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Mesquita CS, Soares-Castro P, Faustino A, Santos HM, Capelo JL, Santos P. Identification of genomic loci associated with genotypic and phenotypic variation among Pseudomonas aeruginosa clinical isolates from pneumonia. Microb Pathog 2019; 136:103702. [PMID: 31472259 DOI: 10.1016/j.micpath.2019.103702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 11/19/2022]
Abstract
In this work, a genotype-phenotype survey of a highly diversified Pseudomonas aeruginosa collection was conducted, aiming to detail pathogen-associated scenarios that clinicians face nowadays. Genetic relation based on RAPD-PCR of 705 isolates, retrieved from 424 patients and several clinical contexts, reported an almost isolate-specific molecular-pattern. Pneumonia-associated isolates HB13 and HB15, clustered in the same RAPD-PCR group, were selected to evaluate the genomic background underlying their contrasting antibiotic resistance and virulence. The HB13 genome harbors antibiotic-inactivating enzymes-coding genes (e.g. aac(3)-Ia, arr, blaVIM-2) and single-nucleotide variations (SNVs) in antibiotic targets, likely accounting for its pan-resistance, whereas HB15 susceptibility correlated to predicted dysfunctional alleles. Isolate HB13 showed the unprecedented rhl-cluster absence and variations in other pathogen competitiveness contributors. Conversely, HB15 genome comprises exoenzyme-coding genes and SNVs linked to increased virulence. Secretome analysis identified signatures features with unknown function as potential novel pathogenic (e.g. a MATE-protein in HB13, a protease in HB15) and antibiotic resistance (a HlyD-like secretion protein in HB13) determinants. Detection of active prophages, proteases (including protease IV and alkaline metalloproteinase), a porin and a peptidase in HB15 highlights the secreted arsenal likely essential for its virulent behavior. The presented phenotype-genome association will contribute to the current knowledge on Pseudomonas aeruginosa pathogenomics.
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Affiliation(s)
- Cristina S Mesquita
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Pedro Soares-Castro
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Alberta Faustino
- Clinical Pathology Service, Hospital de Braga, 4710-243, Braga, Portugal
| | - Hugo M Santos
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Park, Rua dos Inventores, 2825-152, Caparica, Portugal
| | - José L Capelo
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Park, Rua dos Inventores, 2825-152, Caparica, Portugal
| | - Pedro Santos
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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52
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Flynn S, Reen FJ, O'Gara F. Exposure to Bile Leads to the Emergence of Adaptive Signaling Variants in the Opportunistic Pathogen Pseudomonas aeruginosa. Front Microbiol 2019; 10:2013. [PMID: 31555243 PMCID: PMC6727882 DOI: 10.3389/fmicb.2019.02013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 08/16/2019] [Indexed: 12/18/2022] Open
Abstract
The chronic colonization of the respiratory tract by the opportunistic pathogen Pseudomonas aeruginosa is the primary cause of morbidity and mortality in cystic fibrosis (CF) patients. P. aeruginosa has been shown to undergo extensive genomic adaptation facilitating its persistence within the CF lung allowing it to evade the host immune response and outcompete co-colonizing residents of the lung microbiota. However, whilst several studies have described the various mutations that frequently arise in clinical isolates of P. aeruginosa, the environmental factors governing the emergence of these genetic variants is less well characterized. Gastro-oesophageal reflux has recently emerged as a major co-morbidity in CF and is often associated with the presence of bile acids in the lungs most likely by (micro) aspiration. In order to investigate whether bile may select for genetic variants, P. aeruginosa was experimentally evolved in artificial sputum medium, a synthetic media resembling environmental conditions found within the CF lung. Pigmented derivatives of P. aeruginosa emerged exclusively in the presence of bile. Genome sequencing analysis identified single nucleotide polymorphisms (SNPs) in quorum sensing (lasR) and both the pyocyanin (phzS) and pyomelanin (hmgA) biosynthetic pathways. Phenotypic analysis revealed an altered bile response when compared to the ancestral P. aeruginosa progenitor strain. While the recovered pigmented derivatives retained the bile mediated suppression of swarming motility and enhanced antibiotic tolerance, the biofilm, and redox responses to bile were abolished in the adapted mutants. Though loss of pseudomonas quinolone signal (PQS) production in the pigmented isolates was not linked to the altered biofilm response, the loss of redox repression could be explained by defective alkyl-quinolone (AQ) production in the presence of bile. Collectively, these findings suggest that the adaptive variants of P. aeruginosa that arise following long term bile exposure enables the emergence of ecologically competitive sub-populations. Altered pigmentation and AQ signaling may contribute to an enhancement in fitness facilitating population survival within a bile positive environment.
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Affiliation(s)
- Stephanie Flynn
- BIOMERIT Research Centre, School of Microbiology, University College Cork - National University of Ireland, Cork, Ireland
| | - F Jerry Reen
- School of Microbiology, University College Cork - National University of Ireland, Cork, Ireland
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork - National University of Ireland, Cork, Ireland.,Telethon Kids Institute, Perth, WA, Australia.,School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
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53
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Kordes A, Preusse M, Willger SD, Braubach P, Jonigk D, Haverich A, Warnecke G, Häussler S. Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung. Nat Commun 2019; 10:3397. [PMID: 31363089 PMCID: PMC6667473 DOI: 10.1038/s41467-019-11414-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 07/03/2019] [Indexed: 12/20/2022] Open
Abstract
Previous studies have demonstrated substantial genetic diversification of Pseudomonas aeruginosa across sub-compartments in cystic fibrosis (CF) lungs. Here, we isolate P. aeruginosa from five different sampling areas in the upper and lower airways of an explanted CF lung, analyze ex vivo transcriptional profiles by RNA-seq, and use colony re-sequencing and deep population sequencing to determine the genetic diversity within and across the various sub-compartments. We find that, despite genetic variation, the ex vivo transcriptional profiles of P. aeruginosa populations inhabiting different regions of the CF lung are similar. Although we cannot estimate the extent to which the transcriptional response recorded here actually reflects the in vivo transcriptomes, our results indicate that there may be a common in vivo transcriptional profile in the CF lung environment.
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Affiliation(s)
- Adrian Kordes
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, 30625, Germany
| | - Matthias Preusse
- Institute for Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany
| | - Sven D Willger
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, 30625, Germany
- Institute for Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany
| | - Peter Braubach
- Institute of Pathology, Hannover Medical School, Hannover, 30625, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (Deutsches Zentrum für Lungenforschung [DZL]), Hannover, 30625, Germany
| | - Danny Jonigk
- Institute of Pathology, Hannover Medical School, Hannover, 30625, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (Deutsches Zentrum für Lungenforschung [DZL]), Hannover, 30625, Germany
| | - Axel Haverich
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (Deutsches Zentrum für Lungenforschung [DZL]), Hannover, 30625, Germany
- Department of Cardiothoracic, Transplant and Vascular Surgery, Hannover Medical School, Hannover, 30625, Germany
| | - Gregor Warnecke
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (Deutsches Zentrum für Lungenforschung [DZL]), Hannover, 30625, Germany
- Department of Cardiothoracic, Transplant and Vascular Surgery, Hannover Medical School, Hannover, 30625, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, 30625, Germany.
- Institute for Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany.
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Guła G, Dorotkiewicz-Jach A, Korzekwa K, Valvano MA, Drulis-Kawa Z. Complex Signaling Networks Controlling Dynamic Molecular Changes in Pseudomonas aeruginosa Biofilm. Curr Med Chem 2019; 26:1979-1993. [PMID: 30207213 DOI: 10.2174/0929867325666180912110151] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/11/2018] [Accepted: 08/31/2018] [Indexed: 02/06/2023]
Abstract
The environment exerts strong influence on microbes. Adaptation of microbes to changing conditions is a dynamic process regulated by complex networks. Pseudomonas aeruginosa is a life-threating, versatile opportunistic and multi drug resistant pathogen that provides a model to investigate adaptation mechanisms to environmental changes. The ability of P. aeruginosa to form biofilms and to modify virulence in response to environmental changes is coordinated by various mechanisms including two-component systems (TCS), and secondary messengers involved in quorum sensing (QS) and c-di-GMP networks (diguanylate cyclase systems, DGC). In this review, we focus on the role of c-di-GMP during biofilm formation. We describe TCS and QS signal cascades regulated by c-di-GMP in response to changes in the external environment. We present a complex signaling network dynamically changing during the transition of P. aeruginosa from the free-living to sessile mode of growth.
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Affiliation(s)
- Grzegorz Guła
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - Agata Dorotkiewicz-Jach
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - Kamila Korzekwa
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - Miguel A Valvano
- Wellcome- Wolfson Institute for Experimental Medicine, Queen's University Belfast, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
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55
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Chai YH, Xu JF. How does Pseudomonas aeruginosa affect the progression of bronchiectasis? Clin Microbiol Infect 2019; 26:313-318. [PMID: 31306794 DOI: 10.1016/j.cmi.2019.07.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/04/2019] [Accepted: 07/08/2019] [Indexed: 11/17/2022]
Abstract
BACKGROUND Pseudomonas aeruginosa is one of the most common pathogens isolated from respiratory tract specimen in patients with bronchiectasis. It is considered highly responsible for pathogenicity, progression and clinical outcomes of bronchiectasis. AIMS To summarize existing evidence on how different factors of Pseudomonas aeruginosa affect the pathogenicity, progression and clinical outcomes of bronchiectasis, so as to provide possible insights for clinical practice and related research in the future. SOURCES PubMed was searched for studies pertaining to bronchiectasis and P. aeruginosa published to date, with no specific inclusion or exclusion criteria. Reference lists of retrieved reviews were searched for additional articles. CONTENT This review focused on non-cystic fibrosis bronchiectasis and also provided some data on cystic fibrosis when studies in bronchiectasis were limited. We discussed various factors in relation to P. aeruginosa: virulence factors, drug resistance, regulatory systems, genomic diversity and transmission of P. aeruginosa, as well as treatment for P. aeruginosa. Their impacts on bronchiectasis and its management were discussed. IMPLICATIONS The impact of P. aeruginosa on bronchiectasis is definite, although conclusions in some aspects are still vague. Faced with the worrying drug-resistance status and treatment bottleneck, individualized management and novel therapies beyond the classic pathway are most likely to be a future trend. To confirm the independent or integrated impact of various factors of P. aeruginosa on bronchiectasis and to figure out all the problems mentioned, larger randomized control trials are truly needed in the future.
