1
|
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; 12:e0014324. [PMID: 38860784 PMCID: PMC11218531 DOI: 10.1128/spectrum.00143-24] [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: 04/18/2024] [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.
Collapse
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
| |
Collapse
|
2
|
Barp N, Marcacci M, Biagioni E, Serio L, Busani S, Ventura P, Franceschini E, Orlando G, Venturelli C, Menozzi I, Tambassi M, Scaltriti E, Pongolini S, Sarti M, Pietrangelo A, Girardis M, Mussini C, Meschiari M. A Fatal Case of Pseudomonas aeruginosa Community-Acquired Pneumonia in an Immunocompetent Patient: Clinical and Molecular Characterization and Literature Review. Microorganisms 2023; 11:1112. [PMID: 37317086 DOI: 10.3390/microorganisms11051112] [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: 03/16/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 06/16/2023] Open
Abstract
Rare cases of Pseudomonas aeruginosa community-acquired pneumonia (PA-CAP) were reported in non-immunocompromised patients. We describe a case of Pseudomonas aeruginosa (PA) necrotizing cavitary CAP with a fatal outcome in a 53-year-old man previously infected with SARS-CoV-2, who was admitted for dyspnea, fever, cough, hemoptysis, acute respiratory failure and a right upper lobe opacification. Six hours after admission, despite effective antibiotic therapy, he experienced multi-organ failure and died. Autopsy confirmed necrotizing pneumonia with alveolar hemorrhage. Blood and bronchoalveolar lavage cultures were positive for PA serotype O:9 belonging to ST1184. The strain shares the same virulence factor profile with reference genome PA01. With the aim to better investigate the clinical and molecular characteristics of PA-CAP, we considered the literature of the last 13 years concerning this topic. The prevalence of hospitalized PA-CAP is about 4% and has a mortality rate of 33-66%. Smoking, alcohol abuse and contaminated fluid exposure were the recognized risk factors; most cases presented the same symptoms described above and needed intensive care. Co-infection of PA-influenza A is described, which is possibly caused by influenza-inducing respiratory epithelial cell dysfunction: the same pathophysiological mechanism could be assumed with SARS-CoV-2 infection. Considering the high rate of fatal outcomes, additional studies are needed to identify sources of infections and new risk factors, along with genetic and immunological features. Current CAP guidelines should be revised in light of these results.
Collapse
Affiliation(s)
- Nicole Barp
- Infectious Diseases, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Matteo Marcacci
- Internal Medicine, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Emanuela Biagioni
- Intensive Care Unit, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Lucia Serio
- Intensive Care Unit, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Stefano Busani
- Intensive Care Unit, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Paolo Ventura
- Internal Medicine, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Erica Franceschini
- Infectious Diseases, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Gabriella Orlando
- Infectious Diseases, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Claudia Venturelli
- Microbiology, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Ilaria Menozzi
- Risk Analysis and Genomic Epidemiology Unit, Experimental Zooprophylactic Institute of Lombardy and Emilia-Romagna, 43126 Parma, Italy
| | - Martina Tambassi
- Risk Analysis and Genomic Epidemiology Unit, Experimental Zooprophylactic Institute of Lombardy and Emilia-Romagna, 43126 Parma, Italy
| | - Erika Scaltriti
- Risk Analysis and Genomic Epidemiology Unit, Experimental Zooprophylactic Institute of Lombardy and Emilia-Romagna, 43126 Parma, Italy
| | - Stefano Pongolini
- Risk Analysis and Genomic Epidemiology Unit, Experimental Zooprophylactic Institute of Lombardy and Emilia-Romagna, 43126 Parma, Italy
| | - Mario Sarti
- Microbiology, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Antonello Pietrangelo
- Internal Medicine, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Massimo Girardis
- Intensive Care Unit, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Cristina Mussini
- Infectious Diseases, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Marianna Meschiari
- Infectious Diseases, Azienda Ospedaliera-Universitaria of Modena, University of Modena and Reggio Emilia, 41125 Modena, Italy
| |
Collapse
|
3
|
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: 8] [Impact Index Per Article: 8.0] [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.
Collapse
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.
| |
Collapse
|
4
|
Klockgether J, Pust MM, Davenport CF, Bunk B, Spröer C, Overmann J, Tümmler B. Structural genome variants of Pseudomonas aeruginosa clone C and PA14 strains. Front Microbiol 2023; 14:1095928. [PMID: 36992927 PMCID: PMC10040652 DOI: 10.3389/fmicb.2023.1095928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
Plasticity of Pseudomonas aeruginosa chromosomes is mainly driven by an extended accessory genome that is shaped by insertion and deletion events. Further modification of the genome composition can be induced by chromosomal inversion events which lead to relocation of genes in the affected genomic DNA segments, modify the otherwise highly conserved core genome synteny and could even alter the location of the replication terminus. Although the genome of the first sequenced strain, PAO1, displayed such a large genomic inversion, knowledge on such recombination events in the P. aeruginosa population is limited. Several large inversions had been discovered in the late 1990s in cystic fibrosis isolates of the major clonal lineage C by physical genome mapping, and subsequent work on these examples led to the characterization of the DNA at the recombination breakpoints and a presumed recombination mechanism. Since then, the topic was barely addressed in spite of the compilation of thousands of P. aeruginosa genome sequences that are deposited in databases. Due to the use of second-generation sequencing, genome contig assembly had usually followed synteny blueprints provided by the existing reference genome sequences. Inversion detection was not feasible by these approaches, as the respective read lengths did not allow reliable resolution of sequence repeats that are typically found at the borders of inverted segments. In this study, we applied PacBio and MinION long-read sequencing to isolates of the mentioned clone C collection. Confirmation of inversions predicted from the physical mapping data demonstrated that unbiased sequence assembly of such read datasets allows the detection of genomic inversions and the resolution of the recombination breakpoint regions. Additional long-read sequencing of representatives of the other major clonal lineage, PA14, revealed large inversions in several isolates, from cystic fibrosis origin as well as from other sources. These findings indicated that inversion events are not restricted to strains from chronic infection background, but could be widespread in the P. aeruginosa population and contribute to genome plasticity. Moreover, the monitored examples emphasized the role of small mobile DNA units, such as IS elements or transposons, and accessory DNA elements in the inversion-related recombination processes.
