinger I, Karako-Lampert S, Shoshani S, Banin E. An Efficient, Counter-Selection-Based Method for Prophage Curing in Pseudomonas aeruginosa Strains. Viruses 2021; 13:v13020336. [PMID: 33670076 PMCID: PMC7926659 DOI: 10.3390/v13020336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 01/28/2023] Open
Abstract
Prophages are bacteriophages in the lysogenic state, where the viral genome is inserted within the bacterial chromosome. They contribute to strain genetic variability and can influence bacterial phenotypes. Prophages are highly abundant among the strains of the opportunistic pathogen Pseudomonas aeruginosa and were shown to confer specific traits that can promote strain pathogenicity. The main difficulty of studying those regions is the lack of a simple prophage-curing method for P. aeruginosa strains. In this study, we developed a novel, targeted-curing approach for prophages in P. aeruginosa. In the first step, we tagged the prophage for curing with an ampicillin resistance cassette (ampR) and further used this strain for the sacB counter-selection marker’s temporal insertion into the prophage region. The sucrose counter-selection resulted in different variants when the prophage-cured mutant is the sole variant that lost the ampR cassette. Next, we validated the targeted-curing with local PCR amplification and Whole Genome Sequencing. The application of the strategy resulted in high efficiency both for curing the Pf4 prophage of the laboratory wild-type (WT) strain PAO1 and for PR2 prophage from the clinical, hard to genetically manipulate, 39016 strain. We believe this method can support the research and growing interest in prophage biology in P. aeruginosa as well as additional Gram-negative bacteria.
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Affiliation(s)
- Esther Shmidov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel; (E.S.); (I.Z.); (I.L.-L.); (S.S.)
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Itzhak Zander
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel; (E.S.); (I.Z.); (I.L.-L.); (S.S.)
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Ilana Lebenthal-Loinger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel; (E.S.); (I.Z.); (I.L.-L.); (S.S.)
| | - Sarit Karako-Lampert
- Scientific Equipment Center, The Mina & Everard Goodman Faculty of Life Sciences Bar-Ilan University, Ramat Gan 5290002, Israel;
| | - Sivan Shoshani
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel; (E.S.); (I.Z.); (I.L.-L.); (S.S.)
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Ehud Banin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel; (E.S.); (I.Z.); (I.L.-L.); (S.S.)
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
- Correspondence:
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Phenotypic and Genomic Comparison of the Two Most Common ExoU-Positive Pseudomonas aeruginosa Clones, PA14 and ST235. mSystems 2020; 5:5/6/e01007-20. [PMID: 33293405 PMCID: PMC7743143 DOI: 10.1128/msystems.01007-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genotyping of 2,882 Pseudomonas aeruginosa isolates that had been collected during the last 40 years identified the ExoU-positive lineages PA14 (ST253) and ST235 as the second and third most frequent clones in the P. aeruginosa population. Both clones were approximately 2-fold more frequently detected in animate habitats than in soil or aquatic habitats. While ST253 clone isolates were causing mainly acute and chronic infections in humans, ST235 isolates had been preferentially collected from hospitalized patients with severe acute infections, particularly, keratitis, urinary tract infections, burn wounds, and ventilator-associated pneumonia. The two major exoU clones differed substantially in the composition and flexibility of the accessory genome and by more than 8,000 amino acid sequences. Pronounced sequence variation between orthologs was noted in genes encoding elements of secretion systems and secreted effector molecules, including the type III secretion system, indicating the modes of action of the different clones. When comparing representatives of the two clones in batch culture, the PA14 strain orchestrated the quorum sensing circuitry for the expression of pathogenic traits and stopped growing in batch culture when it entered the stationary phase, but the quorum sensing-deficient ST235 strain expressed high type III secretion activity and continued to grow and to divide. In summary, unrestricted growth, high constitutive type III secretion activity, and facilitated uptake of foreign DNA could be major features that have made ST235 a global high-risk clone associated with poor outcomes of acute nosocomial infections.IMPORTANCE The ubiquitous and metabolically versatile environmental bacterium Pseudomonas aeruginosa can cause infections in a wide variety of hosts, including insects, plants, animals, and humans. P. aeruginosa is one of the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens that are the major cause of nosocomial infections in the United States and are a threat all over the world because of their capacity to become increasingly resistant to all available antibiotics. Most experimental work on P. aeruginosa has been performed with reference strains PAO1 and PA14, providing deep insight into key metabolic and regulatory pathways thought to be applicable to all P. aeruginosa strains. However, this comparative study on the two most common exoU-positive clones taught us that there are major lineages in the population such as the global high-risk clone ST235 that exhibit uncommon traits of lifestyle, genome mobility, and pathogenicity distinct from those in our knowledge gained from the studies with the reference strains.