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Affiliation(s)
- Y-H Chai
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - J-F Xu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
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56
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Malhotra S, Hayes D, Wozniak DJ. Cystic Fibrosis and Pseudomonas aeruginosa: the Host-Microbe Interface. Clin Microbiol Rev 2019; 32:e00138-18. [PMID: 31142499 PMCID: PMC6589863 DOI: 10.1128/cmr.00138-18] [Citation(s) in RCA: 244] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In human pathophysiology, the clash between microbial infection and host immunity contributes to multiple diseases. Cystic fibrosis (CF) is a classical example of this phenomenon, wherein a dysfunctional, hyperinflammatory immune response combined with chronic pulmonary infections wreak havoc upon the airway, leading to a disease course of substantial morbidity and shortened life span. Pseudomonas aeruginosa is an opportunistic pathogen that commonly infects the CF lung, promoting an accelerated decline of pulmonary function. Importantly, P. aeruginosa exhibits significant resistance to innate immune effectors and to antibiotics, in part, by expressing specific virulence factors (e.g., antioxidants and exopolysaccharides) and by acquiring adaptive mutations during chronic infection. In an effort to review our current understanding of the host-pathogen interface driving CF pulmonary disease, we discuss (i) the progression of disease within the primitive CF lung, specifically focusing on the role of host versus bacterial factors; (ii) critical, neutrophil-derived innate immune effectors that are implicated in CF pulmonary disease, including reactive oxygen species (ROS) and antimicrobial peptides (e.g., LL-37); (iii) P. aeruginosa virulence factors and adaptive mutations that enable evasion of the host response; and (iv) ongoing work examining the distribution and colocalization of host and bacterial factors within distinct anatomical niches of the CF lung.
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Affiliation(s)
- Sankalp Malhotra
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
- The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Don Hayes
- The Ohio State University College of Medicine, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
- Section of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Daniel J Wozniak
- The Ohio State University College of Medicine, Columbus, Ohio, USA
- Section of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
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57
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Winstanley C, Brockhurst MA. Can We Manipulate the Evolutionary Biology of Pathogens for Clinical Benefit? Am J Respir Cell Mol Biol 2019; 59:143-144. [PMID: 29708392 DOI: 10.1165/rcmb.2018-0113ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Craig Winstanley
- 1 Institute of Infection and Global Health University of Liverpool Liverpool, United Kingdom and
| | - Michael A Brockhurst
- 2 Department of Animal and Plant Sciences University of Sheffield Sheffield, United Kingdom
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58
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Burgener EB, Sweere JM, Bach MS, Secor PR, Haddock N, Jennings LK, Marvig RL, Johansen HK, Rossi E, Cao X, Tian L, Nedelec L, Molin S, Bollyky PL, Milla CE. Filamentous bacteriophages are associated with chronic Pseudomonas lung infections and antibiotic resistance in cystic fibrosis. Sci Transl Med 2019; 11:eaau9748. [PMID: 30996083 PMCID: PMC7021451 DOI: 10.1126/scitranslmed.aau9748] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 01/14/2019] [Accepted: 03/27/2019] [Indexed: 12/31/2022]
Abstract
Filamentous bacteriophage (Pf phage) contribute to the virulence of Pseudomonas aeruginosa infections in animal models, but their relevance to human disease is unclear. We sought to interrogate the prevalence and clinical relevance of Pf phage in patients with cystic fibrosis (CF) using sputum samples from two well-characterized patient cohorts. Bacterial genomic analysis in a Danish longitudinal cohort of 34 patients with CF revealed that 26.5% (n = 9) were consistently Pf phage positive. In the second cohort, a prospective cross-sectional cohort of 58 patients with CF at Stanford, sputum qPCR analysis showed that 36.2% (n = 21) of patients were Pf phage positive. In both cohorts, patients positive for Pf phage were older, and in the Stanford CF cohort, patients positive for Pf phage were more likely to have chronic P. aeruginosa infection and had greater declines in pulmonary function during exacerbations than patients negative for Pf phage presence in the sputum. Last, P. aeruginosa strains carrying Pf phage exhibited increased resistance to antipseudomonal antibiotics. Mechanistically, in vitro analysis showed that Pf phage sequesters these same antibiotics, suggesting that this mechanism may thereby contribute to the selection of antibiotic resistance over time. These data provide evidence that Pf phage may contribute to clinical outcomes in P. aeruginosa infection in CF.
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Affiliation(s)
- Elizabeth B Burgener
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
| | - Johanna M Sweere
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Stanford Immunology, Stanford University, Stanford, CA 94305, USA
| | - Michelle S Bach
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Patrick R Secor
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Naomi Haddock
- Stanford Immunology, Stanford University, Stanford, CA 94305, USA
| | - Laura K Jennings
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Rasmus L Marvig
- Center for Genomic Medicine, Rigshospitalet-Copenhagen University Hospital, Copenhagen, Denmark
| | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen Ø, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Elio Rossi
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen Ø, Denmark
| | - Xiou Cao
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Lu Tian
- Biomedical Data Science Administration and Statistics, Stanford University, Stanford, CA 94305, USA
| | - Laurence Nedelec
- Primary Care and Population Health, Stanford University, Stanford, CA 94305, USA
| | - Søren Molin
- Primary Care and Population Health, Stanford University, Stanford, CA 94305, USA
| | - Paul L Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Stanford Immunology, Stanford University, Stanford, CA 94305, USA
| | - Carlos E Milla
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
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Klockgether J, Cramer N, Fischer S, Wiehlmann L, Tümmler B. Long-Term Microevolution of Pseudomonas aeruginosa Differs between Mildly and Severely Affected Cystic Fibrosis Lungs. Am J Respir Cell Mol Biol 2019; 59:246-256. [PMID: 29470920 DOI: 10.1165/rcmb.2017-0356oc] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Chronic airway infections with Pseudomonas aeruginosa determine morbidity in most individuals with cystic fibrosis (CF). P. aeruginosa may persist for decades in CF lungs, which provides a rare opportunity to study the long-term within-host evolution of a bacterial airway pathogen. In this work, we sought to resolve the genetic adaptation of P. aeruginosa in CF lungs from the onset of colonization until the patient's death or permanent replacement by another P. aeruginosa clone. We followed the microevolution of the first persisting P. aeruginosa clone by whole-genome sequencing of serial isolates from highly divergent clinical courses of airway infection, i.e., a fatal outcome because of respiratory insufficiency within less than 15 years, or a rather normal daily life 25-35 years after acquisition of P. aeruginosa. Nonneutral mutations predominantly emerged in P. aeruginosa genes relevant for protection against and communication with signals from the lung environment, i.e., antibiotic resistance, cell wall components, and two-component systems. Drastic and loss-of-function mutations preferentially happened during the severe courses of infection, and the bacterial lineages of the mild courses more proficiently incorporated extra metabolic genes into their accessory genome. P. aeruginosa followed different evolutionary paths depending on whether the bacterium had taken up residence in a patient with CF and normal or already compromised lung function.
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Affiliation(s)
- Jens Klockgether
- 1 Clinical Research Group "Molecular Pathology of Cystic Fibrosis," Clinic for Pediatric Pneumology, Allergology and Neonatology, and
| | - Nina Cramer
- 1 Clinical Research Group "Molecular Pathology of Cystic Fibrosis," Clinic for Pediatric Pneumology, Allergology and Neonatology, and
| | - Sebastian Fischer
- 1 Clinical Research Group "Molecular Pathology of Cystic Fibrosis," Clinic for Pediatric Pneumology, Allergology and Neonatology, and
| | - Lutz Wiehlmann
- 1 Clinical Research Group "Molecular Pathology of Cystic Fibrosis," Clinic for Pediatric Pneumology, Allergology and Neonatology, and.,2 Research Core Unit Genomics, Hannover Medical School, Hannover, Germany; and
| | - Burkhard Tümmler
- 1 Clinical Research Group "Molecular Pathology of Cystic Fibrosis," Clinic for Pediatric Pneumology, Allergology and Neonatology, and.,3 Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Centre for Lung Research, Hannover, Germany
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60
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Sener Okur D, Yuruyen C, Gungor O, Aktas Z, Erturan Z, Akcakaya N, Camcioglu Y, Cokugras H, Koksalan K. Genotypic characterization of Pseudomonas aeruginosa isolates from Turkish children with cystic fibrosis. Infect Drug Resist 2019; 12:675-685. [PMID: 31114258 PMCID: PMC6497484 DOI: 10.2147/idr.s183151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/15/2019] [Indexed: 02/03/2023] Open
Abstract
Objective: To identify epidemic and other transmissible Pseudomonas aeruginosa strains, genotypic analyses are required. The aim of this study was to assess the distribution of P. aeruginosa strains within the Turkish pediatric cystic fibrosis (CF) clinic population. Methods: Eighteen patients attending the pediatric CF clinic of Cerrahpasa Medical Faculty were investigated in the study. Throat swab and/or sputum samples were taken from each patient at 3-month intervals. The isolates of patients were analyzed by pulsed-field gel electrophoresis (PFGE). The intra- and interpatient genotypic heterogeneity of isolates was examined to determine the clonal isolates of P. aeruginosa within the cohort. Results: A total of 108 clinical isolates of P. aeruginosa were obtained from 18 patients between May 2013 and May 2014. The pulsotypes of the first patient’s isolates could not be obtained by PFGE. From the remaining 17 patients and 101 isolates, 55 distinct pulsotypes were detected. The number of pulsotypes observed in more than one patient (minor clonal strains, cluster strains) was 8 (14.5%), and one of them colonized three patients. However, none of them was detected in more than three patients. These pulsotypes were composed of 20 isolates. In addition, with the PFGE analysis of 81 isolates, we detected 47 (85.6%) pulsotypes, which belonged to only one patient. Over different periods of this study, only 2 (11.8%) patients were colonized with the same pulsotype. Conclusion: Our study indicates that there was considerable genomic diversity among the P. aeruginosa isolates in our clinic. The presence of shared pulsotypes supports cross-transmission between patients.
