1
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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.
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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
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2
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Planet PJ. Adaptation and Evolution of Pathogens in the Cystic Fibrosis Lung. J Pediatric Infect Dis Soc 2022; 11:S23-S31. [PMID: 36069898 PMCID: PMC9451014 DOI: 10.1093/jpids/piac073] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/11/2022] [Indexed: 02/05/2023]
Abstract
As opposed to acute respiratory infections, the persistent bacterial infections of the lung that characterize cystic fibrosis (CF) provide ample time for bacteria to evolve and adapt. The process of adaptation is recorded in mutations that accumulate over time in the genomes of the infecting bacteria. Some of these mutations lead to obvious phenotypic differences such as antibiotic resistance or the well-known mucoid phenotype of Pseudomonas aeruginosa. Other mutations may be just as important but harder to detect such as increased mutation rates, cell surface changes, and shifts in metabolism and nutrient acquisition. Remarkably, many of the adaptations occur again and again in different patients, signaling that bacteria are adapting to solve specific challenges in the CF respiratory tract. This parallel evolution even extends across distinct bacterial species. This review addresses the bacterial systems that are known to change in long-term CF infections with a special emphasis on cross-species comparisons. Consideration is given to how adaptation may impact health in CF, and the possible evolutionary mechanisms that lead to the repeated parallel adaptations.
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Affiliation(s)
- Paul J Planet
- Corresponding Author: Paul J. Planet, MD, PhD, 3615 Civic Center Blvd, Philadelphia, PA 19104. E-mail:
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3
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Langton Hewer SC, Smyth AR, Brown M, Jones AP, Hickey H, Kenna D, Ashby D, Thompson A, Sutton L, Clayton D, Arch B, Tanajewski Ł, Berdunov V, Williamson PR. Intravenous or oral antibiotic treatment in adults and children with cystic fibrosis and Pseudomonas aeruginosa infection: the TORPEDO-CF RCT. Health Technol Assess 2021; 25:1-128. [PMID: 34806975 DOI: 10.3310/hta25650] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND People with cystic fibrosis are susceptible to pulmonary infection with Pseudomonas aeruginosa. This may become chronic and lead to increased mortality and morbidity. If treatment is commenced promptly, infection may be eradicated through prolonged antibiotic treatment. OBJECTIVE To compare the clinical effectiveness, cost-effectiveness and safety of two eradication regimens. DESIGN This was a Phase IV, multicentre, parallel-group, randomised controlled trial. SETTING Seventy UK and two Italian cystic fibrosis centres. PARTICIPANTS Participants were individuals with cystic fibrosis aged > 28 days old who had never had a P. aeruginosa infection or who had been infection free for 1 year. INTERVENTIONS Fourteen days of intravenous ceftazidime and tobramycin or 3 months of oral ciprofloxacin. Inhaled colistimethate sodium was included in both regimens over 3 months. Consenting patients were randomly allocated to either treatment arm in a 1 : 1 ratio using simple block randomisation with random variable block length. MAIN OUTCOME MEASURES The primary outcome was eradication of P. aeruginosa at 3 months and remaining free of infection to 15 months. Secondary outcomes included time to reoccurrence, spirometry, anthropometrics, pulmonary exacerbations and hospitalisations. Primary analysis used intention to treat (powered for superiority). Safety analysis included patients who had received at least one dose of any of the study drugs. Cost-effectiveness analysis explored the cost per successful eradication and the cost per quality-adjusted life-year. RESULTS Between 5 October 2010 and 27 January 2017, 286 patients were randomised: 137 patients to intravenous antibiotics and 149 patients to oral antibiotics. The numbers of participants achieving the primary outcome were 55 out of 125 (44%) in the intravenous group and 68 out of 130 (52%) in the oral group. Participants randomised to the intravenous group were less likely to achieve the primary outcome; although the difference between groups was not statistically significant, the clinically important difference that the trial aimed to detect was not contained within the confidence interval (relative risk 0.84, 95% confidence interval 0.65 to 1.09; p = 0.184). Significantly fewer patients in the intravenous group (40/129, 31%) than in the oral group (61/136, 44.9%) were hospitalised in the 12 months following eradication treatment (relative risk 0.69, 95% confidence interval 0.5 to 0.95; p = 0.02). There were no clinically important differences in other secondary outcomes. There were 32 serious adverse events in 24 participants [intravenous: 10/126 (7.9%); oral: 14/146 (9.6%)]. Oral