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37
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Thomaz L, Gustavo de Almeida L, Silva FRO, Cortez M, Taborda CP, Spira B. In vivo Activity of Silver Nanoparticles Against Pseudomonas aeruginosa Infection in Galleria mellonella. Front Microbiol 2020; 11:582107. [PMID: 33240236 PMCID: PMC7680755 DOI: 10.3389/fmicb.2020.582107] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/16/2020] [Indexed: 01/30/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen associated with life-threatening nosocomial and community-acquired infections. Antibiotic resistance is an immediate threat to public health and demands an urgent action to discovering new antimicrobial agents. One of the best alternatives for pre-clinical tests with animal models is the greater wax moth Galleria mellonella. Here, we evaluated the antipseudomonal activity of silver nanoparticles (AgNPs) against P. aeruginosa strain UCBPP-PA14 using G. mellonella larvae. The AgNPs were synthesized through a non-toxic biogenic process involving microorganism fermentation. The effect of AgNPs was assessed through characterization and quantification of the hemocytic response, nodulation and phenoloxidase cascade. On average, 80% of the larvae infected with P. aeruginosa and prophylactically treated with nanoparticles survived. Both the specific and total larvae hemocyte counts were restored in the treated group. In addition, the nodulation process and the phenoloxidase cascade were less exacerbated when the larvae were exposed to the silver nanoparticles. AgNPs protect the larvae from P. aeruginosa infection by directly killing the bacteria and indirectly by preventing an exacerbated immunological response against the pathogen. Our results suggest that the prophylactic use of AgNPs has a strong protective activity against P. aeruginosa infection.
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Affiliation(s)
- Luciana Thomaz
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Luiz Gustavo de Almeida
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | | | - Mauro Cortez
- Department of Parasitology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Carlos P. Taborda
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
- Laboratory of Medical Mycology/LIM53, Faculty of Medicine, Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, Brazil
| | - Beny Spira
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
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38
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Jackson L, Waters V. Factors influencing the acquisition and eradication of early Pseudomonas aeruginosa infection in cystic fibrosis. J Cyst Fibros 2020; 20:8-16. [PMID: 33172756 DOI: 10.1016/j.jcf.2020.10.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/02/2020] [Accepted: 10/27/2020] [Indexed: 12/21/2022]
Abstract
In recent years considerable improvements have been made in increasing the life expectancy of patients with cystic fibrosis. New highly effective modulator therapies targeting the underlying defect in the cystic fibrosis transmembrane conductance regulator protein are expected to enhance lifespan even further. However, chronic Pseudomonas aeruginosa pulmonary infections continue to threaten CF patient lung health and mortality rates. Early and aggressive antibiotic eradication therapies targeting P. aeruginosa are standard practice, but these eradication therapies fail in 10-40% of patients. The reasons for P. aeruginosa eradication failure remain unclear. Thus, this review summarizes the evidence to date for pseudomonal acquisition and eradication failure in the cystic fibrosis lung. A complex combination of host and bacterial factors are responsible for initial establishment of P. aeruginosa pulmonary infections. Moreover, host and pseudomonal factors, polymicrobial interactions, and antimicrobial limitations in relation to P. aeruginosa eradication therapy failure are summarized.
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Affiliation(s)
- Lindsay Jackson
- Translational Medicine, Hospital for Sick Children, Toronto, Canada.
| | - Valerie Waters
- Translational Medicine, Hospital for Sick Children, Toronto, Canada; Infectious Diseases, Department of Pediatrics, Hospital for Sick Children, Toronto, Canada
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39
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Tümmler B. Molecular epidemiology in current times. Environ Microbiol 2020; 22:4909-4918. [PMID: 32945108 DOI: 10.1111/1462-2920.15238] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 01/04/2023]
Abstract
Motivated to find options for prevention or intervention, molecular epidemiology aims to identify the host and microbial factors that determine the transmission, manifestation and progression of infectious disease. The genotyping of cultivatable bacterial strains is performed by either anonymous fingerprinting techniques or sequence-based exploration of variable genomic sites. Multilocus sequence typing of housekeeping genes and allele profiling of the core genome have become standard techniques of bacterial strain typing that may be supplemented by whole genome sequencing to explore all single nucleotide variants and/or the composition of the accessory genome. Next, novel protocols to investigate host and microbiome based upon smart third generation sequencing technologies are being developed for an effective surveillance, rapid diagnosis and real-time tracking of infectious diseases.