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Affiliation(s)
- Dicle Sener Okur
- Istanbul University Cerrahpasa, Faculty of Medicine, Department of Pediatrics, Division of Pediatric Infectious Diseases, 34098 Kocamustafapasa, Istanbul, Turkey
| | - Caner Yuruyen
- Istanbul University Istanbul, Faculty of Medicine, Department of Microbiology and Clinical Microbiology, 34390 Capa, Istanbul, Turkey
| | - Ozge Gungor
- Istanbul University Istanbul, Faculty of Medicine, Department of Microbiology and Clinical Microbiology, 34390 Capa, Istanbul, Turkey
| | - Zerrin Aktas
- Istanbul University Istanbul, Faculty of Medicine, Department of Microbiology and Clinical Microbiology, 34390 Capa, Istanbul, Turkey
| | - Zayre Erturan
- Istanbul University Istanbul, Faculty of Medicine, Department of Microbiology and Clinical Microbiology, 34390 Capa, Istanbul, Turkey
| | - Necla Akcakaya
- Istanbul University Cerrahpasa, Faculty of Medicine, Department of Pediatrics, Division of Pediatric Infectious Diseases, Clinical Immunology and Allergy, 34098 Kocamustafapasa, Istanbul, Turkey
| | - Yildiz Camcioglu
- Istanbul University Cerrahpasa, Faculty of Medicine, Department of Pediatrics, Division of Pediatric Infectious Diseases, Clinical Immunology and Allergy, 34098 Kocamustafapasa, Istanbul, Turkey
| | - Haluk Cokugras
- Istanbul University Cerrahpasa, Faculty of Medicine, Department of Pediatrics, Division of Pediatric Infectious Diseases, Clinical Immunology and Allergy, 34098 Kocamustafapasa, Istanbul, Turkey
| | - Kaya Koksalan
- Istanbul University, Institute for Medical Experimental Research (DETAE), 34390 Capa, Istanbul, Turkey
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61
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Brockhurst MA, Harrison F, Veening JW, Harrison E, Blackwell G, Iqbal Z, Maclean C. Assessing evolutionary risks of resistance for new antimicrobial therapies. Nat Ecol Evol 2019; 3:515-517. [DOI: 10.1038/s41559-019-0854-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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62
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Andersen SB, Ghoul M, Marvig RL, Lee ZB, Molin S, Johansen HK, Griffin AS. Privatisation rescues function following loss of cooperation. eLife 2018; 7:e38594. [PMID: 30558711 PMCID: PMC6298776 DOI: 10.7554/elife.38594] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 11/17/2018] [Indexed: 12/11/2022] Open
Abstract
A single cheating mutant can lead to the invasion and eventual eradication of cooperation from a population. Consequently, cheat invasion is often considered equal to extinction in empirical and theoretical studies of cooperator-cheat dynamics. But does cheat invasion necessarily equate extinction in nature? By following the social dynamics of iron metabolism in Pseudomonas aeruginosa during cystic fibrosis lung infection, we observed that individuals evolved to replace cooperation with a 'private' behaviour. Phenotypic assays showed that cooperative iron acquisition frequently was upregulated early in infection, which, however, increased the risk of cheat invasion. With whole-genome sequencing we showed that if, and only if, cooperative iron acquisition is lost from the population, a private system was upregulated. The benefit of upregulation depended on iron availability. These findings highlight the importance of social dynamics of natural populations and emphasizes the potential impact of past social interaction on the evolution of private traits.
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Affiliation(s)
- Sandra Breum Andersen
- Department of ZoologyUniversity of OxfordOxfordUnited Kingdom
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
| | - Melanie Ghoul
- Department of ZoologyUniversity of OxfordOxfordUnited Kingdom
| | | | - Zhuo-Bin Lee
- Department of ZoologyUniversity of OxfordOxfordUnited Kingdom
| | - Søren Molin
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
| | - Helle Krogh Johansen
- Department of Clinical MicrobiologyRigshospitaletCopenhagenDenmark
- Department of Clinical Medicine, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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63
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Sousa AM, Monteiro R, Pereira MO. Unveiling the early events of Pseudomonas aeruginosa adaptation in cystic fibrosis airway environment using a long-term in vitro maintenance. Int J Med Microbiol 2018; 308:1053-1064. [PMID: 30377031 DOI: 10.1016/j.ijmm.2018.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/16/2018] [Accepted: 10/10/2018] [Indexed: 01/22/2023] Open
Abstract
Pseudomonas aeruginosa chronic infections are the major cause of high morbidity and mortality in cystic fibrosis (CF) patients due to the use of sophisticated mechanisms of adaptation, including clonal diversification into specialized CF-adapted phenotypes. In contrast to chronic infections, very little is known about what occurs after CF lungs colonization and at early infection stages. This study aims to investigate the early events of P. aeruginosa adaptation to CF environment, in particular, to inspect the occurrence of clonal diversification at early stages of infection development and its impact on antibiotherapy effectiveness. To mimic CF early infections, three P. aeruginosa strains were long-term grown in artificial sputum (ASM) over 10 days and phenotypic diversity verified through colony morphology characterization. Biofilm sub- and inhibitory concentrations of ciprofloxacin were applied to non- and diversified populations to evaluate antibiotic effectiveness on P. aeruginosa eradication. Our results demonstrated that clonal diversification might occur after ASM colonization and growth. However, this phenotypic diversification did not compromise ciprofloxacin efficacy in P. aeruginosa eradication since a biofilm minimal inhibitory dosage would be applied. The expected absence of mutators in P. aeruginosa populations led us to speculate that clonal diversification in the absence of ciprofloxacin treatments could be driven by niche specialization. Yet, biofilm sub-inhibitory concentrations of ciprofloxacin seemed to overlap niche specialization as "fitter" variants emerged, such as mucoid, small colony and pinpoint variants, known to be highly resistant to antibiotics. The pathogenic potential of all emergent colony morphotypes-associated bacteria, distinct from the wild-morphotypes, revealed that P. aeruginosa evolved to a non-swimming phenotype. Impaired swimming motility seemed to be one of the first evolutionary steps of P. aeruginosa in CF lungs that could pave the way for further adaptation steps including biofilm formation and progress to chronic infection. Based on our findings, impaired swimming motility seemed to be a candidate to disease marker of P. aeruginosa infection development. Despite our in vitro CF model represents a step forward towards in vivo scenario simulation and provided valuable insights about the early events, more and distinct P. aeruginosa strains should be studied to strengthen our results.
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Affiliation(s)
- Ana Margarida Sousa
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Rosana Monteiro
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Maria Olívia Pereira
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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64
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Parkins MD, Somayaji R, Waters VJ. Epidemiology, Biology, and Impact of Clonal Pseudomonas aeruginosa Infections in Cystic Fibrosis. Clin Microbiol Rev 2018; 31:e00019-18. [PMID: 30158299 PMCID: PMC6148191 DOI: 10.1128/cmr.00019-18] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chronic lower airway infection with Pseudomonas aeruginosa is a major contributor to morbidity and mortality in individuals suffering from the genetic disease cystic fibrosis (CF). Whereas it was long presumed that each patient independently acquired unique strains of P. aeruginosa present in their living environment, multiple studies have since demonstrated that shared strains of P. aeruginosa exist among individuals with CF. Many of these shared strains, often referred to as clonal or epidemic strains, can be transmitted from one CF individual to another, potentially reaching epidemic status. Numerous epidemic P. aeruginosa strains have been described from different parts of the world and are often associated with an antibiotic-resistant phenotype. Importantly, infection with these strains often portends a worse prognosis than for infection with nonclonal strains, including an increased pulmonary exacerbation rate, exaggerated lung function decline, and progression to end-stage lung disease. This review describes the global epidemiology of clonal P. aeruginosa strains in CF and summarizes the current literature regarding the underlying biology and clinical impact of globally important CF clones. Mechanisms associated with patient-to-patient transmission are discussed, and best-evidence practices to prevent infections are highlighted. Preventing new infections with epidemic P. aeruginosa strains is of paramount importance in mitigating CF disease progression.