therapy led to reductions in costs compared with intravenous therapy (-£5938.50, 95% confidence interval -£7190.30 to -£4686.70). Intravenous therapy usually necessitated hospital admission, which accounted for a large part of this cost. LIMITATIONS Only 15 out of the 286 participants recruited were adults - partly because of the smaller number of adult centres participating in the trial. The possibility that the trial participants may be different from the rest of the cystic fibrosis population and may have had a better clinical status, and so be more likely to agree to the uncertainty of trial participation, cannot be ruled out. CONCLUSIONS Intravenous antibiotics did not achieve sustained eradication of P. aeruginosa in a greater proportion of cystic fibrosis patients. Although there were fewer hospitalisations in the intravenous group during follow-up, this confers no advantage over the oral therapy group, as intravenous eradication frequently requires hospitalisation. These results do not support the use of intravenous antibiotics to eradicate P. aeruginosa in cystic fibrosis. FUTURE WORK Future research studies should combine long-term follow-up with regimens to reduce reoccurrence after eradication. TRIAL REGISTRATION Current Controlled Trials ISRCTN02734162 and EudraCT 2009-012575-10. FUNDING This project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 25, No. 65. See the NIHR Journals Library website for further project information.
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Affiliation(s)
- Simon C Langton Hewer
- Department of Paediatric Respiratory Medicine, Bristol Royal Hospital for Children.,University of Bristol, Bristol, UK
| | - Alan R Smyth
- Division of Child Health, Obstetrics and Gynaecology, University of Nottingham, Nottingham, UK
| | - Michaela Brown
- Liverpool Clinical Trials Centre, University of Liverpool, a member of the Liverpool Health Partners, Liverpool, UK
| | - Ashley P Jones
- Liverpool Clinical Trials Centre, University of Liverpool, a member of the Liverpool Health Partners, Liverpool, UK
| | - Helen Hickey
- Liverpool Clinical Trials Centre, University of Liverpool, a member of the Liverpool Health Partners, Liverpool, UK
| | - Dervla Kenna
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, London, UK
| | - Deborah Ashby
- School of Public Health, Imperial College London, London, UK
| | - Alexander Thompson
- Manchester Centre for Health Economics, The University of Manchester, Manchester, UK
| | - Laura Sutton
- Liverpool Clinical Trials Centre, University of Liverpool, a member of the Liverpool Health Partners, Liverpool, UK
| | - Dannii Clayton
- Liverpool Clinical Trials Centre, University of Liverpool, a member of the Liverpool Health Partners, Liverpool, UK
| | - Barbara Arch
- Liverpool Clinical Trials Centre, University of Liverpool, a member of the Liverpool Health Partners, Liverpool, UK
| | - Łukasz Tanajewski
- Division of Pharmacy Practice and Policy, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Vladislav Berdunov
- Division of Pharmacy Practice and Policy, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Paula R Williamson
- Liverpool Clinical Trials Centre, University of Liverpool, a member of the Liverpool Health Partners, Liverpool, UK
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4
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Armbruster CR, Marshall CW, Garber AI, Melvin JA, Zemke AC, Moore J, Zamora PF, Li K, Fritz IL, Manko CD, Weaver ML, Gaston JR, Morris A, Methé B, DePas WH, Lee SE, Cooper VS, Bomberger JM. Adaptation and genomic erosion in fragmented Pseudomonas aeruginosa populations in the sinuses of people with cystic fibrosis. Cell Rep 2021; 37:109829. [PMID: 34686349 PMCID: PMC8667756 DOI: 10.1016/j.celrep.2021.109829] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/09/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022] Open
Abstract
Pseudomonas aeruginosa notoriously adapts to the airways of people with cystic fibrosis (CF), yet how infection-site biogeography and associated evolutionary processes vary as lifelong infections progress remains unclear. Here we test the hypothesis that early adaptations promoting aggregation influence evolutionary-genetic trajectories by examining longitudinal P. aeruginosa from the sinuses of six adults with CF. Highly host-adapted lineages harbored mutator genotypes displaying signatures of early genome degradation associated with recent host restriction. Using an advanced imaging technique (MiPACT-HCR [microbial identification after passive clarity technique]), we find population structure tracks with genome degradation, with the most host-adapted, genome-degraded P. aeruginosa (the mutators) residing in small, sparse aggregates. We propose that following initial adaptive evolution in larger populations under strong selection for aggregation, P. aeruginosa persists in small, fragmented populations that experience stronger effects of genetic drift. These conditions enrich for mutators and promote degenerative genome evolution. Our findings underscore the importance of infection-site biogeography to pathogen evolution.