Collapse
Affiliation(s)
- Jens Klockgether
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hanover, Germany
- *Correspondence: Jens Klockgether,
| | - Marie-Madlen Pust
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hanover, Germany
| | - Colin F. Davenport
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hanover, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Center for Infection Research, Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Burkhard Tümmler
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hanover, Germany
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hanover, Germany
| |
Collapse
|
5
|
Job V, Gomez-Valero L, Renier A, Rusniok C, Bouillot S, Chenal-Francisque V, Gueguen E, Adrait A, Robert-Genthon M, Jeannot K, Panchev P, Elsen S, Fauvarque MO, Couté Y, Buchrieser C, Attrée I. Genomic erosion and horizontal gene transfer shape functional differences of the ExlA toxin in Pseudomonas spp. iScience 2022; 25:104596. [PMID: 35789842 PMCID: PMC9250014 DOI: 10.1016/j.isci.2022.104596] [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: 11/17/2021] [Revised: 03/15/2022] [Accepted: 06/08/2022] [Indexed: 12/31/2022] Open
Abstract
Two-partner secretion (TPS) is widespread in the bacterial world. The pore-forming TPS toxin ExlA of Pseudomonas aeruginosa is conserved in pathogenic and environmental Pseudomonas. While P. chlororaphis and P. entomophila displayed ExlA-dependent killing, P. putida did not cause damage to eukaryotic cells. ExlA proteins interacted with epithelial cell membranes; however, only ExlAPch induced the cleavage of the adhesive molecule E-cadherin. ExlA proteins participated in insecticidal activity toward the larvae of Galleria mellonella and the fly Drosophila melanogaster. Evolutionary analyses demonstrated that the differences in the C-terminal domains are partly due to horizontal movements of the operon within the genus Pseudomonas. Reconstruction of the evolutionary history revealed the complex horizontal acquisitions. Together, our results provide evidence that conserved TPS toxins in environmental Pseudomonas play a role in bacteria-insect interactions and discrete differences in CTDs may determine their specificity and mode of action toward eukaryotic cells. ExlA is a two-partner secreted toxin conserved across Pseudomonas spp. Environmental Pseudomonas strains encode ExlA with different cytotoxic activities ExlA of environmental Pseudomonas strains play a role in bacteria-insect interactions ExlBA operon shows a complex evolutionary history of horizontal gene transfer
Collapse
Affiliation(s)
- Viviana Job
- Université Grenoble Alpes, Institute of Structural Biology, Bacterial Pathogenesis and Cellular Responses Team, UMR5075 CNRS, IRIG, CEA, Grenoble, France
| | - Laura Gomez-Valero
- Institut Pasteur, Université de Paris, CNRS UMR 6047, Unité Biologie des Bactéries Intracellulaires, 75015 Paris, France
| | - Adèle Renier
- Université Grenoble Alpes, Institute of Structural Biology, Bacterial Pathogenesis and Cellular Responses Team, UMR5075 CNRS, IRIG, CEA, Grenoble, France
| | - Christophe Rusniok
- Institut Pasteur, Université de Paris, CNRS UMR 6047, Unité Biologie des Bactéries Intracellulaires, 75015 Paris, France
| | - Stephanie Bouillot
- Université Grenoble Alpes, Institute of Structural Biology, Bacterial Pathogenesis and Cellular Responses Team, UMR5075 CNRS, IRIG, CEA, Grenoble, France
| | - Viviane Chenal-Francisque
- Institut Pasteur, Université de Paris, CNRS UMR 6047, Unité Biologie des Bactéries Intracellulaires, 75015 Paris, France
| | - Erwan Gueguen
- University of Lyon, Université Lyon 1, INSA de Lyon, CNRS UMR 5240 Microbiologie Adaptation et Pathogénie, Lyon, France
| | - Annie Adrait
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, Grenoble, France
| | - Mylène Robert-Genthon
- Université Grenoble Alpes, Institute of Structural Biology, Bacterial Pathogenesis and Cellular Responses Team, UMR5075 CNRS, IRIG, CEA, Grenoble, France
| | - Katy Jeannot
- Centre National de Référence de la Résistance aux Antibiotiques, Laboratoire de Bactériologie, Centre Hospitalier Universitaire Jean Minjoz, UMR6249 CNRS, Université de Bourgogne-Franche Comté, Besançon, France
| | - Peter Panchev
- Université Grenoble Alpes, Institute of Structural Biology, Bacterial Pathogenesis and Cellular Responses Team, UMR5075 CNRS, IRIG, CEA, Grenoble, France
| | - Sylvie Elsen
- Université Grenoble Alpes, Institute of Structural Biology, Bacterial Pathogenesis and Cellular Responses Team, UMR5075 CNRS, IRIG, CEA, Grenoble, France
| | | | - Yohann Couté
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, Grenoble, France
- CNRS, CEA, FR2048, Grenoble, France
| | - Carmen Buchrieser
- Institut Pasteur, Université de Paris, CNRS UMR 6047, Unité Biologie des Bactéries Intracellulaires, 75015 Paris, France
- Corresponding author
| | - Ina Attrée
- Université Grenoble Alpes, Institute of Structural Biology, Bacterial Pathogenesis and Cellular Responses Team, UMR5075 CNRS, IRIG, CEA, Grenoble, France
- Corresponding author
| |
Collapse
|
6
|
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).
Collapse
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
| |
Collapse
|
7
|
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]
|
8
|
Lebreton F, Snesrud E, Hall L, Mills E, Galac M, Stam J, Ong A, Maybank R, Kwak YI, Johnson S, Julius M, Ly M, Swierczewski B, Waterman PE, Hinkle M, Jones A, Lesho E, Bennett JW, McGann P. A panel of diverse Pseudomonas aeruginosa clinical isolates for research and development. JAC Antimicrob Resist 2021; 3:dlab179. [PMID: 34909689 DOI: 10.1093/jacamr/dlab179] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 11/05/2021] [Indexed: 11/15/2022] Open
Abstract
Objectives Pseudomonas aeruginosa is a leading cause of community- and hospital-acquired infections. Successful treatment is hampered by its remarkable ability to rapidly develop resistance to antimicrobial agents, primarily through mutation. In response, WHO listed carbapenem-resistant P. aeruginosa as a Priority 1 (Critical) pathogen for research and development of new treatments. A key resource in developing effective countermeasures is access to diverse and clinically relevant strains for testing. Herein we describe a panel of 100 diverse P. aeruginosa strains to support this endeavour. Methods WGS was performed on 3785 P. aeruginosa isolates in our repository. Isolates were cultured from clinical samples collected from healthcare facilities around the world between 2003 and 2017. Core-genome MLST and high-resolution SNP-based phylogenetic analyses were used to select a panel of 100 strains that captured the genetic diversity of this collection. Antibiotic susceptibility testing was also performed using 14 clinically relevant antibiotics. Results This 100-strain diversity panel contained representative strains from 91 different STs, including genetically distinct strains from major epidemic clones ST-111, ST-235, ST-244 and ST-253. Seventy-one distinct antibiotic susceptibility profiles were identified ranging from pan-susceptible to pan-resistant. Known resistance alleles as well as the most prevalent mutations underlying the antibiotic susceptibilities were characterized for all isolates. Conclusions This panel provides a diverse and comprehensive set of P. aeruginosa strains for use in developing solutions to antibiotic resistance. The isolates and available metadata, including genome sequences, are available to industry, academia, federal and other laboratories at no additional cost.