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Affiliation(s)
- Michael D Parkins
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ranjani Somayaji
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Valerie J Waters
- Translational Medicine, Research Institute, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Department of Pediatrics, Division of Infectious Diseases, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
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65
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Rapid diversification of Pseudomonas aeruginosa in cystic fibrosis lung-like conditions. Proc Natl Acad Sci U S A 2018; 115:10714-10719. [PMID: 30275334 DOI: 10.1073/pnas.1721270115] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chronic infection of the cystic fibrosis (CF) airway by the opportunistic pathogen Pseudomonas aeruginosa is the leading cause of morbidity and mortality for adult CF patients. Prolonged infections are accompanied by adaptation of P. aeruginosa to the unique conditions of the CF lung environment, as well as marked diversification of the pathogen into phenotypically and genetically distinct strains that can coexist for years within a patient. Little is known, however, about the causes of this diversification and its impact on patient health. Here, we show experimentally that, consistent with ecological theory of diversification, the nutritional conditions of the CF airway can cause rapid and extensive diversification of P. aeruginosa Mucin, the substance responsible for the increased viscosity associated with the thick mucus layer in the CF airway, had little impact on within-population diversification but did promote divergence among populations. Furthermore, in vitro evolution recapitulated traits thought to be hallmarks of chronic infection, including reduced motility and increased biofilm formation, and the range of phenotypes observed in a collection of clinical isolates. Our results suggest that nutritional complexity and reduced dispersal can drive evolutionary diversification of P. aeruginosa independent of other features of the CF lung such as an active immune system or the presence of competing microbial species. We suggest that diversification, by generating extensive phenotypic and genetic variation on which selection can act, may be a key first step in the development of chronic infections.
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66
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Great phenotypic and genetic variation among successive chronic Pseudomonas aeruginosa from a cystic fibrosis patient. PLoS One 2018; 13:e0204167. [PMID: 30212579 PMCID: PMC6136817 DOI: 10.1371/journal.pone.0204167] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 09/03/2018] [Indexed: 12/31/2022] Open
Abstract
Background/Objectives Different adapted Pseudomonas aeruginosa morphotypes are found during chronic infections. Relevant biological determinants in P. aeruginosa successively isolated from a cystic fibrosis (CF) patient were analyzed in this work to gain insight into P. aeruginosa heterogeneity during chronic infection. Methods Seventeen P. aeruginosa isolates collected from a patient over a 3 year period were included, 5 small colony variants (SCV) and 12 mucoids. The following analyses were performed: Pulsed-Field-Gel-Electrophoresis (PFGE)/Multilocus- sequence-typing (MLST)/serotype, antimicrobial susceptibility, growth curves, capacity to form biofilm, pigment production, elastase activity, motility; presence/expression of virulence/quorum sensing genes, and identification of resistance mechanisms. Results All isolates had closely related PFGE patterns and belonged to ST412. Important phenotypic and genotypic differences were found. SCVs were more resistant to antimicrobials than mucoid isolates. AmpC hyperproduction and efflux pump activity were detected. Seven isolates contained two integrons and nine isolates only one integron. All SCVs showed the same OprD profile, while three different profiles were identified among mucoids. No amino acid changes were found in MutL and MutS. All isolates were slow-growing, generally produced high biofilm, had reduced their toxin expression and their quorum sensing, and showed low motility. Nevertheless, statistically significant differences were found among SCV and mucoid isolates. SCVs grew faster, presented higher biofilm formation and flicA expression; but produced less pyorubin and pyocyanin, showed lower elastase activity and rhlR, algD, and lasB expression than mucoid isolates. Conclusion These results help to understand the molecular behavior of chronic P. aeruginosa isolates in CF patients.
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67
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Wee BA, Tai AS, Sherrard LJ, Ben Zakour NL, Hanks KR, Kidd TJ, Ramsay KA, Lamont I, Whiley DM, Bell SC, Beatson SA. Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre. BMC Genomics 2018; 19:644. [PMID: 30165811 PMCID: PMC6117919 DOI: 10.1186/s12864-018-5018-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 08/14/2018] [Indexed: 11/18/2022] Open
Abstract
Background Chronic lung infections caused by Pseudomonas aeruginosa are a significant cause of morbidity and mortality in people with cystic fibrosis (CF). Shared P. aeruginosa strains, that can be transmitted between patients, are of concern and in Australia the AUST-02 shared strain is predominant in individuals attending CF centres in Queensland and Western Australia. M3L7 is a multidrug resistant sub-type of AUST-02 that was recently identified in a Queensland CF centre and was shown to be associated with poorer clinical outcomes. The main aim of this study was to resolve the relationship of the emergent M3L7 sub-type within the AUST-02 group of strains using whole genome sequencing. Results A whole genome core phylogeny of 63 isolates indicated that M3L7 is a monophyletic sub-lineage within the context of the broader AUST-02 group. Relatively short branch lengths connected all of the M3L7 isolates. A phylogeny based on nucleotide polymorphisms present across the genome showed that the chronological estimation of the most recent common ancestor was around 2001 (± 3 years). SNP differences between sequential non-hypermutator M3L7 isolates collected 3–4 years apart from five patients suggested both continuous infection of the same strain and cross-infection of some M3L7 variants between patients. The majority of polymorphisms that were characteristic of M3L7 (i.e. acquired after divergence from all other AUST-02 isolates sequenced) were found to produce non-synonymous mutations in virulence and antibiotic resistance genes. Conclusions M3L7 has recently diverged from a common ancestor, indicating descent from a single carrier at a CF treatment centre in Australia. Both adaptation to the lung and transmission of M3L7 between adults attending this centre may have contributed to its rapid dissemination. Further genomic investigations are required on multiple intra-sample isolates of this sub-type to decipher potential mechanisms which facilitates its epidemiological success. Electronic supplementary material The online version of this article (10.1186/s12864-018-5018-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bryan A Wee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.,Present Address: Usher Institute of Population Health Sciences & Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Anna S Tai
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia.,Department of Respiratory Medicine, Western Australia Adult Cystic Fibrosis Centre, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Laura J Sherrard
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Present Address: School of Pharmacy, Queen's University Belfast, Belfast, United Kingdom
| | - Nouri L Ben Zakour
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Kirt R Hanks
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.,Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK.,Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Kay A Ramsay
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Present Address: Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Iain Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - David M Whiley
- Faculty of Medicine, UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia.,Microbiology Department, Pathology Queensland Central Laboratory, Brisbane, QLD, Australia
| | - Scott C Bell
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia.,Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia. .,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.
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68
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Granato ET, Ziegenhain C, Marvig RL, Kümmerli R. Low spatial structure and selection against secreted virulence factors attenuates pathogenicity in Pseudomonas aeruginosa. ISME JOURNAL 2018; 12:2907-2918. [PMID: 30065310 DOI: 10.1038/s41396-018-0231-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/14/2018] [Accepted: 06/19/2018] [Indexed: 02/01/2023]
Abstract
Bacterial opportunistic pathogens are feared for their difficult-to-treat nosocomial infections and for causing morbidity in immunocompromised patients. Here, we study how such a versatile opportunist, Pseudomonas aeruginosa, adapts to conditions inside and outside its model host Caenorhabditis elegans, and use phenotypic and genotypic screens to identify the mechanistic basis of virulence evolution. We found that virulence significantly dropped in unstructured environments both in the presence and absence of the host, but remained unchanged in spatially structured environments. Reduction of virulence was either driven by a substantial decline in the production of siderophores (in treatments without hosts) or toxins and proteases (in treatments with hosts). Whole-genome sequencing of evolved clones revealed positive selection and parallel evolution across replicates, and showed an accumulation of mutations in regulator genes controlling virulence factor expression. Our study identifies the spatial structure of the non-host environment as a key driver of virulence evolution in an opportunistic pathogen.
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Affiliation(s)
- Elisa T Granato
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland. .,Department of Zoology, University of Oxford, Oxford, United Kingdom.
| | - Christoph Ziegenhain
- Department Biology II, Ludwig-Maximilians-University, Munich, Germany.,Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden
| | - Rasmus L Marvig
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Rolf Kümmerli
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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69
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Abstract
Any two lineages, no matter how distant they are now, began their divergence as one population splitting into two lineages that could coexist indefinitely. The rate of origin of higher-level taxa is therefore the product of the rate of speciation times the probability that two new species coexist long enough to reach a particular level of divergence. Here I have explored these two parameters of disparification in bacteria. Owing to low recombination rates, sexual isolation is not a necessary milestone of bacterial speciation. Rather, irreversible and indefinite divergence begins with ecological diversification, that is, transmission of a bacterial lineage to a new ecological niche, possibly to a new microhabitat but at least to new resources. Several algorithms use sequence data from a taxon of focus to identify phylogenetic groups likely to bear the dynamic properties of species. Identifying these newly divergent lineages allows us to characterize the genetic bases of speciation, as well as the ecological dimensions upon which new species diverge. Speciation appears to be least frequent when a given lineage has few new resources it can adopt, as exemplified by photoautotrophs, C1 heterotrophs, and obligately intracellular pathogens; speciation is likely most rapid for generalist heterotrophs. The genetic basis of ecological divergence may determine whether ecological divergence is irreversible and whether lineages will diverge indefinitely into the future. Long-term coexistence is most likely when newly divergent lineages utilize at least some resources not shared with the other and when the resources themselves will coexist into the remote future.
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70
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Lim SZP, Fitzgerald DA. Treating resistant Pseudomonas aeruginosa lung disease in young children with cystic fibrosis. Paediatr Respir Rev 2018; 27:33-36. [PMID: 29033215 DOI: 10.1016/j.prrv.2017.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 08/25/2017] [Indexed: 12/28/2022]
Abstract
Pseudomonas aeruginosa is a common bacterial pathogen in the evolution of bronchiectasis in cystic fibrosis. The appearance of resistant strains of pseudomonas is increasing with the earlier and more liberal use of a range of anti-pseudomonal antibiotics for the treatment of bacterial chest infections. The rationale for treatment and potential benefits of aggressive treatment of resistant strains of Pseudomonas aeruginosa from early in life are discussed.