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Affiliation(s)
- Catherine R Armbruster
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | | | - Arkadiy I Garber
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Jeffrey A Melvin
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Anna C Zemke
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - John Moore
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Paula F Zamora
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Ian L Fritz
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Christopher D Manko
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Madison L Weaver
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Jordan R Gaston
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Alison Morris
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Barbara Methé
- Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - William H DePas
- Department of Pediatrics, Children's Hospital of Pittsburgh and University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Stella E Lee
- Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA.
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA; Center for Medicine and the Microbiome, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA; Pittsburgh Center for Evolutionary Biology & Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| | - Jennifer M Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
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5
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Lee C, Klockgether J, Fischer S, Trcek J, Tümmler B, Römling U. Why? - Successful Pseudomonas aeruginosa clones with a focus on clone C. FEMS Microbiol Rev 2021; 44:740-762. [PMID: 32990729 PMCID: PMC7685784 DOI: 10.1093/femsre/fuaa029] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/12/2020] [Indexed: 12/20/2022] Open
Abstract
The environmental species Pseudomonas aeruginosa thrives in a variety of habitats. Within the epidemic population structure of P. aeruginosa, occassionally highly successful clones that are equally capable to succeed in the environment and the human host arise. Framed by a highly conserved core genome, individual members of successful clones are characterized by a high variability in their accessory genome. The abundance of successful clones might be funded in specific features of the core genome or, although not mutually exclusive, in the variability of the accessory genome. In clone C, one of the most predominant clones, the plasmid pKLC102 and the PACGI-1 genomic island are two ubiquitous accessory genetic elements. The conserved transmissible locus of protein quality control (TLPQC) at the border of PACGI-1 is a unique horizontally transferred compository element, which codes predominantly for stress-related cargo gene products such as involved in protein homeostasis. As a hallmark, most TLPQC xenologues possess a core genome equivalent. With elevated temperature tolerance as a characteristic of clone C strains, the unique P. aeruginosa and clone C specific disaggregase ClpG is a major contributor to tolerance. As other successful clones, such as PA14, do not encode the TLPQC locus, ubiquitous denominators of success, if existing, need to be identified.
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Affiliation(s)
- Changhan Lee
- Department of Microbiology, Tumor and Cell Biology, Biomedicum C8, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Jens Klockgether
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover Medical School, D-30625 Hannover, Germany
| | - Sebastian Fischer
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover Medical School, D-30625 Hannover, Germany
| | - Janja Trcek
- Faculty of Natural Sciences and Mathematics, Department of Biology, University of Maribor, Maribor, 2000, Slovenia
| | - Burkhard Tümmler
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover Medical School, D-30625 Hannover, Germany
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Biomedicum C8, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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6
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Morello E, Pérez-Berezo T, Boisseau C, Baranek T, Guillon A, Bréa D, Lanotte P, Carpena X, Pietrancosta N, Hervé V, Ramphal R, Cenac N, Si-Tahar M. Pseudomonas aeruginosa Lipoxygenase LoxA Contributes to Lung Infection by Altering the Host Immune Lipid Signaling. Front Microbiol 2019; 10:1826. [PMID: 31474948 PMCID: PMC6702342 DOI: 10.3389/fmicb.2019.01826] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 07/24/2019] [Indexed: 01/17/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic bacteria and a major cause of nosocomial pneumonia. P. aeruginosa has many virulence factors contributing to its ability to colonize the host. LoxA is a lipoxygenase enzyme secreted by P. aeruginosa that oxidizes polyunsaturated fatty acids. Based on previous in vitro biochemical studies, several biological roles of LoxA have been hypothesized, including interference of the host lipid signaling, and modulation of bacterial invasion properties. However, the contribution of LoxA to P. aeruginosa lung pathogenesis per se remained unclear. In this study, we used complementary in vitro and in vivo approaches, clinical strains of P. aeruginosa as well as lipidomics technology to investigate the role of LoxA in lung infection. We found that several P. aeruginosa clinical isolates express LoxA. When secreted in the lungs, LoxA processes a wide range of host polyunsaturated fatty acids, which further results in the production of bioactive lipid mediators (including lipoxin A4). LoxA also inhibits the expression of major chemokines (e.g., MIPs and KC) and the recruitment of key leukocytes. Remarkably, LoxA promotes P. aeruginosa persistence in lungs tissues. Hence, our study suggests that LoxA-dependent interference of the host lipid pathways may contribute to P. aeruginosa lung pathogenesis.