Collapse
Affiliation(s)
- Francois Lebreton
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Erik Snesrud
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Lindsey Hall
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Emma Mills
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Madeline Galac
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jason Stam
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Ana Ong
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Rosslyn Maybank
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Yoon I Kwak
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sheila Johnson
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Michael Julius
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Melissa Ly
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Brett Swierczewski
- Bacterial Disease Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Mary Hinkle
- Infectious Diseases Unit, Rochester General Hospital, Rochester, NY, USA
| | - Anthony Jones
- Department of Virology, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Emil Lesho
- Infectious Diseases Unit, Rochester General Hospital, Rochester, NY, USA
| | - Jason W Bennett
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Patrick McGann
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD, USA
| |
Collapse
|
9
|
Abstract
The transcriptomes of Pseudomonas aeruginosa clone C isolates NN2 and SG17M during the mid-exponential and early stationary phase of planktonic growth were evaluated by direct RNA sequencing on the nanopore platform and compared with established short-read cDNA sequencing on the Illumina platform. Fifty to ninety percent of the sense RNAs turned out to be rRNA molecules followed by similar proportions of mRNA transcripts and non-coding RNAs. Both platforms detected similar proportions of uncharged tRNAs and 29 yet undescribed antisense tRNAs. For example, the rarest arginine codon was paired with the most abundant tRNAArg, and the tRNAArg gene is missing for the most frequent arginine codon. More than 90% of the antisense RNA molecules were complementary to a coding sequence. The antisense RNAs were evenly distributed in the genomes. Direct RNA sequencing identified more than 4,000 distinct non-overlapping antisense RNAs during exponential and stationary growth. Besides highly expressed small antisense RNAs less than 200 bases in size, a population of longer antisense RNAs was sequenced that covered a broad range of a few hundred to thousands of bases and could be complementary to a contig of several genes. In summary, direct RNA sequencing identified yet undescribed RNA molecules and an unexpected composition of the pools of tRNAs, sense and antisense RNAs. IMPORTANCE Genome-wide gene expression of bacteria is commonly studied by high-throughput sequencing of size-selected cDNA fragment libraries of reverse-transcribed RNA preparations. However, the depletion of ribosomal RNAs, enzymatic reverse transcription and the fragmentation, size selection and amplification during library preparation lead to inevitable losses of information about the initial composition of the RNA pool. We demonstrate that direct RNA sequencing on the nanopore platform can overcome these limitations. Nanopore sequencing of total RNA yielded novel insights into the Pseudomonas aeruginosa transcriptome that - if replicated in other species - will change our view of the bacterial RNA world. The discovery of sense - antisense pairs of tmRNA, tRNAs and mRNAs indicates a further and unknown level of gene regulation in bacteria.
Collapse
|
10
|
Irum S, Naz K, Ullah N, Mustafa Z, Ali A, Arslan M, Khalid K, Andleeb S. Antimicrobial Resistance and Genomic Characterization of Six New Sequence Types in Multidrug-Resistant Pseudomonas aeruginosa Clinical Isolates from Pakistan. Antibiotics (Basel) 2021; 10:antibiotics10111386. [PMID: 34827324 PMCID: PMC8615273 DOI: 10.3390/antibiotics10111386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/06/2021] [Accepted: 08/13/2021] [Indexed: 01/13/2023] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is a major bacterial pathogen associated with a variety of infections with high mortality rates. Most of the clinical P. aeruginosa isolates belong to a limited number of genetic subgroups characterized by multiple housekeeping genes’ sequences (usually 5–7) through the Multi-Locus Sequence Typing (MLST) scheme. The emergence and dissemination of novel multidrug-resistant (MDR) sequence types (ST) in P. aeruginosa pose serious clinical concerns. We performed whole-genome sequencing on a cohort (n = 160) of MDR P. aeruginosa isolates collected from a tertiary care hospital lab in Pakistan and found six isolates belonging to six unique MLST allelic profiles. The genomes were submitted to the PubMLST database and new ST numbers (ST3493, ST3494, ST3472, ST3489, ST3491, and ST3492) were assigned to the respective allele combinations. MLST and core-genome-based phylogenetic analysis confirmed the divergence of these isolates and positioned them in separate branches. Analysis of the resistome of the new STs isolates revealed the presence of genes blaOXA-50, blaPAO, blaPDC, blaVIM-2, aph(3′)-IIb, aac(6′)-II, aac(3)-Id, fosA, catB7, dfrB2, crpP, merP and a number of missense and frame-shift mutations in chromosomal genes conferring resistance to various antipseudomonal antibiotics. The exoS, exoT, pvdE, rhlI, rhlR, lasA, lasB, lasI, and lasR genes were the most prevalent virulence-related genes among the new ST isolates. The different genotypic features revealed the adaptation of these new clones to a variety of infections by various mutations in genes affecting antimicrobial resistance, quorum sensing and biofilm formation. Close monitoring of these antibiotic-resistant pathogens and surveillance mechanisms needs to be adopted to reduce their spread to the healthcare facilities of Pakistan. We believe that these strains can be used as reference strains for future comparative analysis of isolates belonging to the same STs.