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Affiliation(s)
- Sandy Z P Lim
- Sydney Medical School, University of Sydney, Australia
| | - Dominic A Fitzgerald
- The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, Discipline Paediatrics & Child Health, University of Sydney, Australia.
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71
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O'Brien S, Fothergill JL. The role of multispecies social interactions in shaping Pseudomonas aeruginosa pathogenicity in the cystic fibrosis lung. FEMS Microbiol Lett 2018; 364:3958795. [PMID: 28859314 PMCID: PMC5812498 DOI: 10.1093/femsle/fnx128] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/11/2017] [Indexed: 02/07/2023] Open
Abstract
Pseudomonas aeruginosa is a major pathogen in the lungs of cystic fibrosis (CF) patients. However, it is now recognised that a diverse microbial community exists in the airways comprising aerobic and anaerobic bacteria as well as fungi and viruses. This rich soup of microorganisms provides ample opportunity for interspecies interactions, particularly when considering secreted compounds. Here, we discuss how P. aeruginosa-secreted products can have community-wide effects, with the potential to ultimately shape microbial community dynamics within the lung. We focus on three well-studied traits associated with worsening clinical outcome in CF: phenazines, siderophores and biofilm formation, and discuss how secretions can shape interactions between P. aeruginosa and other commonly encountered members of the lung microbiome: Staphylococcus aureus, the Burkholderia cepacia complex, Candida albicans and Aspergillus fumigatus. These interactions may shape the evolutionary trajectory of P. aeruginosa while providing new opportunities for therapeutic exploitation of the CF lung microbiome.
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Affiliation(s)
- Siobhán O'Brien
- Center for Adaptation to a Changing Environment (ACE), ETH Zürich, 8092 Zürich, Switzerland.,Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Joanne L Fothergill
- Institute of Infection and Global Health, University of Liverpool, 8 West Derby Street, Liverpool L69 7B3, UK
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72
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Williams D, Fothergill JL, Evans B, Caples J, Haldenby S, Walshaw MJ, Brockhurst MA, Winstanley C, Paterson S. Transmission and lineage displacement drive rapid population genomic flux in cystic fibrosis airway infections of a Pseudomonas aeruginosa epidemic strain. Microb Genom 2018; 4. [PMID: 29547097 PMCID: PMC5885019 DOI: 10.1099/mgen.0.000167] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Pseudomonas aeruginosa chronic infections of cystic fibrosis (CF) airways are a paradigm for within-host evolution with abundant evidence for rapid evolutionary adaptation and diversification. Recently emerged transmissible strains have spread globally, with the Liverpool Epidemic Strain (LES) the most common strain infecting the UK CF population. Previously we have shown that highly divergent lineages of LES can be found within a single infection, consistent with super-infection among a cross-sectional cohort of patients. However, despite its clinical importance, little is known about the impact of transmission on the genetic structure of these infections over time. To characterize this, we longitudinally sampled a meta-population of 15 genetic lineages within the LES over 13 months among seven chronically infected CF patients by genome sequencing. Comparative genome analyses of P. aeruginosa populations revealed that the presence of coexisting lineages contributed more to genetic diversity within an infection than diversification in situ. We observed rapid and substantial shifts in the relative abundance of lineages and replacement of dominant lineages, likely to represent super-infection by repeated transmissions. Lineage dynamics within patients led to rapid changes in the frequencies of mutations across suites of linked loci carried by each lineage. Many loci were associated with important infection phenotypes such as antibiotic resistance, mucoidy and quorum sensing, and were repeatedly mutated in different lineages. These findings suggest that transmission leads to rapid shifts in the genetic structure of CF infections, including in clinically important phenotypes such as antimicrobial resistance, and is likely to impede accurate diagnosis and treatment.
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Affiliation(s)
- David Williams
- 1Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Joanne L Fothergill
- 2Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Benjamin Evans
- 1Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Jessica Caples
- 2Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Sam Haldenby
- 1Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Martin J Walshaw
- 3Liverpool Heart and Chest Hospital, NHS Foundation Trust, Liverpool, UK
| | | | - Craig Winstanley
- 2Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Steve Paterson
- 1Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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73
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Flanagan L, Steen RR, Saxby K, Klatter M, Aucott BJ, Winstanley C, Fairlamb IJS, Lynam JM, Parkin A, Friman VP. The Antimicrobial Activity of a Carbon Monoxide Releasing Molecule (EBOR-CORM-1) Is Shaped by Intraspecific Variation within Pseudomonas aeruginosa Populations. Front Microbiol 2018; 9:195. [PMID: 29472912 PMCID: PMC5809400 DOI: 10.3389/fmicb.2018.00195] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/29/2018] [Indexed: 11/13/2022] Open
Abstract
Carbon monoxide releasing molecules (CORMs) have been suggested as a new synthetic class of antimicrobials to treat bacterial infections. Here we utilized a novel EBOR-CORM-1 ([NEt4][MnBr2(CO)4]) capable of water-triggered CO-release, and tested its efficacy against a collection of clinical Pseudomonas aeruginosa strains that differ in infection-related virulence traits. We found that while EBOR-CORM-1 was effective in clearing planktonic and biofilm cells of P. aeruginosa strain PAO1 in a concentration dependent manner, this effect was less clear and varied considerably between different P. aeruginosa cystic fibrosis (CF) lung isolates. While a reduction in cell growth was observed after 8 h of CORM application, either no effect or even a slight increase in cell densities and the amount of biofilm was observed after 24 h. This variation could be partly explained by differences in bacterial virulence traits: while CF isolates showed attenuated in vivo virulence and growth compared to strain PAO1, they formed much more biofilm, which could have potentially protected them from the CORM. Even though no clear therapeutic benefits against a subset of isolates was observed in an in vivo wax moth acute infection model, EBOR-CORM-1 was more efficient at reducing the growth of CF isolate co-culture populations harboring intraspecific variation, in comparison with efficacy against more uniform single isolate culture populations. Together these results suggest that CORMs could be effective at controlling genetically diverse P. aeruginosa populations typical for natural chronic CF infections and that the potential benefits of some antibiotics might not be observed if tested only against clonal bacterial populations.
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Affiliation(s)
- Lindsey Flanagan
- Department of Biology, University of York, York, United Kingdom
- Department of Chemistry, University of York, York, United Kingdom
| | - Rachel R. Steen
- Department of Chemistry, University of York, York, United Kingdom
| | - Karinna Saxby
- Department of Biology, University of York, York, United Kingdom
- Department of Chemistry, University of York, York, United Kingdom
| | - Mirre Klatter
- Department of Biology, University of York, York, United Kingdom
| | | | - Craig Winstanley
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | | | - Jason M. Lynam
- Department of Chemistry, University of York, York, United Kingdom
| | - Alison Parkin
- Department of Chemistry, University of York, York, United Kingdom
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74
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Reemergence of Lower-Airway Microbiota in Lung Transplant Patients with Cystic Fibrosis. Ann Am Thorac Soc 2018; 13:2132-2142. [PMID: 27925791 DOI: 10.1513/annalsats.201606-431oc] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
RATIONALE Chronic lung infections are a hallmark of cystic fibrosis; they are responsible for progressive airway destruction and ultimately lead to respiratory death or the requirement for life-saving bilateral lung transplant. Furthermore, recurrent isolation of airway pathogens such as Pseudomonas aeruginosa in the allograft after transplant is associated with adverse outcomes, including bronchiolitis obliterans syndrome and acute infections. Little information exists on the impact of bilateral lung transplant on the lower-airway microbiota. OBJECTIVES To compare, at a microbiome and single-pathogen level (P. aeruginosa), the bacterial communities in pre- and post-transplant samples. METHODS We retrospectively accessed our biobank of sputum samples and sputum-derived bacterial pathogens for patients who had matched samples, including those who were clinically stable before transplant, those who had a pulmonary exacerbation before transplant, and those who had pulmonary exacerbation after transplant. We used 16S ribosomal RNA gene sequencing to characterize the lower-airway microbiome of 14 adult transplant patients with cystic fibrosis. Genotyping and phenotyping of P. aeruginosa isolates from 12 of these patients with matched isolates was performed. MEASUREMENTS AND MAIN RESULTS Although α-diversity (richness and evenness) of patient microbiomes was similar before and after transplant, β- diversity (core microbiome composition) measures stratified patients evenly into two groups with more similar and more dissimilar communities. P. aeruginosa strains isolated before transplant were found to reemerge in 11 of 12 patients; however, phenotypic variation was observed. CONCLUSIONS These findings indicate that recolonization by P. aeruginosa after transplant is almost always strain specific, suggesting a within-host source. The polymicrobial colonization of the airways after transplant does not always reflect the pretransplant sputum microbiota.