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Affiliation(s)
- Burkhard Tümmler
- Clinical Research Group, Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
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40
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Çekin ZK, Dabos L, Malkoçoğlu G, Fortineau N, Bayraktar B, Iorga BI, Naas T, Aktaş E. Carbapenemase -producing Pseudomonas aeruginosa isolates from Turkey: first report of P. aeruginosa high-risk clones with VIM-5- and IMP-7-type carbapenemases in a tertiary hospital. Diagn Microbiol Infect Dis 2020; 99:115174. [PMID: 32980808 DOI: 10.1016/j.diagmicrobio.2020.115174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 02/08/2023]
Abstract
We investigated the presence of carbapenemases in carbapenem-resistant Pseudomonas aeruginosa isolates, which were collected over a 14-month period in a Turkish hospital, with in-depth molecular characterization of carbapenemase-producing isolates. Among 45 study isolates, 2 isolates were identified as carbapenemase producers by both Carba NP and Carbapenem Inactivation Method tests, and only 1 of them gave a positive result in polymerase chain reaction tests for a carbapenemase gene (blaVIM). Whole genome sequencing of the 2 isolates revealed the presence of blaVIM-5 gene in an ST308 isolate, while the other one expressed IMP-7 in an ST357 isolate; both STs are considered high-risk clones. The 2 carbapenemase-producing isolates were multidrug resistant, as they harbored other resistance determinants, including a variant of the recently described plasmid-encoded fluoroquinolone resistance determinant crpP gene, crpP-2. We report for the first time P. aeruginosa high-risk clones carrying VIM-5- and IMP-7-type carbapenemases with multiple resistance determinants in Turkey.
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Affiliation(s)
- Zuhal Kalaycı Çekin
- Şişli Hamidiye Etfal Training and Research Hospital, Clinical Microbiology Laboratory, Istanbul, Turkey
| | - Laura Dabos
- UMR1184, Team RESIST, INSERM, University Paris-Saclay, Faculty of Medicine, Le Kremlin-Bicêtre, France; Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France
| | | | - Nicolas Fortineau
- UMR1184, Team RESIST, INSERM, University Paris-Saclay, Faculty of Medicine, Le Kremlin-Bicêtre, France; Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France; Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France; French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Banu Bayraktar
- Şişli Hamidiye Etfal Training and Research Hospital, Clinical Microbiology Laboratory, Istanbul, Turkey
| | - Bogdan I Iorga
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Thierry Naas
- UMR1184, Team RESIST, INSERM, University Paris-Saclay, Faculty of Medicine, Le Kremlin-Bicêtre, France; Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France; Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France; French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France.
| | - Elif Aktaş
- Şişli Hamidiye Etfal Training and Research Hospital, Clinical Microbiology Laboratory, Istanbul, Turkey.
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41
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Yin Q, Wu S, Wu L, Wang Z, Mu Y, Zhang R, Dong C, Zhou B, Zhao B, Zheng J, Sun Y, Cheng X, Yang L. A novel in silico antimicrobial peptide DP7 combats MDR Pseudomonas aeruginosa and related biofilm infections. J Antimicrob Chemother 2020; 75:3248-3259. [PMID: 32737484 DOI: 10.1093/jac/dkaa308] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/11/2020] [Indexed: 02/06/2023] Open
Abstract
Abstract
Background
Antimicrobial peptides are promising alternative antimicrobial agents to combat MDR. DP7, an antimicrobial peptide designed in silico, possesses broad-spectrum antimicrobial activities and immunomodulatory effects. However, the effects of DP7 against Pseudomonas aeruginosa and biofilm infection remain largely unexplored.
Objectives
To assess (i) the antimicrobial activity of DP7 against MDR P. aeruginosa; and (ii) the antibiofilm activity against biofilm infection. Also, to preliminarily investigate the possible antimicrobial mode of action.
Methods
The MICs of DP7 for 104 clinical P. aeruginosa strains (including 57 MDR strains) and the antibiofilm activity were determined. RNA-Seq, genome sequencing and cell morphology were conducted. Both acute and chronic biofilm infection mouse models were established. Two mutants, resulting from point mutations associated with LPS and biofilms, were constructed to investigate the potential mode of action.
Results
DP7, at 8–32 mg/L, inhibited the growth of clinical P. aeruginosa strains and, at 64 mg/L, reduced biofilm formation by 43% to 68% in vitro. In acute lung infection, 0.5 mg/kg DP7 exhibited a 70% protection rate and reduced bacterial colonization by 50% in chronic infection. DP7 mainly suppressed gene expression involving LPS and outer membrane proteins and disrupted cell wall structure. Genome sequencing of the DP7-resistant strain DP7R revealed four SNPs controlling LPS and biofilm production. gshA44 and wbpJ139 mutants displayed LPS reduction and motility deficiency, conferring the reduction of LPS and biofilm biomass of strain DP7R and indicating that LPS was a potential target of DP7.
Conclusions
These results demonstrate that DP7 may hold potential as an effective antimicrobial agent against MDR P. aeruginosa and related infections.