Collapse
Affiliation(s)
- Sidra Irum
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Kanwal Naz
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Nimat Ullah
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Zeeshan Mustafa
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Amjad Ali
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Muhammad Arslan
- Pakistan Institute of Medical Sciences (PIMS), Islamabad 44000, Pakistan;
| | - Kashaf Khalid
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Saadia Andleeb
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
- Correspondence: or
| |
Collapse
|
11
|
Sanz-García F, Hernando-Amado S, Martínez JL. Evolution under low antibiotic concentrations: a risk for the selection of Pseudomonas aeruginosa multidrug-resistant mutants in nature. Environ Microbiol 2021; 24:1279-1293. [PMID: 34666420 DOI: 10.1111/1462-2920.15806] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/05/2021] [Indexed: 11/30/2022]
Abstract
Antibiotic pollution of non-clinical environments might have a relevant impact on human health if resistant pathogens are selected. However, this potential risk is often overlooked, since drug concentrations in nature are usually below their minimal inhibitory concentrations (MICs). Albeit, antibiotic resistant bacteria can be selected even at sub-MIC concentrations, in a range known as the sub-MIC selective window. Using short-term evolution experiments, we have determined the sub-MIC selective windows of the opportunistic pathogen Pseudomonas aeruginosa for seven antibiotics of clinical relevance, finding the ones of quinolones to be the widest, and the ones of polymyxin B and imipenem, the narrowest. Clinically relevant multidrug-resistant mutants arose within the sub-MIC selective windows of most antibiotics tested, being some of these phenotypes mediated by efflux pumps' activity. The fact that the concentration of antibiotics reported in aquatic ecosystems - colonizable by P. aeruginosa - are, in occasions, higher than the ones that select multidrug-resistant mutants in our assays, has implications for understanding the role of different ecosystems and conditions in the emergence of antibiotic resistance from a One-Health perspective. Further, it reinforces the importance of procuring accurate information on the sub-MIC selective windows for drugs of clinical value in pathogens with environmental niches.
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
|
14
|
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.
Collapse
Affiliation(s)
- Burkhard Tümmler
- Clinical Research Group, Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| |
Collapse
|
15
|
A comparative genomics approach identifies contact-dependent growth inhibition as a virulence determinant. Proc Natl Acad Sci U S A 2020; 117:6811-6821. [PMID: 32156726 DOI: 10.1073/pnas.1919198117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Emerging evidence suggests the Pseudomonas aeruginosa accessory genome is enriched with uncharacterized virulence genes. Identification and characterization of such genes may reveal novel pathogenic mechanisms used by particularly virulent isolates. Here, we utilized a mouse bacteremia model to quantify the virulence of 100 individual P. aeruginosa bloodstream isolates and performed whole-genome sequencing to identify accessory genomic elements correlated with increased bacterial virulence. From this work, we identified a specific contact-dependent growth inhibition (CDI) system enriched among highly virulent P. aeruginosa isolates. CDI systems contain a large exoprotein (CdiA) with a C-terminal toxin (CT) domain that can vary between different isolates within a species. Prior work has revealed that delivery of a CdiA-CT domain upon direct cell-to-cell contact can inhibit replication of a susceptible target bacterium. Aside from mediating interbacterial competition, we observed our virulence-associated CdiA-CT domain to promote toxicity against mammalian cells in culture and lethality during mouse bacteremia. Structural and functional studies revealed this CdiA-CT domain to have in vitro tRNase activity, and mutations that abrogated this tRNAse activity in vitro also attenuated virulence. Furthermore, CdiA contributed to virulence in mice even in the absence of contact-dependent signaling. Overall, our findings indicate that this P. aeruginosa CDI system functions as both an interbacterial inhibition system and a bacterial virulence factor against a mammalian host. These findings provide an impetus for continued studies into the complex role of CDI systems in P. aeruginosa pathogenesis.
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Kamal SM, Rybtke ML, Nimtz M, Sperlein S, Giske C, Trček J, Deschamps J, Briandet R, Dini L, Jänsch L, Tolker-Nielsen T, Lee C, Römling U. Two FtsH Proteases Contribute to Fitness and Adaptation of Pseudomonas aeruginosa Clone C Strains. Front Microbiol 2019; 10:1372. [PMID: 31338071 PMCID: PMC6629908 DOI: 10.3389/fmicb.2019.01372] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 05/31/2019] [Indexed: 12/30/2022] Open
Abstract
Pseudomonas aeruginosa is an environmental bacterium and a nosocomial pathogen with clone C one of the most prevalent clonal groups. The P. aeruginosa clone C specific genomic island PACGI-1 harbors a xenolog of ftsH encoding a functionally diverse membrane-spanning ATP-dependent metalloprotease on the core genome. In the aquatic isolate P. aeruginosa SG17M, the core genome copy ftsH1 significantly affects growth and dominantly mediates a broad range of phenotypes, such as secretion of secondary metabolites, swimming and twitching motility and resistance to aminoglycosides, while the PACGI-1 xenolog ftsH2 backs up the phenotypes in the ftsH1 mutant background. The two proteins, with conserved motifs for disaggregase and protease activity present in FtsH1 and FtsH2, have the ability to form homo- and hetero-oligomers with ftsH2 distinctively expressed in the late stationary phase of growth. However, mainly FtsH1 degrades a major substrate, the heat shock transcription factor RpoH. Pull-down experiments with substrate trap-variants inactive in proteolytic activity indicate both FtsH1 and FtsH2 to interact with the inhibitory protein HflC, while the phenazine biosynthesis protein PhzC was identified as a substrate of FtsH1. In summary, as an exception in P. aeruginosa, clone C harbors two copies of the ftsH metallo-protease, which cumulatively are required for the expression of a diversity of phenotypes.
Collapse
Affiliation(s)
- Shady Mansour Kamal
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Microbiology and Immunology, Faculty of Pharmaceutical Sciences & Pharmaceutical Industries, Future University in Egypt, New Cairo, Egypt
| | - Morten Levin Rybtke
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manfred Nimtz
- Department of Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefanie Sperlein
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Christian Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Janja Trček
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, Maribor, Slovenia
| | - Julien Deschamps
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Romain Briandet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Luciana Dini
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Lothar Jänsch
- Department of Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Changhan Lee
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
19
|
Weiser R, Green AE, Bull MJ, Cunningham-Oakes E, Jolley KA, Maiden MCJ, Hall AJ, Winstanley C, Weightman AJ, Donoghue D, Amezquita A, Connor TR, Mahenthiralingam E. Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes. Microb Genom 2019; 5:e000276. [PMID: 31170060 PMCID: PMC6700666 DOI: 10.1099/mgen.0.000276] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/24/2019] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa is a highly versatile, antibiotic-resistant Gram-negative bacterium known for causing opportunistic infections and contamination of industrial products. Despite extensive genomic analysis of clinical P. aeruginosa strains, no genomes exist for preservative-tolerant industrial strains. A unique collection of 69 industrial isolates was assembled and compared to clinical and environmental strains; 16 genetically distinct industrial strains were subjected to array tube genotyping, multilocus sequence typing and whole-genome sequencing. The industrial strains possessed high preservative tolerance and were dispersed widely across P. aeruginosa as a species, but recurrence of strains from the same lineage within specific industrial products and locations was identified. The industrial P. aeruginosa genomes (mean=7.0 Mb) were significantly larger than those of previously sequenced environmental (mean=6.5 Mb; n=19) and clinical (mean=6.6 Mb; n=66) strains. Complete sequencing of the P. aeruginosa industrial strain RW109, which encoded the largest genome (7.75 Mb), revealed a multireplicon structure including a megaplasmid (555 265 bp) and large plasmid (151 612 bp). The RW109 megaplasmid represented an emerging plasmid family conserved in seven industrial and two clinical P. aeruginosa strains, and associated with extremely stress-resilient phenotypes, including antimicrobial resistance and solvent tolerance. Here, by defining the detailed phylogenomics of P. aeruginosa industrial strains, we show that they uniquely possess multireplicon, megaplasmid-bearing genomes, and significantly greater genomic content worthy of further study.