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75
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Tai AS, Sherrard LJ, Kidd TJ, Ramsay KA, Buckley C, Syrmis M, Grimwood K, Bell SC, Whiley DM. Antibiotic perturbation of mixed-strain Pseudomonas aeruginosa infection in patients with cystic fibrosis. BMC Pulm Med 2017; 17:138. [PMID: 29096618 PMCID: PMC5667482 DOI: 10.1186/s12890-017-0482-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/25/2017] [Indexed: 12/20/2022] Open
Abstract
Background Pulmonary exacerbations in cystic fibrosis (CF) remain poorly understood and treatment is usually targeted at Pseudomonas aeruginosa. Within Australia a predominant shared P. aeruginosa strain (AUST-02) is associated with greater treatment needs. This single centre study assessed temporal shared strain population dynamics during and after antibiotic treatment of exacerbations. Methods Sputum was collected from 12 adult patients with a history of chronic AUST-02 infection at four time-points during and after treatment of an exacerbation. Forty-eight P. aeruginosa isolates within each sample underwent AUST-02 allele-specific PCR and SNP-based strain genotyping. Results Various commonly shared Australian strains (AUST-01, 0.1%; AUST-02, 54.3%; AUST-06, 36.6%; AUST-07, 4.6%; AUST-11, 4.3%) and two unique strains (0.1%) were identified from 45 sputum samples (2160 isolates). Based on within-patient relative abundance of strains, a “single-strain infection” (n = 7) or “mixed-strain infection” (n = 5) was assigned to each patient. A significant temporal variation in the P. aeruginosa population composition was found for those with mixed-strain infection (P < 0.001). Patients with mixed-strain infections had more long-term treatment requirements than those with single-strain infection. Moreover, despite both groups having similar lung function at study entry, patients with single-strain infection had greater improvement in FEV1% predicted following their exacerbation treatment (P = 0.02). Conclusion Pulmonary exacerbations may reveal multiple, unrelated P. aeruginosa strains whose relative abundance with one another may change rapidly, in a sustained and unpredictable manner. Electronic supplementary material The online version of this article (10.1186/s12890-017-0482-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna S Tai
- School of Medicine, The University of Queensland, Brisbane, QLD, Australia. .,Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia. .,Western Australia Adult Cystic Fibrosis Centre, Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Hospital Avenue, Perth, WA, 6009, Australia.
| | - Laura J Sherrard
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.,Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK.,Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Kay A Ramsay
- School of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Cameron Buckley
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Melanie Syrmis
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia.,Pathology Queensland, Microbiology Department, Brisbane, QLD, Australia
| | - Keith Grimwood
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia.,Menzies Health Institute Queensland, Griffith University and Gold Coast Health, Gold Coast, QLD, Australia
| | - Scott C Bell
- Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia.,Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - David M Whiley
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia.,Pathology Queensland, Microbiology Department, Brisbane, QLD, Australia
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76
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Harrison F, McNally A, da Silva AC, Heeb S, Diggle SP. Optimised chronic infection models demonstrate that siderophore 'cheating' in Pseudomonas aeruginosa is context specific. THE ISME JOURNAL 2017; 11:2492-2509. [PMID: 28696423 PMCID: PMC5649161 DOI: 10.1038/ismej.2017.103] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 12/25/2022]
Abstract
The potential for siderophore mutants of Pseudomonas aeruginosa to attenuate virulence during infection, and the possibility of exploiting this for clinical ends, have attracted much discussion. This has largely been based on the results of in vitro experiments conducted in iron-limited growth medium, in which siderophore mutants act as social 'cheats:' increasing in frequency at the expense of the wild type to result in low-productivity, low-virulence populations dominated by mutants. We show that insights from in vitro experiments cannot necessarily be transferred to infection contexts. First, most published experiments use an undefined siderophore mutant. Whole-genome sequencing of this strain revealed a range of mutations affecting phenotypes other than siderophore production. Second, iron-limited medium provides a very different environment from that encountered in chronic infections. We conducted cheating assays using defined siderophore deletion mutants, in conditions designed to model infected fluids and tissue in cystic fibrosis lung infection and non-healing wounds. Depending on the environment, siderophore loss led to cheating, simple fitness defects, or no fitness effect at all. Our results show that it is crucial to develop defined in vitro models in order to predict whether siderophores are social, cheatable and suitable for clinical exploitation in specific infection contexts.
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Affiliation(s)
- Freya Harrison
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, UK
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Ana C da Silva
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Stephan Heeb
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Stephen P Diggle
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham, UK
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77
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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.
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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
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78
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Maunders E, Welch M. Matrix exopolysaccharides; the sticky side of biofilm formation. FEMS Microbiol Lett 2017; 364:3866592. [PMID: 28605431 PMCID: PMC5812517 DOI: 10.1093/femsle/fnx120] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/07/2017] [Indexed: 12/20/2022] Open
Abstract
The Gram-negative pathogen Pseudomonas aeruginosa is found ubiquitously within the environment and is recognised as an opportunistic human pathogen that commonly infects burn wounds and immunocompromised individuals, or patients suffering from the autosomal recessive disorder cystic fibrosis (CF). During chronic infection, P. aeruginosa is thought to form structured aggregates known as biofilms characterised by a self-produced matrix which encases the bacteria, protecting them from antimicrobial attack and the host immune response. In many cases, antibiotics are ineffective at eradicating P. aeruginosa from chronically infected CF airways. Cyclic-di-GMP has been identified as a key regulator of biofilm formation; however, the way in which its effector proteins elicit a change in biofilm formation remains unclear. Identifying regulators of biofilm formation is a key theme of current research and understanding the factors that activate biofilm formation may help to expose potential new drug targets that slow the onset of chronic infection. This minireview outlines the contribution made by exopolysaccharides to biofilm formation, and describes the current understanding of biofilm regulation in P. aeruginosa with a particular focus on CF airway-associated infections.
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Affiliation(s)
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Hopkins Building, Cambridge CB2 1QW, UK. Tel: +44 01223 333653; E-mail:
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79
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Pseudomonas aeruginosa-Derived Rhamnolipids and Other Detergents Modulate Colony Morphotype and Motility in the Burkholderia cepacia Complex. J Bacteriol 2017; 199:JB.00171-17. [PMID: 28439038 DOI: 10.1128/jb.00171-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 04/16/2017] [Indexed: 12/16/2022] Open
Abstract
Competitive interactions mediated by released chemicals (e.g., toxins) are prominent in multispecies communities, but the effects of these chemicals at subinhibitory concentrations on susceptible bacteria are poorly understood. Although Pseudomonas aeruginosa and species of the Burkholderia cepacia complex (Bcc) can exist together as a coinfection in cystic fibrosis airways, P. aeruginosa toxins can kill Bcc species in vitro Consequently, these bacteria become an ideal in vitro model system to study the impact of sublethal levels of toxins on the biology of typical susceptible bacteria, such as the Bcc, when exposed to P. aeruginosa toxins. Using P. aeruginosa spent medium as a source of toxins, we showed that a small window of subinhibitory concentrations modulated the colony morphotype and swarming motility of some but not all tested Bcc strains, for which rhamnolipids were identified as the active molecule. Using a random transposon mutagenesis approach, we identified several genes required by the Bcc to respond to low concentrations of rhamnolipids and consequently affect the ability of this microbe to change its morphotype and swarm over surfaces. Among those genes identified were those coding for type IVb-Tad pili, which are often required for virulence in various bacterial pathogens. Our study demonstrates that manipulating chemical gradients in vitro can lead to the identification of bacterial behaviors relevant to polymicrobial infections.IMPORTANCE Interspecies interactions can have profound effects on the development and outcomes of polymicrobial infections. Consequently, improving the molecular understanding of these interactions could provide us with new insights on the possible long-term consequences of these chronic infections. In this study, we show that P. aeruginosa-derived rhamnolipids, which participate in Bcc killing at high concentrations, can also trigger biological responses in Burkholderia spp. at low concentrations. The modulation of potential virulence phenotypes in the Bcc by P. aeruginosa suggests that these interactions contribute to pathogenesis and disease severity in the context of polymicrobial infections.
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80
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Jeukens J, Freschi L, Kukavica-Ibrulj I, Emond-Rheault JG, Tucker NP, Levesque RC. Genomics of antibiotic-resistance prediction in Pseudomonas aeruginosa. Ann N Y Acad Sci 2017; 1435:5-17. [PMID: 28574575 PMCID: PMC7379567 DOI: 10.1111/nyas.13358] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/10/2017] [Accepted: 03/22/2017] [Indexed: 12/17/2022]
Abstract
Antibiotic resistance is a worldwide health issue spreading quickly among human and animal pathogens, as well as environmental bacteria. Misuse of antibiotics has an impact on the selection of resistant bacteria, thus contributing to an increase in the occurrence of resistant genotypes that emerge via spontaneous mutation or are acquired by horizontal gene transfer. There is a specific and urgent need not only to detect antimicrobial resistance but also to predict antibiotic resistance in silico. We now have the capability to sequence hundreds of bacterial genomes per week, including assembly and annotation. Novel and forthcoming bioinformatics tools can predict the resistome and the mobilome with a level of sophistication not previously possible. Coupled with bacterial strain collections and databases containing strain metadata, prediction of antibiotic resistance and the potential for virulence are moving rapidly toward a novel approach in molecular epidemiology. Here, we present a model system in antibiotic-resistance prediction, along with its promises and limitations. As it is commonly multidrug resistant, Pseudomonas aeruginosa causes infections that are often difficult to eradicate. We review novel approaches for genotype prediction of antibiotic resistance. We discuss the generation of microbial sequence data for real-time patient management and the prediction of antimicrobial resistance.