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Affiliation(s)
- Qi Yin
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, 3688 Nanhai Avenue, Nanshan Section, Shenzhen 518060, People’s Republic of China
| | - Siwen Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
| | - Lei Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
| | - Zhenling Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
| | - Yandong Mu
- Stomatology Department, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 611731, People’s Republic of China
| | - Rui Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
| | - Chunyan Dong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
| | - Bailing Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
| | - Binyan Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
| | - Jiajun Zheng
- Stomatology Department, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 611731, People’s Republic of China
| | - Ying Sun
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
| | - Xingjun Cheng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
| | - Li Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
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42
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Hornischer K, Khaledi A, Pohl S, Schniederjans M, Pezoldt L, Casilag F, Muthukumarasamy U, Bruchmann S, Thöming J, Kordes A, Häussler S. BACTOME-a reference database to explore the sequence- and gene expression-variation landscape of Pseudomonas aeruginosa clinical isolates. Nucleic Acids Res 2020; 47:D716-D720. [PMID: 30272193 PMCID: PMC6324029 DOI: 10.1093/nar/gky895] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/21/2018] [Indexed: 12/26/2022] Open
Abstract
Extensive use of next-generation sequencing (NGS) for pathogen profiling has the potential to transform our understanding of how genomic plasticity contributes to phenotypic versatility. However, the storage of large amounts of NGS data and visualization tools need to evolve to offer the scientific community fast and convenient access to these data. We introduce BACTOME as a database system that links aligned DNA- and RNA-sequencing reads of clinical Pseudomonas aeruginosa isolates with clinically relevant pathogen phenotypes. The database allows data extraction for any single isolate, gene or phenotype as well as data filtering and phenotypic grouping for specific research questions. With the integration of statistical tools we illustrate the usefulness of a relational database structure for the identification of phenotype-genotype correlations as an essential part of the discovery pipeline in genomic research. Furthermore, the database provides a compilation of DNA sequences and gene expression values of a plethora of clinical isolates to give a consensus DNA sequence and consensus gene expression signature. Deviations from the consensus thereby describe the genomic landscape and the transcriptional plasticity of the species P. aeruginosa. The database is available at https://bactome.helmholtz-hzi.de.
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Affiliation(s)
- Klaus Hornischer
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany.,Molecular Health GmbH, D-69115 Heidelberg, Germany
| | - Ariane Khaledi
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany
| | - Sarah Pohl
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany
| | - Monika Schniederjans
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany
| | - Lorena Pezoldt
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany
| | - Fiordiligie Casilag
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany
| | - Uthayakumar Muthukumarasamy
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany
| | - Sebastian Bruchmann
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany.,Pathogen Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Janne Thöming
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany
| | - Adrian Kordes
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany
| | - Susanne Häussler
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany
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43
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The aerobic respiratory chain of Pseudomonas aeruginosa cultured in artificial urine media: Role of NQR and terminal oxidases. PLoS One 2020; 15:e0231965. [PMID: 32324772 PMCID: PMC7179901 DOI: 10.1371/journal.pone.0231965] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 04/04/2020] [Indexed: 12/26/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative γ-proteobacterium that forms part of the normal human microbiota and it is also an opportunistic pathogen, responsible for 30% of all nosocomial urinary tract infections. P. aeruginosa carries a highly branched respiratory chain that allows the colonization of many environments, such as the urinary tract, catheters and other medical devices. P. aeruginosa respiratory chain contains three different NADH dehydrogenases (complex I, NQR and NDH-2), whose physiologic roles have not been elucidated, and up to five terminal oxidases: three cytochrome c oxidases (COx), a cytochrome bo3 oxidase (CYO) and a cyanide-insensitive cytochrome bd-like oxidase (CIO). In this work, we studied the composition of the respiratory chain of P. aeruginosa cells cultured in Luria Broth (LB) and modified artificial urine media (mAUM), to understand the metabolic adaptations of this microorganism to the growth in urine. Our results show that the COx oxidases play major roles in mAUM, while P. aeruginosa relies on CYO when growing in LB medium. Moreover, our data demonstrate that the proton-pumping NQR complex is the main NADH dehydrogenase in both LB and mAUM. This enzyme is resistant to HQNO, an inhibitory molecule produced by P. aeruginosa, and may provide an advantage against the natural antibacterial agents produced by this organism. This work offers a clear picture of the composition of this pathogen’s aerobic respiratory chain and the main roles that NQR and terminal oxidases play in urine, which is essential to understand its physiology and could be used to develop new antibiotics against this notorious multidrug-resistant microorganism.