Collapse
Affiliation(s)
- Rebecca Weiser
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Angharad E. Green
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
- University of Liverpool, Institute of Infection and Global Health, Liverpool, UK
| | - Matthew J. Bull
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Edward Cunningham-Oakes
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Keith A. Jolley
- Department of Zoology, The Tinbergen Building, University of Oxford, Oxford, UK
| | - Martin C. J. Maiden
- Department of Zoology, The Tinbergen Building, University of Oxford, Oxford, UK
| | - Amanda J. Hall
- University of Liverpool, Institute of Infection and Global Health, Liverpool, UK
| | - Craig Winstanley
- University of Liverpool, Institute of Infection and Global Health, Liverpool, UK
| | - Andrew J. Weightman
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Denise Donoghue
- Unilever Research and Development, Port Sunlight, Wirral, UK
| | - Alejandro Amezquita
- Unilever Research and Development, Safety and Environmental Assurance Centre, Colworth House, Sharnbrook, Bedford, UK
| | - Thomas R. Connor
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
| |
Collapse
|
20
|
Sentausa E, Basso P, Berry A, Adrait A, Bellement G, Couté Y, Lory S, Elsen S, Attrée I. Insertion sequences drive the emergence of a highly adapted human pathogen. Microb Genom 2019; 6. [PMID: 30946644 PMCID: PMC7643977 DOI: 10.1099/mgen.0.000265] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pseudomonas aeruginosa is a highly adaptive opportunistic pathogen that can have serious health consequences in patients with lung disorders. Taxonomic outliers of P. aeruginosa of environmental origin have recently emerged as infectious for humans. Here, we present the first genome-wide analysis of an isolate that caused fatal haemorrhagic pneumonia. In two clones, CLJ1 and CLJ3, sequentially recovered from a patient with chronic pulmonary disease, insertion of a mobile genetic element into the P. aeruginosa chromosome affected major virulence-associated phenotypes and led to increased resistance to the antibiotics used to combat the infection. Comparative genome, proteome and transcriptome analyses revealed that this ISL3-family insertion sequence disrupted the genes for flagellar components, type IV pili, O-specific antigens, translesion polymerase and enzymes producing hydrogen cyanide. Seven-fold more insertions were detected in the later isolate, CLJ3, than in CLJ1, some of which modified strain susceptibility to antibiotics by disrupting the genes for the outer-membrane porin OprD and the regulator of β-lactamase expression AmpD. In the Galleria mellonella larvae model, the two strains displayed different levels of virulence, with CLJ1 being highly pathogenic. This study revealed insertion sequences to be major players in enhancing the pathogenic potential of a P. aeruginosa taxonomic outlier by modulating both its virulence and its resistance to antimicrobials, and explains how this bacterium adapts from the environment to a human host.
Collapse
Affiliation(s)
- Erwin Sentausa
- Université Grenoble Alpes, CNRS ERL5261, INSERM U1036, CEA, Laboratory Biology of Cancer and Infection, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, 38000 Grenoble, France.,Present address: Evotec ID (Lyon) SAS, Marcy l'Étoile, France
| | - Pauline Basso
- Université Grenoble Alpes, CNRS ERL5261, INSERM U1036, CEA, Laboratory Biology of Cancer and Infection, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, 38000 Grenoble, France.,Present address: Department of Microbiology and Immunology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Alice Berry
- Université Grenoble Alpes, CNRS ERL5261, INSERM U1036, CEA, Laboratory Biology of Cancer and Infection, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, 38000 Grenoble, France
| | - Annie Adrait
- Université Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
| | - Gwendoline Bellement
- Université Grenoble Alpes, CNRS ERL5261, INSERM U1036, CEA, Laboratory Biology of Cancer and Infection, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, 38000 Grenoble, France.,Université Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France.,Present address: Biozentrum, University of Basel, Basel, Switzerland
| | - Yohann Couté
- Université Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
| | - Stephen Lory
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Sylvie Elsen
- Université Grenoble Alpes, CNRS ERL5261, INSERM U1036, CEA, Laboratory Biology of Cancer and Infection, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, 38000 Grenoble, France
| | - Ina Attrée
- Université Grenoble Alpes, CNRS ERL5261, INSERM U1036, CEA, Laboratory Biology of Cancer and Infection, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, 38000 Grenoble, France
| |
Collapse
|
21
|
Cramer N, Sedlacek L, Tümmler B, Welte T. Low transmission risk of Pseudomonas aeruginosa in a bronchiectasis clinic based on the knowledge of bacterial population biology. Eur Respir J 2019; 53:13993003.02191-2018. [PMID: 30635293 DOI: 10.1183/13993003.02191-2018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 12/19/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Nina Cramer
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Ludwig Sedlacek
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, Hannover, Germany
| | - Tobias Welte
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, Hannover, Germany.,Dept for Respiratory Medicine, Hannover Medical School, Hannover, Germany
| |
Collapse
|
22
|
Munder A, Rothschuh J, Schirmer B, Klockgether J, Kaever V, Tümmler B, Seifert R, Kloth C. The Pseudomonas aeruginosa ExoY phenotype of high-copy-number recombinants is not detectable in natural isolates. Open Biol 2019; 8:rsob.170250. [PMID: 29386405 PMCID: PMC5795057 DOI: 10.1098/rsob.170250] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/03/2018] [Indexed: 12/31/2022] Open
Abstract
The nucleotidyl cyclase ExoY is an effector protein of the type III secretion system of Pseudomonas aeruginosa. We compared the cyclic nucleotide production and lung disease phenotypes caused by the ExoY-overexpressing strain PA103ΔexoUexoT::Tc pUCPexoY, its vector control strain PA103ΔexoUexoT::Tc pUCP18, its loss-of-function control PA103ΔexoUexoT::Tc pUCPexoY K81M and natural ExoY-positive and ExoY-negative isolates in a murine acute airway infection model. Only the P. aeruginosa carrier of the exoY-plasmid produced high levels of cUMP and caused the most severe course of infection. The pathology ascribed to ExoY from studies using the high-copy-number plasmid on mammalian cells in vitro and in vivo was not observed with natural P. aeruginosa isolates. This indicates that the role of ExoY during infection with real-life P. aeruginosa still needs to be resolved.