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Affiliation(s)
- Julie Jeukens
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Luca Freschi
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Irena Kukavica-Ibrulj
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | | | - Nicholas P Tucker
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
| | - Roger C Levesque
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
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81
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Hilliam Y, Moore MP, Lamont IL, Bilton D, Haworth CS, Foweraker J, Walshaw MJ, Williams D, Fothergill JL, De Soyza A, Winstanley C. Pseudomonas aeruginosa adaptation and diversification in the non-cystic fibrosis bronchiectasis lung. Eur Respir J 2017; 49:49/4/1602108. [PMID: 28446558 PMCID: PMC5898933 DOI: 10.1183/13993003.02108-2016] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/21/2017] [Indexed: 11/05/2022]
Abstract
To characterise Pseudomonas aeruginosa populations during chronic lung infections of non-cystic fibrosis bronchiectasis patients, we used whole-genome sequencing to 1) assess the diversity of P. aeruginosa and the prevalence of multilineage infections; 2) seek evidence for cross-infection or common source acquisition; and 3) characterise P. aeruginosa adaptations.189 isolates, obtained from the sputa of 91 patients attending 16 adult bronchiectasis centres in the UK, were whole-genome sequenced.Bronchiectasis isolates were representative of the wider P. aeruginosa population. Of 24 patients from whom multiple isolates were examined, there were seven examples of multilineage infections, probably arising from multiple infection events. The number of nucleotide variants between genomes of isolates from different patients was in some cases similar to the variations observed between isolates from individual patients, implying the possible occurrence of cross-infection or common source acquisition.Our data indicate that during infections of bronchiectasis patients, P. aeruginosa populations adapt by accumulating loss-of-function mutations, leading to changes in phenotypes including different modes of iron acquisition and variations in biofilm-associated polysaccharides. The within-population diversification suggests that larger scale longitudinal surveillance studies will be required to capture cross-infection or common source acquisition events at an early stage.
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Affiliation(s)
- Yasmin Hilliam
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.,These authors contributed equally
| | - Matthew P Moore
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.,These authors contributed equally
| | - Iain L Lamont
- Dept of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Diana Bilton
- Dept of Respiratory Medicine, Royal Brompton Hospital, London, UK
| | - Charles S Haworth
- Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK
| | - Juliet Foweraker
- Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK
| | - Martin J Walshaw
- Dept of Respiratory Medicine, Liverpool Heart and Chest Hospital, Liverpool, UK
| | - David Williams
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.,Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Joanne L Fothergill
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Anthony De Soyza
- Institute for Cellular Medicine, Newcastle University, Newcastle-upon-Tyne, UK.,These authors contributed equally
| | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK .,These authors contributed equally
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82
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Sherrard LJ, Tai AS, Wee BA, Ramsay KA, Kidd TJ, Ben Zakour NL, Whiley DM, Beatson SA, Bell SC. Within-host whole genome analysis of an antibiotic resistant Pseudomonas aeruginosa strain sub-type in cystic fibrosis. PLoS One 2017; 12:e0172179. [PMID: 28273168 PMCID: PMC5342179 DOI: 10.1371/journal.pone.0172179] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/31/2017] [Indexed: 02/07/2023] Open
Abstract
A Pseudomonas aeruginosa AUST-02 strain sub-type (M3L7) has been identified in Australia, infects the lungs of some people with cystic fibrosis and is associated with antibiotic resistance. Multiple clonal lineages may emerge during treatment with mutations in chromosomally encoded antibiotic resistance genes commonly observed. Here we describe the within-host diversity and antibiotic resistance of M3L7 during and after antibiotic treatment of an acute pulmonary exacerbation using whole genome sequencing and show both variation and shared mutations in important genes. Eleven isolates from an M3L7 population (n = 134) isolated over 3 months from an individual with cystic fibrosis underwent whole genome sequencing. A phylogeny based on core genome SNPs identified three distinct phylogenetic groups comprising two groups with higher rates of mutation (hypermutators) and one non-hypermutator group. Genomes were screened for acquired antibiotic resistance genes with the result suggesting that M3L7 resistance is principally driven by chromosomal mutations as no acquired mechanisms were detected. Small genetic variations, shared by all 11 isolates, were found in 49 genes associated with antibiotic resistance including frame-shift mutations (mexA, mexT), premature stop codons (oprD, mexB) and mutations in quinolone-resistance determining regions (gyrA, parE). However, whole genome sequencing also revealed mutations in 21 genes that were acquired following divergence of groups, which may also impact the activity of antibiotics and multi-drug efflux pumps. Comparison of mutations with minimum inhibitory concentrations of anti-pseudomonal antibiotics could not easily explain all resistance profiles observed. These data further demonstrate the complexity of chronic and antibiotic resistant P. aeruginosa infection where a multitude of co-existing genotypically diverse sub-lineages might co-exist during and after intravenous antibiotic treatment.
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Affiliation(s)
- Laura J. Sherrard
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Anna S. Tai
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
- Western Australia Adult Cystic Fibrosis Centre, Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Bryan A. Wee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Kay A. Ramsay
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Timothy J. Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Centre for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Nouri L. Ben Zakour
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - David M. Whiley
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
- Pathology Queensland, Microbiology Department, Brisbane, QLD, Australia
| | - Scott A. Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Scott C. Bell
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
- * E-mail:
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83
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High virulence sub-populations in Pseudomonas aeruginosa long-term cystic fibrosis airway infections. BMC Microbiol 2017; 17:30. [PMID: 28158967 PMCID: PMC5291983 DOI: 10.1186/s12866-017-0941-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/25/2017] [Indexed: 11/24/2022] Open
Abstract
Background Pseudomonas aeruginosa typically displays loss of virulence-associated secretions over the course of chronic cystic fibrosis infections. This has led to the suggestion that virulence is a costly attribute in chronic infections. However, previous reports suggest that overproducing (OP) virulent pathotypes can coexist with non-producing mutants in the CF lung for many years. The consequences of such within-patient phenotypic diversity for the success of this pathogen are not fully understood. Here, we provide in-depth quantification of within-host variation in the production of three virulence associated secretions in the Liverpool cystic fibrosis epidemic strain of P. aeruginosa, and investgate the effect of this phenotypic variation on virulence in acute infections of an insect host model. Results Within-patient variation was present for all three secretions (pyoverdine, pyocyanin and LasA protease). In two out of three patients sampled, OP isolates coexisted with under-producing mutants. In the third patient, all 39 isolates were under-producers of all three secretions relative to the transmissible ancestor LESB58. Finally, this phenotypic variation translated into variation in virulence in an insect host model. Conclusions Within population variation in the production of P. aeruginosa virulence-associated secretions can lead to high virulence sub-populations persisting in patients with chronic CF infections. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0941-6) contains supplementary material, which is available to authorized users.
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84
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Beaume M, Köhler T, Greub G, Manuel O, Aubert JD, Baerlocher L, Farinelli L, Buckling A, van Delden C. Rapid adaptation drives invasion of airway donor microbiota by Pseudomonas after lung transplantation. Sci Rep 2017; 7:40309. [PMID: 28094327 PMCID: PMC5240337 DOI: 10.1038/srep40309] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 12/06/2016] [Indexed: 01/02/2023] Open
Abstract
In cystic fibrosis (CF) patients, chronic airway infection by Pseudomonas leads to progressive lung destruction ultimately requiring lung transplantation (LT). Following LT, CF-adapted Pseudomonas strains, potentially originating from the sinuses, may seed the allograft leading to infections and reduced allograft survival. We investigated whether CF-adapted Pseudomonas populations invade the donor microbiota and adapt to the non-CF allograft. We collected sequential Pseudomonas isolates and airway samples from a CF-lung transplant recipient during two years, and followed the dynamics of the microbiota and Pseudomonas populations. We show that Pseudomonas invaded the host microbiota within three days post-LT, in association with a reduction in richness and diversity. A dominant mucoid and hypermutator mutL lineage was replaced after 11 days by non-mucoid strains. Despite antibiotic therapy, Pseudomonas dominated the allograft microbiota until day 95. We observed positive selection of pre-LT variants and the appearance of novel mutations. Phenotypic adaptation resulted in increased biofilm formation and swimming motility capacities. Pseudomonas was replaced after 95 days by a microbiota dominated by Actinobacillus. In conclusion, mucoid Pseudomonas adapted to the CF-lung remained able to invade the allograft. Selection of both pre-existing non-mucoid subpopulations and of novel phenotypic traits suggests rapid adaptation of Pseudomonas to the non-CF allograft.
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Affiliation(s)
- M Beaume
- Service of Infectious Diseases, University Hospitals of Geneva and Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - T Köhler
- Service of Infectious Diseases, University Hospitals of Geneva and Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - G Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.,Service of Infectious Diseases, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - O Manuel
- Service of Infectious Diseases, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.,Transplantation Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - J-D Aubert
- Transplantation Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.,Service of Pulmonary Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | | | | | - A Buckling
- ESI &CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall, United Kingdom
| | - C van Delden
- Service of Infectious Diseases, University Hospitals of Geneva and Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
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85
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Davies EV, James CE, Brockhurst MA, Winstanley C. Evolutionary diversification of Pseudomonas aeruginosa in an artificial sputum model. BMC Microbiol 2017; 17:3. [PMID: 28056789 PMCID: PMC5216580 DOI: 10.1186/s12866-016-0916-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/15/2016] [Indexed: 12/20/2022] Open
Abstract
Background During chronic lung infections of cystic fibrosis patients Pseudomonas aeruginosa populations undergo extensive evolutionary diversification. However, the selective drivers of this evolutionary process are poorly understood. To test the effects of temperate phages on diversification in P. aeruginosa biofilms we experimentally evolved populations of P. aeruginosa for approximately 240 generations in artificial sputum medium with or without a community of three temperate phages. Results Analysis of end-point populations using a suite of phenotypic tests revealed extensive phenotypic diversification within populations, but no significant differences between the populations evolved with or without phages. The most common phenotypic variant observed was loss of all three types of motility (swimming, swarming and twitching) and resistance to all three phages. Despite the absence of selective pressure, some members of the population evolved antibiotic resistance. The frequency of antibiotic resistant isolates varied according to population and the antibiotic tested. However, resistance to ceftazidime and tazobactam-piperacillin was observed more frequently than resistance to other antibiotics, and was associated with higher prevelence of isolates exhibiting a hypermutable phenotype and increased beta-lactamase production. Conclusions We observed considerable within-population phenotypic diversity in P. aeruginosa populations evolving in the artificial sputum medium biofilm model. Replicate populations evolved both in the presence and absence of phages converged upon similar sets of phenotypes. The evolved phenotypes, including antimicrobial resistance, were similar to those observed amongst clinical isolates from cystic fibrosis infections. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0916-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emily V Davies
- Institute of Infection and Global Health, University of Liverpool, 8 West Derby Street, Liverpool, L69 7BE, UK
| | - Chloe E James
- Institute of Infection and Global Health, University of Liverpool, 8 West Derby Street, Liverpool, L69 7BE, UK.,School of Environment and Life Sciences, University of Salford, Manchester, M5 4WT, UK
| | | | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool, 8 West Derby Street, Liverpool, L69 7BE, UK.