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44
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Moura-Alves P, Puyskens A, Stinn A, Klemm M, Guhlich-Bornhof U, Dorhoi A, Furkert J, Kreuchwig A, Protze J, Lozza L, Pei G, Saikali P, Perdomo C, Mollenkopf HJ, Hurwitz R, Kirschhoefer F, Brenner-Weiss G, Weiner J, Oschkinat H, Kolbe M, Krause G, Kaufmann SHE. Host monitoring of quorum sensing during Pseudomonas aeruginosa infection. Science 2020; 366:366/6472/eaaw1629. [PMID: 31857448 DOI: 10.1126/science.aaw1629] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 07/25/2019] [Accepted: 11/13/2019] [Indexed: 01/01/2023]
Abstract
Pseudomonas aeruginosa rapidly adapts to altered conditions by quorum sensing (QS), a communication system that it uses to collectively modify its behavior through the production, release, and detection of signaling molecules. QS molecules can also be sensed by hosts, although the respective receptors and signaling pathways are poorly understood. We describe a pattern of regulation in the host by the aryl hydrocarbon receptor (AhR) that is critically dependent on qualitative and quantitative sensing of P. aeruginosa quorum. QS molecules bind to AhR and distinctly modulate its activity. This is mirrored upon infection with P. aeruginosa collected from diverse growth stages and with QS mutants. We propose that by spying on bacterial quorum, AhR acts as a major sensor of infection dynamics, capable of orchestrating host defense according to the status quo of infection.
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Affiliation(s)
- Pedro Moura-Alves
- Department of Immunology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany. .,Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Andreas Puyskens
- Department of Immunology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Anne Stinn
- Department of Immunology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany.,Structural Systems Biology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany.,Department of Structural Infection Biology, Centre for Structural Systems Biology, Helmholtz Centre for Infection Research (HZI), 22607 Hamburg, Germany.,Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, 20148 Hamburg, Germany
| | - Marion Klemm
- Department of Immunology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Ute Guhlich-Bornhof
- Department of Immunology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Anca Dorhoi
- Department of Immunology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany.,Institute of Immunology, Friedrich-Loeffler Institut, Greifswald-Insel Riems, Germany.,Faculty of Mathematics and Natural Sciences, University of Greifswald, Greifswald, Germany
| | - Jens Furkert
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Annika Kreuchwig
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Jonas Protze
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Laura Lozza
- Department of Immunology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany.,Epiontis GmbH-Precision for Medicine, 12489 Berlin, Germany
| | - Gang Pei
- Department of Immunology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Philippe Saikali
- Department of Immunology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Carolina Perdomo
- Department of Immunology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Hans J Mollenkopf
- Microarray Core Facility, Max Planck Institute for Infection Biology, Department of Immunology, 10117 Berlin, Germany
| | - Robert Hurwitz
- Protein Purification Core Facility, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Frank Kirschhoefer
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Gerald Brenner-Weiss
- Protein Purification Core Facility, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - January Weiner
- Department of Immunology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Hartmut Oschkinat
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Michael Kolbe
- Structural Systems Biology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany.,Department of Structural Infection Biology, Centre for Structural Systems Biology, Helmholtz Centre for Infection Research (HZI), 22607 Hamburg, Germany.,Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, 20148 Hamburg, Germany
| | - Gerd Krause
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Stefan H E Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany. .,Hagler Institute for Advanced Study at Texas A&M University, College Station, TX 77843, USA
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45
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Gil-Gil T, Martínez JL, Blanco P. Mechanisms of antimicrobial resistance in Stenotrophomonas maltophilia: a review of current knowledge. Expert Rev Anti Infect Ther 2020; 18:335-347. [PMID: 32052662 DOI: 10.1080/14787210.2020.1730178] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Stenotrophomonas maltophilia is a prototype of bacteria intrinsically resistant to antibiotics. The reduced susceptibility of this microorganism to antimicrobials mainly relies on the presence in its chromosome of genes encoding efflux pumps and antibiotic inactivating enzymes. Consequently, the therapeutic options for treating S. maltophilia infections are limited.Areas covered: Known mechanisms of intrinsic, acquired and phenotypic resistance to antibiotics of S. maltophilia and the consequences of such resistance for treating S. maltophilia infections are discussed. Acquisition of some genes, mainly those involved in co-trimoxazole resistance, contributes to acquired resistance. Mutation, mainly in the regulators of chromosomally-encoded antibiotic resistance genes, is a major cause for S. maltophilia acquisition of resistance. The expression of some of these genes is triggered by specific signals or stressors, which can lead to transient phenotypic resistance.Expert opinion: Treatment of S. maltophilia infections is difficult because this organism presents low susceptibility to antibiotics. Besides, it can acquire resistance to antimicrobials currently in use. Particularly problematic is the selection of mutants overexpressing efflux pumps since they present a multidrug resistance phenotype. The use of novel antimicrobials alone or in combination, together with the development of efflux pumps' inhibitors may help in fighting S. maltophilia infections.