Collapse
Affiliation(s)
- Antje Munder
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany .,Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, Hannover, Germany
| | - Justin Rothschuh
- Institute of Pharmacology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Bastian Schirmer
- Institute of Pharmacology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Jens Klockgether
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Hannover Medical School, 30625 Hannover, Germany
| | - Burkhard Tümmler
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, Hannover, Germany
| | - Roland Seifert
- Institute of Pharmacology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Christina Kloth
- Institute of Pharmacology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.,Institute of Functional and Applied Anatomy, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| |
Collapse
|
23
|
Abstract
Inspection of the genomes of bacterial pathogens indicates that their pathogenic potential relies, at least in part, on the activity of different elements that have been acquired by horizontal gene transfer from other (usually unknown) microorganisms. Similarly, in the case of resistance to antibiotics, besides mutation-driven resistance, the incorporation of novel resistance genes is a widespread evolutionary procedure for the acquisition of this phenotype. Current information in the field supports the idea that most (if not all) genes acquired by horizontal gene transfer by bacterial pathogens and contributing to their virulence potential or to antibiotic resistance originate in environmental, not human-pathogenic, microorganisms. Herein I discuss the potential functions that the genes that are dubbed virulence or antibiotic resistance genes may have in their original hosts in nonclinical, natural ecosystems. In addition, I discuss the potential bottlenecks modulating the transfer of virulence and antibiotic resistance determinants and the consequences in terms of speciation of acquiring one or another of both categories of genes. Finally, I propose that exaptation, a process by which a change of function is achieved by a change of habitat and not by changes in the element with the new functionality, is the basis of the evolution of virulence determinants and of antibiotic resistance genes.
Collapse
|
24
|
Comparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites. Sci Rep 2018; 8:15668. [PMID: 30353070 PMCID: PMC6199293 DOI: 10.1038/s41598-018-34020-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/04/2018] [Indexed: 12/17/2022] Open
Abstract
The large and complex genome of Pseudomonas aeruginosa, which consists of significant portions (up to 20%) of transferable genetic elements contributes to the rapid development of antibiotic resistance. The whole genome sequences of 22 strains isolated from eye and cystic fibrosis patients in Australia and India between 1992 and 2007 were used to compare genomic divergence and phylogenetic relationships as well as genes for antibiotic resistance and virulence factors. Analysis of the pangenome indicated a large variation in the size of accessory genome amongst 22 stains and the size of the accessory genome correlated with number of genomic islands, insertion sequences and prophages. The strains were diverse in terms of sequence type and dissimilar to that of global epidemic P. aeruginosa clones. Of the eye isolates, 62% clustered together within a single lineage. Indian eye isolates possessed genes associated with resistance to aminoglycoside, beta-lactams, sulphonamide, quaternary ammonium compounds, tetracycline, trimethoprims and chloramphenicols. These genes were, however, absent in Australian isolates regardless of source. Overall, our results provide valuable information for understanding the genomic diversity of P. aeruginosa isolated from two different infection types and countries.
Collapse
|
25
|
Brüggemann H, Migliorini LB, Sales ROD, Koga PCM, Souza AVD, Jensen A, Poehlein A, Brzuszkiewicz E, Doi AM, Pasternak J, Martino MDV, Severino P. Comparative Genomics of Nonoutbreak Pseudomonas aeruginosa Strains Underlines Genome Plasticity and Geographic Relatedness of the Global Clone ST235. Genome Biol Evol 2018; 10:1852-1857. [PMID: 29982603 PMCID: PMC6063271 DOI: 10.1093/gbe/evy139] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2018] [Indexed: 02/07/2023] Open
Abstract
Pseudomonas aeruginosa is an important opportunistic pathogen in hospitals, responsible for various infections that are difficult to treat due to intrinsic and acquired antibiotic resistance. Here, 20 epidemiologically unrelated strains isolated from patients in a general hospital over a time period of two decades were analyzed using whole genome sequencing. The genomes were compared in order to assess the presence of a predominant clone or sequence type (ST). No clonal structure was identified, but core genome-based single nucleotide polymorphism (SNP) analysis distinguished two major, previously identified phylogenetic groups. Interestingly, most of the older strains isolated between 1994 and 1998 harbored exoU, encoding a cytotoxic phospholipase. In contrast, most strains isolated between 2011 and 2016 were exoU-negative and phylogenetically very distinct from the older strains, suggesting a population shift of nosocomial P. aeruginosa over time. Three out of 20 strains were ST235 strains, a global high-risk clonal lineage; these carried several additional resistance determinants including aac(6’)Ib-cr encoding an aminoglycoside N-acetyltransferase that confers resistance to fluoroquinolones. Core genome comparison with ST235 strains from other parts of the world showed that the three strains clustered together with other Brazilian/Argentinean isolates. Despite this regional relatedness, the individuality of each of the three ST235 strains was revealed by core genome-based SNPs and the presence of genomic islands in the accessory genome. Similarly, strain-specific characteristics were detected for the remaining strains, indicative of individual evolutionary histories and elevated genome plasticity.
Collapse
Affiliation(s)
| | - Leticia Busato Migliorini
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | - Romario Oliveira de Sales
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | | | - Andrea Vieira de Souza
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | - Anders Jensen
- Department of Biomedicine, Aarhus University, Denmark
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Germany
| | - Elzbieta Brzuszkiewicz
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Germany
| | - Andre Mario Doi
- Laboratorio Clinico, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | - Jacyr Pasternak
- Laboratorio Clinico, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | | | - Patricia Severino
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| |
Collapse
|
26
|
Rutherford V, Yom K, Ozer EA, Pura O, Hughes A, Murphy KR, Cudzilo L, Mitchel D, Hauser AR. Environmental reservoirs for exoS+ and exoU+ strains of Pseudomonas aeruginosa. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:485-492. [PMID: 29687624 PMCID: PMC6108916 DOI: 10.1111/1758-2229.12653] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 04/15/2018] [Indexed: 06/08/2023]
Abstract
Pseudomonas aeruginosa uses its type III secretion system to inject the effector proteins ExoS and ExoU into eukaryotic cells, which subverts these cells to the bacterium's advantage and contributes to severe infections. We studied the environmental reservoirs of exoS+ and exoU+ strains of P. aeruginosa by collecting water, soil, moist substrates and plant samples from environments in the Chicago region and neighbouring states. Whole-genome sequencing was used to determine the phylogeny and type III secretion system genotypes of 120 environmental isolates. No correlation existed between geographic separation of isolates and their genetic relatedness, which confirmed previous findings of both high genetic diversity within a single site and the widespread distribution of P. aeruginosa clonal complexes. After excluding clonal isolates cultured from the same samples, 74 exoS+ isolates and 16 exoU+ isolates remained. Of the exoS+ isolates, 41 (55%) were from natural environmental sites and 33 (45%) were from man-made sites. Of the exoU+ isolates, only 3 (19%) were from natural environmental sites and 13 (81%) were from man-made sites (p < 0.05). These findings suggest that man-made water systems may be a reservoir from which patients acquire exoU+ P. aeruginosa strains.