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Affiliation(s)
- Eric Morello
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France.,Université de Tours, Tours, France
| | - Teresa Pérez-Berezo
- Institut de Recherche en Santé Digestive, Université de Toulouse, INSERM, INRA, Ecole Nationale Vétérinaire de Toulouse, Toulouse, France
| | - Chloé Boisseau
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France.,Université de Tours, Tours, France
| | - Thomas Baranek
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France.,Université de Tours, Tours, France
| | - Antoine Guillon
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France.,Université de Tours, Tours, France
| | - Déborah Bréa
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France.,Université de Tours, Tours, France
| | - Philippe Lanotte
- CHRU de Tours, Service de Bactériologie-Virologie, Tours, France.,Université de Tours, UMR1282 ISP, Faculté de Médecine, Equipe Bactéries et Risque Materno-Foetal, Tours, France
| | - Xavier Carpena
- Institut de Biologia Molecular de Barcelona, Parc Científic de Barcelona, Barcelona, Spain.,XALOC Beamline, ALBA Synchrotron, Cerdanyola del Vallès, Spain
| | - Nicolas Pietrancosta
- Plateau 2MI, CNRS UMR8601, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Centre Universitaire des Saints-Pères, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Virginie Hervé
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France.,Université de Tours, Tours, France
| | - Reuben Ramphal
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France.,Université de Tours, Tours, France.,Department of Medicine, University of Florida, Gainesville, FL, United States
| | - Nicolas Cenac
- Institut de Recherche en Santé Digestive, Université de Toulouse, INSERM, INRA, Ecole Nationale Vétérinaire de Toulouse, Toulouse, France
| | - Mustapha Si-Tahar
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France.,Université de Tours, Tours, France
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7
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Marvig RL, Sommer LM, Jelsbak L, Molin S, Johansen HK. Evolutionary insight from whole-genome sequencing of Pseudomonas aeruginosa from cystic fibrosis patients. Future Microbiol 2015; 10:599-611. [DOI: 10.2217/fmb.15.3] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
ABSTRACT The opportunistic pathogen Pseudomonas aeruginosa causes chronic airway infections in patients with cystic fibrosis (CF), and it is directly associated with the morbidity and mortality connected with this disease. The ability of P. aeruginosa to establish chronic infections in CF patients is suggested to be due to the large genetic repertoire of P. aeruginosa and its ability to genetically adapt to the host environment. Here, we review the recent work that has applied whole-genome sequencing to understand P. aeruginosa population genomics, within-host microevolution and diversity, mutational mechanisms, genetic adaptation and transmission events. Finally, we summarize the advances in relation to medical applications and laboratory evolution experiments.
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Affiliation(s)
| | - Lea M Sommer
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lars Jelsbak
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Søren Molin
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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8
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Lavenir R, Petit SMC, Alliot N, Ribun S, Loiseau L, Marjolet L, Briolay J, Nazaret S, Cournoyer B. Structure and fate of a Pseudomonas aeruginosa population originating from a combined sewer and colonizing a wastewater treatment lagoon. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:5402-5418. [PMID: 24407782 DOI: 10.1007/s11356-013-2454-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
The efficacy of a wastewater treatment lagoon (WWTL) at preventing the spread of Pseudomonas aeruginosa into natural aquatic habitats was investigated. A WWTL and its connected combined sewer and brook were exhaustively sampled. Physico-chemical analyses showed a stratification of the first pond according to pH, temperature and oxygen content. The P. aeruginosa counts partially matched this stratification with higher values among the bottom anaerobic waters of the first half of this pond. Genotyping of 494 WWTL P. aeruginosa strains was performed and led to the definition of 85 lineages. Dominant lineages were observed, with some being found all over the WWTL including the connected brook. IS5 was used as an indicator of genomic changes, and 1 to 12 elements were detected among 16 % of the strains. IS-driven lasR (genetic regulator) disruptions were detected among nine strains that were not part of the dominant lineages. These insertional mutants did not show significant elastase activities but showed better growth than the PAO1 reference strain in WWTL waters. Differences in growth patterns were related to a better survival of these mutants at an alkaline pH and a better ability at using some C-sources such as alanine. The opportunistic colonization of a WWTL by P. aeruginosa can involve several metabolic strategies which appeared lineage specific. Some clones appeared more successful than others at disseminating from a combined sewer toward the overflow of a WWTL.