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Affiliation(s)
| | | | - Paula Blanco
- Molecular Basis of Adaptation Laboratory, Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
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46
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Cabral MP, Correia A, Vilanova M, Gärtner F, Moscoso M, García P, Vallejo JA, Pérez A, Francisco-Tomé M, Fuentes-Valverde V, Bou G. A live auxotrophic vaccine confers mucosal immunity and protection against lethal pneumonia caused by Pseudomonas aeruginosa. PLoS Pathog 2020; 16:e1008311. [PMID: 32040500 PMCID: PMC7034913 DOI: 10.1371/journal.ppat.1008311] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 02/21/2020] [Accepted: 01/06/2020] [Indexed: 12/28/2022] Open
Abstract
Pseudomonas aeruginosa is one of the leading causes of nosocomial pneumonia and its associated mortality. Moreover, extensively drug-resistant high-risk clones are globally widespread, presenting a major challenge to the healthcare systems. Despite this, no vaccine is available against this high-concerning pathogen. Here we tested immunogenicity and protective efficacy of an experimental live vaccine against P. aeruginosa pneumonia, consisting of an auxotrophic strain which lacks the key enzyme involved in D-glutamate biosynthesis, a structural component of the bacterial cell wall. As the amounts of free D-glutamate in vivo are trace substances in most cases, blockage of the cell wall synthesis occurs, compromising the growth of this strain, but not its immunogenic properties. Indeed, when delivered intranasally, this vaccine stimulated production of systemic and mucosal antibodies, induced effector memory, central memory and IL-17A-producing CD4+ T cells, and recruited neutrophils and mononuclear phagocytes into the airway mucosa. A significant improvement in mice survival after lung infection caused by ExoU-producing PAO1 and PA14 strains was observed. Nearly one third of the mice infected with the XDR high-risk clone ST235 were also protected. These findings highlight the potential of this vaccine for the control of acute pneumonia caused by this bacterial pathogen. Pseudomonas aeruginosa is an opportunistic bacterium and one of the most common causes of healthcare-associated diseases, including acute pneumonia, causing high mortality within immunocompromised hosts. Most of these infections are strikingly difficult to treat using conventional antibiotic therapies, since this microorganism displays high intrinsic resistance to a wide range of antibiotics. Moreover, to date, no vaccine is available for prevention. Here we used a mutated bacterial strain, which is unable to replicate in vivo and to cause disease, as a live vaccine against acute pneumonia caused by this pathogen. When applied intranasally, this vaccine induced immunity both at local and distant body sites, activating immune cells which were recruited into the airway mucosa. This evoked immune response reduced the number of non-surviving mice after infection with two cytotoxic P. aeruginosa strains causing acute lung infection. Some protection was also observed against an internationally disseminated cytotoxic strain. These data indicate that this is a promising vaccine candidate against P. aeruginosa-pneumonia.
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Affiliation(s)
- Maria P. Cabral
- Department of Microbiology, University Hospital A Coruña (CHUAC)–Biomedical Research Institute A Coruña (INIBIC), A Coruña, Spain
| | - Alexandra Correia
- i3S –Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC–Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Manuel Vilanova
- i3S –Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC–Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Fátima Gärtner
- i3S –Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Miriam Moscoso
- Department of Microbiology, University Hospital A Coruña (CHUAC)–Biomedical Research Institute A Coruña (INIBIC), A Coruña, Spain
| | - Patricia García
- Department of Microbiology, University Hospital A Coruña (CHUAC)–Biomedical Research Institute A Coruña (INIBIC), A Coruña, Spain
| | - Juan A. Vallejo
- Department of Microbiology, University Hospital A Coruña (CHUAC)–Biomedical Research Institute A Coruña (INIBIC), A Coruña, Spain
| | - Astrid Pérez
- Department of Microbiology, University Hospital A Coruña (CHUAC)–Biomedical Research Institute A Coruña (INIBIC), A Coruña, Spain
| | - Mónica Francisco-Tomé
- Department of Microbiology, Galicia Sur Health Research Institute (IISGS), Vigo, Spain
| | - Víctor Fuentes-Valverde
- Department of Microbiology, University Hospital A Coruña (CHUAC)–Biomedical Research Institute A Coruña (INIBIC), A Coruña, Spain
| | - Germán Bou
- Department of Microbiology, University Hospital A Coruña (CHUAC)–Biomedical Research Institute A Coruña (INIBIC), A Coruña, Spain
- * E-mail:
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47
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Cramer N, Fischer S, Hedtfeld S, Dorda M, Tümmler B. Intraclonal competitive fitness of longitudinal cystic fibrosis Pseudomonas aeruginosa airway isolates in liquid cultures. Environ Microbiol 2020; 22:2536-2549. [PMID: 31985137 DOI: 10.1111/1462-2920.14924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 01/22/2020] [Indexed: 12/31/2022]
Abstract
The metabolically versatile Pseudomonas aeruginosa inhabits biotic and abiotic environments including the niche of cystic fibrosis (CF) airways. This study investigated how the adaptation to CF lungs affects the within-clone fitness of P. aeruginosa to grow and persist in liquid cultures in the presence of the clonal ancestors. Longitudinal clonal P. aeruginosa isolates that had been collected from 12 CF donors since the onset of colonization for up to 30 years was subjected to within-clone competition experiments. The relative quantities of individual strains were determined by marker-free amplicon sequencing of multiplex PCR products of strain-specific nucleotide sequence variants, a novel method that is generally applicable to studies in evolutionary genetics and microbial ecology with real-world strain collections. For 10 of the 12 examined patient courses, P. aeruginosa isolates of the first years of colonization grew faster in the presence of their clonal progeny than alone. Single growth of individual strains showed no temporal trend with colonization time, but in co-culture, the early isolates out-competed their clonal progeny. Irrespective of the genetic make-up of the clone and its genomic microevolution in CF lungs, the early isolates expressed fitness traits to win the within-clone competition that were absent in their progeny.