Collapse
Affiliation(s)
- Victoria Rutherford
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Kelly Yom
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Egon A. Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Olivia Pura
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ami Hughes
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Katherine R. Murphy
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Laura Cudzilo
- Department of Biology, St. John’s University, Collegeville, Minnesota
| | - David Mitchel
- Department of Biology, St. John’s University, Collegeville, Minnesota
| | - Alan R. Hauser
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| |
Collapse
|
27
|
Reboud E, Basso P, Maillard AP, Huber P, Attrée I. Exolysin Shapes the Virulence of Pseudomonas aeruginosa Clonal Outliers. Toxins (Basel) 2017; 9:toxins9110364. [PMID: 29120408 PMCID: PMC5705979 DOI: 10.3390/toxins9110364] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 10/30/2017] [Accepted: 11/02/2017] [Indexed: 12/12/2022] Open
Abstract
Bacterial toxins are important weapons of toxicogenic pathogens. Depending on their origin, structure and targets, they show diverse mechanisms of action and effects on eukaryotic cells. Exolysin is a secreted 170 kDa pore-forming toxin employed by clonal outliers of Pseudomonas aeruginosa providing to some strains a hyper-virulent behaviour. This group of strains lacks the major virulence factor used by classical strains, the Type III secretion system. Here, we review the structural features of the toxin, the mechanism of its secretion and the effects of the pore formation on eukaryotic cells.
Collapse
Affiliation(s)
- Emeline Reboud
- CNRS-ERL5261, INSERM, U1036, CEA, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, University Grenoble Alpes, 17 rue des Martyrs, CEA-Grenoble, 38054 Grenoble, France.
| | - Pauline Basso
- CNRS-ERL5261, INSERM, U1036, CEA, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, University Grenoble Alpes, 17 rue des Martyrs, CEA-Grenoble, 38054 Grenoble, France.
| | - Antoine P Maillard
- CNRS-ERL5261, INSERM, U1036, CEA, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, University Grenoble Alpes, 17 rue des Martyrs, CEA-Grenoble, 38054 Grenoble, France.
| | - Philippe Huber
- CNRS-ERL5261, INSERM, U1036, CEA, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, University Grenoble Alpes, 17 rue des Martyrs, CEA-Grenoble, 38054 Grenoble, France.
| | - Ina Attrée
- CNRS-ERL5261, INSERM, U1036, CEA, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, University Grenoble Alpes, 17 rue des Martyrs, CEA-Grenoble, 38054 Grenoble, France.
| |
Collapse
|
28
|
Abstract
The versatile and ubiquitous
Pseudomonas aeruginosa is an opportunistic pathogen causing acute and chronic infections in predisposed human subjects. Here we review recent progress in understanding
P. aeruginosa population biology and virulence, its cyclic di-GMP-mediated switches of lifestyle, and its interaction with the mammalian host as well as the role of the type III and type VI secretion systems in
P. aeruginosa infection.
Collapse
Affiliation(s)
- Jens Klockgether
- Molecular Pathology of Cystic Fibrosis Clinical Research Group, Clinic for Paediatric Pneumology, Allergology, and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Molecular Pathology of Cystic Fibrosis Clinical Research Group, Clinic for Paediatric Pneumology, Allergology, and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Centre for Lung Research, Hannover, Germany
| |
Collapse
|
29
|
Environmental Pseudomonads Inhibit Cystic Fibrosis Patient-Derived Pseudomonas aeruginosa. Appl Environ Microbiol 2016; 83:AEM.02701-16. [PMID: 27881418 PMCID: PMC5203635 DOI: 10.1128/aem.02701-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 10/28/2016] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen which is evolving resistance to many currently used antibiotics. While much research has been devoted to the roles of pathogenic P. aeruginosa in cystic fibrosis (CF) patients, less is known of its ecological properties. P. aeruginosa dominates the lungs during chronic infection in CF patients, yet its abundance in some environments is less than that of other diverse groups of pseudomonads. Here, we sought to determine if clinical isolates of P. aeruginosa are vulnerable to environmental pseudomonads that dominate soil and water habitats in one-to-one competitions which may provide a source of inhibitory factors. We isolated a total of 330 pseudomonads from diverse habitats of soil and freshwater ecosystems and competed these strains against one another to determine their capacity for antagonistic activity. Over 900 individual inhibitory events were observed. Extending the analysis to P. aeruginosa isolates revealed that clinical isolates, including ones with increased alginate production, were susceptible to competition by multiple environmental strains. We performed transposon mutagenesis on one isolate and identified an ∼14.8-kb locus involved in antagonistic activity. Only two other environmental isolates were observed to carry the locus, suggesting the presence of additional unique compounds or interactions among other isolates involved in outcompeting P. aeruginosa. This collection of strains represents a source of compounds that are active against multiple pathogenic strains. With the evolution of resistance of P. aeruginosa to currently used antibiotics, these environmental strains provide opportunities for novel compound discovery against drug-resistant clinical strains. IMPORTANCE We demonstrate that clinical CF-derived isolates of P. aeruginosa are susceptible to competition in the presence of environmental pseudomonads. We observed that many diverse environmental strains exhibited varied antagonistic profiles against a panel of clinical P. aeruginosa isolates, suggesting the presence of distinct mechanisms of inhibition among these ecological strains. Understanding the properties of these antagonistic events offers the potential for discoveries of antimicrobial compounds or metabolic pathways important to the development of novel treatments for P. aeruginosa infections.