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9
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Emergence of carbapenem resistance due to the novel insertion sequence ISPa8 in Pseudomonas aeruginosa. PLoS One 2014; 9:e91299. [PMID: 24614163 PMCID: PMC3948848 DOI: 10.1371/journal.pone.0091299] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 02/09/2014] [Indexed: 11/19/2022] Open
Abstract
Chronic lung infections due to the persistence of Pseudomonas aeruginosa in cystic fibrosis patients are typically associated with the emergence of antibiotic resistance. The purpose of this study was to investigate the mechanisms responsible for the emergence of carbapenem resistance when a clinical isolate of P. aeruginosa collected from a patient with cystic fibrosis was challenged with meropenem. Nine carbapenem-resistant mutants were selected with subinhibitory concentrations of meropenem from a clinical isolate of P. aeruginosa and characterized for carbapenem resistance. Increased carbapenem MICs were associated with the identification of the novel insertion sequence ISPa8 within oprD or its promoter region in all the mutants. The position of ISPa8 was different for each of the mutants evaluated. In addition, Southern blot analyses identified multiple copies of ISPa8 within the genomes of the mutants and their parent isolate. These data demonstrate that transposition of IS elements within the Pseudomonas genome can influence antibiotic susceptibility. Understanding the selective pressures associated with the emergence of antibiotic resistance is critical for the judicious use of antimicrobial chemotherapy and the successful treatment of bacterial infections.
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10
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Diene SM, L’homme T, Bellulo S, Stremler N, Dubus JC, Mely L, Leroy S, Degand N, Rolain JM. ISPa46, a novel insertion sequence in the oprD porin gene of an imipenem-resistant Pseudomonas aeruginosa isolate from a cystic fibrosis patient in Marseille, France. Int J Antimicrob Agents 2013; 42:268-71. [DOI: 10.1016/j.ijantimicag.2013.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 06/03/2013] [Indexed: 01/08/2023]
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11
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Clusters of genetically similar isolates of Pseudomonas aeruginosa from multiple hospitals in the UK. J Med Microbiol 2013; 62:988-1000. [DOI: 10.1099/jmm.0.054841-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Variable number tandem repeat (VNTR) analysis at nine loci of isolates of Pseudomonas aeruginosa submitted to the national reference laboratory from UK hospitals, from over 2000 patients, between June 2010 and June 2012 revealed four widely found types that collectively were received from approximately a fifth of patients, including from those with cystic fibrosis. These types were also prevalent among related submissions from the clinical environment and were received from up to 54 (out of 143) hospitals. Multi-locus sequence typing and bla
OXA-50-like sequencing confirmed the clonal relationship within each cluster, and representatives from multiple centres clustered within about 70 % by pulsed-field gel electrophoresis. Illumina sequencing of 12 isolates of cluster A of VNTR profile 8, 3, 4, 5, 2, 3, 5, 2, x (where the repeat number at the last, most discriminatory locus is variable) revealed a large number of variably present targets in the accessory genome and seven of these were sought by PCR among a larger set of isolates. Representatives from patients within a single centre mostly had distinct accessory gene profiles, suggesting that these patients acquired the strain independently, while those with clear epidemiological links shared the same profile. Profiles also varied between representatives from different centres. Epidemiological investigations of widely found types such as these require the use of finer-typing methods, which increasingly will be informed by next generation sequencing.