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Affiliation(s)
- Nina Cramer
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Sebastian Fischer
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover, Germany
| | - Silke Hedtfeld
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover, Germany
| | - Marie Dorda
- Research Core Unit Genomics, Hannover, Germany
| | - Burkhard Tümmler
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', 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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48
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Magalhães B, Valot B, Abdelbary MMH, Prod'hom G, Greub G, Senn L, Blanc DS. Combining Standard Molecular Typing and Whole Genome Sequencing to Investigate Pseudomonas aeruginosa Epidemiology in Intensive Care Units. Front Public Health 2020; 8:3. [PMID: 32047733 PMCID: PMC6997133 DOI: 10.3389/fpubh.2020.00003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/07/2020] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa is one of the main pathogens responsible for nosocomial infections, particularly in Intensive Care Units (ICUs). Due to the complexity of P. aeruginosa ecology, only powerful typing methods can efficiently allow its surveillance and the detection during expanding outbreaks. An increase in P. aeruginosa incidence was observed in the ICUs of the Lausanne University Hospital between 2010 and 2014. All clinical and environmental isolates retrieved during this period were typed with Double locus sequence typing (DLST), which detected the presence of three major genotypes: DLST 1–18, DLST 1–21, and DLST 6–7. DLST 1–18 (ST1076) isolates were previously associated with an epidemiologically well-described outbreak in the burn unit. Nevertheless, DLST 1–21 (ST253) and DLST 6–7 (ST17) showed sporadic occurrence with only few cases of possible transmission between patients. Whole genome sequencing (WGS) was used to further investigate the epidemiology of these three major P. aeruginosa genotypes in the ICUs. WGS was able to differentiate between outbreak and non-outbreak isolates and confirm suspected epidemiological links. Additionally, whole-genome single nucleotide polymorphisms (SNPs) results considered isolates as closely related for which no epidemiological links were suspected, expanding the epidemiological investigation to unsuspected links. The combination of a first-line molecular typing tool (DLST) with a more discriminatory method (WGS) proved to be an accurate and cost-efficient typing strategy for the investigation of P. aeruginosa epidemiology in the ICUs.
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Affiliation(s)
- Bárbara Magalhães
- Service of Hospital Preventive Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Benoit Valot
- Chrono-Environment, Franche-Comté University, Besançon, France
| | - Mohamed M H Abdelbary
- Service of Hospital Preventive Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Guy Prod'hom
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Laurence Senn
- Service of Hospital Preventive Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dominique S Blanc
- Service of Hospital Preventive Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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49
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Ducey TF, Durso LM, Ibekwe AM, Dungan RS, Jackson CR, Frye JG, Castleberry BL, Rashash DMC, Rothrock MJ, Boykin D, Whitehead TR, Ramos Z, McManus M, Cook KL. A newly developed Escherichia coli isolate panel from a cross section of U.S. animal production systems reveals geographic and commodity-based differences in antibiotic resistance gene carriage. JOURNAL OF HAZARDOUS MATERIALS 2020; 382:120991. [PMID: 31446353 DOI: 10.1016/j.jhazmat.2019.120991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 08/08/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
There are limited numbers of Escherichia coli isolate panels that represent United States food animal production. The majority of existing Escherichia coli isolate panels are typically designed: (i) to optimize genetic and/or phenotypic diversity; or (ii) focus on human isolates. To address this shortfall in agriculturally-related resources, we have assembled a publicly-available isolate panel (AgEc) from the four major animal production commodities in the United States, including beef, dairy, poultry, and swine, as well as isolates from agriculturally-impacted environments, and other commodity groups. Diversity analyses by phylotyping and Pulsed-field Gel Electrophoresis revealed a highly diverse composition, with the 300 isolates clustered into 71 PFGE sub-types based upon an 80% similarity cutoff. To demonstrate the panel's utility, tetracycline and sulfonamide resistance genes were assayed, which identified 131 isolates harboring genes involved in tetracycline resistance, and 41 isolates containing sulfonamide resistance genes. There was strong overlap in the two pools of isolates, 38 of the 41 isolates harboring sulfonamide resistance genes also contained tetracycline resistance genes. Analysis of antimicrobial resistance gene patterns revealed significant differences along commodity and geographical lines. This panel therefore provides the research community an E. coli isolate panel for study of issues pertinent to U.S. food animal production.