Collapse
|
30
|
Molecular Epidemiology of Mutations in Antimicrobial Resistance Loci of Pseudomonas aeruginosa Isolates from Airways of Cystic Fibrosis Patients. Antimicrob Agents Chemother 2016; 60:6726-6734. [PMID: 27572404 DOI: 10.1128/aac.00724-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/23/2016] [Indexed: 01/30/2023] Open
Abstract
The chronic airway infections with Pseudomonas aeruginosa in people with cystic fibrosis (CF) are treated with aerosolized antibiotics, oral fluoroquinolones, and/or intravenous combination therapy with aminoglycosides and β-lactam antibiotics. An international strain collection of 361 P. aeruginosa isolates from 258 CF patients seen at 30 CF clinics was examined for mutations in 17 antimicrobial susceptibility and resistance loci that had been identified as hot spots of mutation by genome sequencing of serial isolates from a single CF clinic. Combinatorial amplicon sequencing of pooled PCR products identified 1,112 sequence variants that were not present in the genomes of representative strains of the 20 most common clones of the global P. aeruginosa population. A high frequency of singular coding variants was seen in spuE, mexA, gyrA, rpoB, fusA1, mexZ, mexY, oprD, ampD, parR, parS, and envZ (amgS), reflecting the pressure upon P. aeruginosa in lungs of CF patients to generate novel protein variants. The proportion of nonneutral amino acid exchanges was high. Of the 17 loci, mexA, mexZ, and pagL were most frequently affected by independent stop mutations. Private and de novo mutations seem to play a pivotal role in the response of P. aeruginosa populations to the antimicrobial load and the individual CF host.
Collapse
|
31
|
Morán Losada P, Tümmler B. SNP synteny analysis of Staphylococcus aureus and Pseudomonas aeruginosa population genomics. FEMS Microbiol Lett 2016; 363:fnw229. [PMID: 27702754 DOI: 10.1093/femsle/fnw229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/31/2016] [Accepted: 09/29/2016] [Indexed: 01/04/2023] Open
Abstract
Genomic sequence diversity of a bacterial species mainly results from the frequency distribution of single nucleotide polymorphisms (SNPs). Here we report on an SNP matrix-based binary algorithm to determine the intraclonal or interclonal genomic diversity by the number of shared sequential SNPs, the so-called SNP synteny or haplotype. All SNP positions and the frequency and length distribution of haplotypes are determined from pairwise alignment of completely sequenced genomes. This metric is invariant regarding the reference genome chosen. Information is obtained about the size of haplotypes, genomic gradients of recombination frequency, relatedness of strains and population composition of a taxon or clonal populations. The approach is illustrated with whole genome data sets of Staphylococcus aureus and Pseudomonas aeruginosa strains.
Collapse
Affiliation(s)
- Patricia Morán Losada
- Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Hannover D-30625, Germany
| | - Burkhard Tümmler
- Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Hannover D-30625, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover D-30625, Germany
| |
Collapse
|
32
|
Fischer S, Klockgether J, Morán Losada P, Chouvarine P, Cramer N, Davenport CF, Dethlefsen S, Dorda M, Goesmann A, Hilker R, Mielke S, Schönfelder T, Suerbaum S, Türk O, Woltemate S, Wiehlmann L, Tümmler B. Intraclonal genome diversity of the major Pseudomonas aeruginosa clones C and PA14. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:227-234. [PMID: 26711897 PMCID: PMC4819714 DOI: 10.1111/1758-2229.12372] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/16/2015] [Indexed: 06/05/2023]
Abstract
Bacterial populations differentiate at the subspecies level into clonal complexes. Intraclonal genome diversity was studied in 100 isolates of the two dominant Pseudomonas aeruginosa clones C and PA14 collected from the inanimate environment, acute and chronic infections. The core genome was highly conserved among clone members with a median pairwise within-clone single nucleotide sequence diversity of 8 × 10(-6) for clone C and 2 × 10(-5) for clone PA14. The composition of the accessory genome was, on the other hand, as variable within the clone as between unrelated clones. Each strain carried a large cargo of unique genes. The two dominant worldwide distributed P. aeruginosa clones combine an almost invariant core with the flexible gain and loss of genetic elements that spread by horizontal transfer.
Collapse
Affiliation(s)
- Sebastian Fischer
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Hannover, Germany
| | - Jens Klockgether
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Hannover, Germany
| | - Patricia Morán Losada
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Hannover, Germany
| | - Philippe Chouvarine
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Hannover, Germany
| | - Nina Cramer
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Hannover, Germany
| | - Colin F Davenport
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Hannover, Germany
| | - Sarah Dethlefsen
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Hannover, Germany
| | - Marie Dorda
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Hannover, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-Universität, Gießen, Germany
| | - Rolf Hilker
- Bioinformatics and Systems Biology, Justus-Liebig-Universität, Gießen, Germany
| | - Samira Mielke
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Hannover, Germany
| | - Torben Schönfelder
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Hannover, Germany
| | - Sebastian Suerbaum
- Institute for Medical Microbiology and Hospital Epidemiology, OE 5210, Hannover Medical School, Hannover, Germany
| | - Oliver Türk
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Hannover, Germany
| | - Sabrina Woltemate
- Institute for Medical Microbiology and Hospital Epidemiology, OE 5210, Hannover Medical School, Hannover, Germany
| | - Lutz Wiehlmann
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Clinical Research Group 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, Hannover, Germany
| |
Collapse
|
33
|
Lee C, Wigren E, Lünsdorf H, Römling U. Protein homeostasis-more than resisting a hot bath. Curr Opin Microbiol 2016; 30:147-154. [PMID: 26974352 DOI: 10.1016/j.mib.2016.02.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 02/10/2016] [Accepted: 02/22/2016] [Indexed: 12/13/2022]
Abstract
Maintenance of protein homeostasis is essential for survival of all organisms. In bacteria, the protein quality control system has a broad physiological impact beyond heat shock resistance, being involved in virulence, antibiotic resistance, as well as protection against environmental stresses. Its contribution to rejuvenation and growth arrest suggests interference with protein quality control to be a novel antimicrobial strategy. Remarkably, a protein quality control module originating from environmental strains has been found to be horizontally transferred to predominant clonal groups of bacteria providing exquisite thermotolerance to recently emerged global pathogens suggesting that novel features related to protein homeostasis contribute to the transition to new environments.
Collapse
Affiliation(s)
- Changhan Lee
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 77, Sweden.
| | - Edvard Wigren
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Heinrich Lünsdorf
- The Helmholtz Center for Infection Research, Braunschweig 38124, Germany
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 77, Sweden.
| |
Collapse
|