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Coyne S, Courvalin P, Galimand M. Acquisition of multidrug resistance transposon Tn6061 and IS6100-mediated large chromosomal inversions in Pseudomonas aeruginosa clinical isolates. MICROBIOLOGY-SGM 2010; 156:1448-1458. [PMID: 20110294 DOI: 10.1099/mic.0.033639-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pseudomonas aeruginosa is a major human opportunistic pathogen, especially for patients in intensive care units or with cystic fibrosis. Multidrug resistance is a common feature of this species. In a previous study we detected the ant(4')-IIb gene in six multiresistant clinical isolates of P. aeruginosa, and determination of the environment of the gene led to characterization of Tn6061. This 26 586 bp element, a member of the Tn3 family of transposons, carried 10 genes conferring resistance to six drug classes. The ant(4')-IIb sequence was flanked by directly repeated copies of ISCR6 in all but one of the strains studied, consistent with ISCR6-mediated gene acquisition. Tn6061 was chromosomally located in six strains and plasmid-borne in the remaining isolate, suggesting horizontal acquisition. Duplication-insertion of IS6100, that ended Tn6061, was responsible for large chromosomal inversions. Acquisition of Tn6061 and chromosomal inversions are further examples of intricate mechanisms that contribute to the genome plasticity of P. aeruginosa.
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Affiliation(s)
- Sébastien Coyne
- Institut Pasteur, Unité des Agents Antibactériens, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Patrice Courvalin
- Institut Pasteur, Unité des Agents Antibactériens, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Marc Galimand
- Institut Pasteur, Unité des Agents Antibactériens, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
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Wolter DJ, Acquazzino D, Goering RV, Sammut P, Khalaf N, Hanson ND. Emergence of carbapenem resistance in Pseudomonas aeruginosa isolates from a patient with cystic fibrosis in the absence of carbapenem therapy. Clin Infect Dis 2008; 46:e137-41. [PMID: 18462098 DOI: 10.1086/588484] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The emergence of carbapenem-resistant Pseudomonas aeruginosa in the lung of a patient with cystic fibrosis was evaluated. A single strain of P. aeruginosa persisted during a 3-year study despite antipseudomonal treatment. A stepwise decrease in carbapenem susceptibility leading to resistance was observed in the absence of carbapenem treatment. These data suggest that chronic exposure to unrelated drug classes may be an important determinant for the emergence of carbapenem resistance in P. aeruginosa.
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Affiliation(s)
- Daniel J Wolter
- Center for Research in Anti-Infectives and Biotechnology, Creighton University School of Medicine, Omaha, Nebraska 68178, USA
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D'Argenio DA, Wu M, Hoffman LR, Kulasekara HD, Déziel E, Smith EE, Nguyen H, Ernst RK, Larson Freeman TJ, Spencer DH, Brittnacher M, Hayden HS, Selgrade S, Klausen M, Goodlett DR, Burns JL, Ramsey BW, Miller SI. Growth phenotypes of Pseudomonas aeruginosa lasR mutants adapted to the airways of cystic fibrosis patients. Mol Microbiol 2007; 64:512-33. [PMID: 17493132 PMCID: PMC2742308 DOI: 10.1111/j.1365-2958.2007.05678.x] [Citation(s) in RCA: 269] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa undergoes genetic change during chronic airway infection of cystic fibrosis (CF) patients. One common change is a mutation inactivating lasR, which encodes a transcriptional regulator that responds to a homoserine lactone signal to activate expression of acute virulence factors. Colonies of lasR mutants visibly accumulated the iridescent intercellular signal 4-hydroxy-2-heptylquinoline. Using this colony phenotype, we identified P. aeruginosa lasR mutants that emerged in the airway of a CF patient early during chronic infection, and during growth in the laboratory on a rich medium. The lasR loss-of-function mutations in these strains conferred a growth advantage with particular carbon and nitrogen sources, including amino acids, in part due to increased expression of the catabolic pathway regulator CbrB. This growth phenotype could contribute to selection of lasR mutants both on rich medium and within the CF airway, supporting a key role for bacterial metabolic adaptation during chronic infection. Inactivation of lasR also resulted in increased beta-lactamase activity that increased tolerance to ceftazidime, a widely used beta-lactam antibiotic. Loss of LasR function may represent a marker of an early stage in chronic infection of the CF airway with clinical implications for antibiotic resistance and disease progression.
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Affiliation(s)
- David A D'Argenio
- Department of Microbiology, University of Washington, Seattle, WA, USA
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