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Affiliation(s)
- Thomas F Ducey
- Coastal Plains Soil, Water, and Plant Research Center, Agricultural Research Service, Department of Agriculture, Florence, SC, United States.
| | - Lisa M Durso
- Agroecosystem Management Research Unit, Agricultural Research Service, Department of Agriculture, Lincoln, NE, United States
| | - Abasiofiok M Ibekwe
- U.S. Salinity Laboratory, Agricultural Research Service, Department of Agriculture, Riverside, CA, United States
| | - Robert S Dungan
- Northwest Irrigation and Soils Research Laboratory, Agricultural Research Service, Department of Agriculture, Kimberly, ID, United States
| | - Charlene R Jackson
- Bacterial Epidemiology & Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Department of Agriculture, Athens, GA, United States
| | - Jonathan G Frye
- Bacterial Epidemiology & Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Department of Agriculture, Athens, GA, United States
| | - B Lana Castleberry
- Livestock Nutrient Management Research Unit, Agricultural Research Service, Department of Agriculture, Bushland, TX, United States
| | - Diana M C Rashash
- North Carolina Cooperative Extension Service, Jacksonville, NC, United States
| | - Michael J Rothrock
- Egg Safety & Quality Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Department of Agriculture, Athens, GA, United States
| | - Debbie Boykin
- Jamie Whitten Delta States Research Center, Agricultural Research Service, Department of Agriculture, Stoneville, MS, United States
| | - Terence R Whitehead
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, Department of Agriculture, Peoria, IL, United States
| | - Zeanmarj Ramos
- South Carolina Governor's School for Science and Mathematics, Hartsville, SC, United States
| | - Morgan McManus
- South Carolina Governor's School for Science and Mathematics, Hartsville, SC, United States
| | - Kimberly L Cook
- Bacterial Epidemiology & Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Department of Agriculture, Athens, GA, United States
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50
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Ozer EA, Nnah E, Didelot X, Whitaker RJ, Hauser AR. The Population Structure of Pseudomonas aeruginosa Is Characterized by Genetic Isolation of exoU+ and exoS+ Lineages. Genome Biol Evol 2019; 11:1780-1796. [PMID: 31173069 PMCID: PMC6690169 DOI: 10.1093/gbe/evz119] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2019] [Indexed: 02/06/2023] Open
Abstract
The diversification of microbial populations may be driven by many factors including adaptation to distinct ecological niches and barriers to recombination. We examined the population structure of the bacterial pathogen Pseudomonas aeruginosa by analyzing whole-genome sequences of 739 isolates from diverse sources. We confirmed that the population structure of P. aeruginosa consists of two major groups (referred to as Groups A and B) and at least two minor groups (Groups C1 and C2). Evidence for frequent intragroup but limited intergroup recombination in the core genome was observed, consistent with sexual isolation of the groups. Likewise, accessory genome analysis demonstrated more gene flow within Groups A and B than between these groups, and a few accessory genomic elements were nearly specific to one or the other group. In particular, the exoS gene was highly overrepresented in Group A compared with Group B isolates (99.4% vs. 1.1%) and the exoU gene was highly overrepresented in Group B compared with Group A isolates (95.2% vs. 1.8%). The exoS and exoU genes encode effector proteins secreted by the P. aeruginosa type III secretion system. Together these results suggest that the major P. aeruginosa groups defined in part by the exoS and exoU genes are divergent from each other, and that these groups are genetically isolated and may be ecologically distinct. Although both groups were globally distributed and caused human infections, certain groups predominated in some clinical contexts.
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Affiliation(s)
- Egon A Ozer
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine
| | - Ekpeno Nnah
- Lurie Children's Hospital, Chicago, Illinois
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Rachel J Whitaker
- Department of Microbiology and the Carl R. Woese Institute of Genomic Biology, University of Illinois, Urbana-Champaign
| | - Alan R Hauser
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine.,Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine
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