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86
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Microbiome in the pathogenesis of cystic fibrosis and lung transplant-related disease. Transl Res 2017; 179:84-96. [PMID: 27559681 DOI: 10.1016/j.trsl.2016.07.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 07/26/2016] [Accepted: 07/27/2016] [Indexed: 01/01/2023]
Abstract
Significant advances in culture-independent methods have expanded our knowledge about the diversity of the lung microbial environment. Complex microorganisms and microbial communities can now be identified in the distal airways in a variety of respiratory diseases, including cystic fibrosis (CF) and the posttransplantation lung. Although there are significant methodologic concerns about sampling the lung microbiome, several studies have now shown that the microbiome of the lower respiratory tract is distinct from the upper airway. CF is a disease characterized by chronic airway infections that lead to significant morbidity and mortality. Traditional culture-dependent methods have identified a select group of pathogens that cause exacerbations in CF, but studies using bacterial 16S rRNA gene-based microarrays have shown that the CF microbiome is an intricate and dynamic bacterial ecosystem, which influences both host immune health and disease pathogenesis. These microbial communities can shift with external influences, including antibiotic exposure. In addition, there have been a number of studies suggesting a link between the gut microbiome and respiratory health in CF. Compared with CF, there is significantly less knowledge about the microbiome of the transplanted lung. Risk factors for bronchiolitis obliterans syndrome, one of the leading causes of death, include microbial infections. Lung transplant patients have a unique lung microbiome that is different than the pretransplanted microbiome and changes with time. Understanding the host-pathogen interactions in these diseases may suggest targeted therapies and improve long-term survival in these patients.
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87
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Impact of High Diversity of Achromobacter Populations within Cystic Fibrosis Sputum Samples on Antimicrobial Susceptibility Testing. J Clin Microbiol 2016; 55:206-215. [PMID: 27807149 DOI: 10.1128/jcm.01843-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 10/25/2016] [Indexed: 01/31/2023] Open
Abstract
Chronic colonization by opportunistic environmental bacteria is frequent in the airways of cystic fibrosis (CF) patients. Studies of Pseudomonas aeruginosa evolution during persistence have highlighted the emergence of pathoadaptive genotypes and phenotypes, leading to complex and diversified inpatient colonizing populations also observed at the intraspecimen level. Such diversity, including heterogeneity in resistance profiles, has been considered an adaptive strategy devoted to host persistence. Longitudinal genomic diversity has been shown for the emergent opportunistic pathogen Achromobacter, but phenotypic and genomic diversity has not yet been studied within a simple CF sputum sample. Here, we studied the genomic diversity and antimicrobial resistance heterogeneity of 132 Achromobacter species strains (8 to 27 strains of identical or distinct colonial morphotypes per specimen) recovered from the sputum samples of 9 chronically colonized CF patients. We highlighted the high within-sample and within-morphotype diversity of antimicrobial resistance (disk diffusion) and genomic (pulsed-field gel electrophoresis) profiles. No sputum sample included strains with identical pulsotypes or antibiotic susceptibility patterns. Differences in clinical categorization were observed for the 9 patients and concerned 3 to 11 antibiotics, including antibiotics recommended for use against Achromobacter Within-sample antimicrobial resistance heterogeneity, not predictable from colonial morphology, suggested that it may represent a selective advantage against antibiotics in an Achromobacter persisting population and potentially compromise the antibiotic management of CF airway infections.
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88
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Gonçalves SM, Lagrou K, Duarte-Oliveira C, Maertens JA, Cunha C, Carvalho A. The microbiome-metabolome crosstalk in the pathogenesis of respiratory fungal diseases. Virulence 2016; 8:673-684. [PMID: 27820674 DOI: 10.1080/21505594.2016.1257458] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Filamentous fungi of the genus Aspergillus are responsible for several superficial and invasive infections and allergic syndromes. The risk of infection and its clinical outcome vary significantly even among patients with similar predisposing clinical factors and pathogen exposure. There is increasing evidence that the individual microbiome supervises the outcome of the host-fungus interaction by influencing mechanisms of immune regulation, inflammation, metabolism, and other physiological processes. Microbiome-mediated mechanisms of resistance allow therefore the control of fungal colonization, preventing the onset of overt disease, particularly in patients with underlying immune dysfunction. Here, we review this emerging area of research and discuss the contribution of the microbiota (and its dysbiosis), including its immunoregulatory properties and relationship with the metabolic activity of commensals, to respiratory fungal diseases. Finally, we highlight possible strategies aimed at decoding the microbiome-metabolome dialog and at its exploitation toward personalized medical interventions in patients at high risk of infection.
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Affiliation(s)
- Samuel M Gonçalves
- a Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho , Braga , Portugal.,b ICVS/3B's - PT Government Associate Laboratory , Guimarães , Portugal
| | - Katrien Lagrou
- c Department of Microbiology and Immunology , KU Leuven - University of Leuven , Leuven , Belgium.,d Department of Laboratory Medicine and National Reference Center for Medical Mycology , University Hospitals Leuven , Leuven , Belgium
| | - Cláudio Duarte-Oliveira
- a Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho , Braga , Portugal.,b ICVS/3B's - PT Government Associate Laboratory , Guimarães , Portugal
| | - Johan A Maertens
- e Department of Hematology , University Hospitals Leuven , Leuven , Belgium
| | - Cristina Cunha
- a Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho , Braga , Portugal.,b ICVS/3B's - PT Government Associate Laboratory , Guimarães , Portugal
| | - Agostinho Carvalho
- a Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho , Braga , Portugal.,b ICVS/3B's - PT Government Associate Laboratory , Guimarães , Portugal
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89
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Lorenz A, Pawar V, Häussler S, Weiss S. Insights into host-pathogen interactions from state-of-the-art animal models of respiratory Pseudomonas aeruginosa infections. FEBS Lett 2016; 590:3941-3959. [PMID: 27730639 DOI: 10.1002/1873-3468.12454] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 10/04/2016] [Accepted: 10/07/2016] [Indexed: 12/29/2022]
Abstract
Pseudomonas aeruginosa is an important opportunistic pathogen that can cause acute respiratory infections in immunocompetent patients or chronic infections in immunocompromised individuals and in patients with cystic fibrosis. When acquiring the chronic infection state, bacteria are encapsulated within biofilm structures enabling them to withstand diverse environmental assaults, including immune reactions and antimicrobial therapy. Understanding the molecular interactions within the bacteria, as well as with the host or other bacteria, is essential for developing innovative treatment strategies. Such knowledge might be accumulated in vitro. However, it is ultimately necessary to confirm these findings in vivo. In the present Review, we describe state-of-the-art in vivo models that allow studying P. aeruginosa infections in molecular detail. The portrayed mammalian models exclusively focus on respiratory infections. The data obtained by alternative animal models which lack lung tissue, often provide molecular insights that are easily transferable to mammals. Importantly, these surrogate in vivo systems reveal complex molecular interactions of P. aeruginosa with the host. Herein, we also provide a critical assessment of the advantages and disadvantages of such models.
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Affiliation(s)
- Anne Lorenz
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research, TWINCORE GmbH, A Joint Venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Germany
| | - Vinay Pawar
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany.,Department of Molecular Immunology, Helmholtz Center for Infection Research, Braunschweig, Germany.,Institute of Immunology, Medical School Hannover, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research, TWINCORE GmbH, A Joint Venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Germany.,Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Siegfried Weiss
- Department of Molecular Immunology, Helmholtz Center for Infection Research, Braunschweig, Germany.,Institute of Immunology, Medical School Hannover, Germany
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90
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Fernández-Barat L, Ciofu O, Kragh KN, Pressler T, Johansen U, Motos A, Torres A, Hoiby N. Phenotypic shift in Pseudomonas aeruginosa populations from cystic fibrosis lungs after 2-week antipseudomonal treatment. J Cyst Fibros 2016; 16:222-229. [PMID: 27651273 DOI: 10.1016/j.jcf.2016.08.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 08/25/2016] [Accepted: 08/25/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND The influence of suppressive therapy on the different P. aeruginosa phenotypes harbored in the lungs of cystic fibrosis (CF) patients remains unclear. Our aim was to investigate the phenotypic changes (mucoidy, hypermutability, antibiotic resistance, transcriptomic profiles and biofilm) in P. aeruginosa populations before and after a 2-week course of suppressive antimicrobial therapy in chronically infected CF patients in Denmark. MATERIAL AND METHODS Prospective observational clinical study. Sputum samples were assessed before and after treatment for P. aeruginosa, with regard to: a) colony-forming units (CFU/mL), b) frequency of mucoids and non-mucoids, c) resistance pattern to anti-pseudomonal drugs, d) hypermutability, e) transcriptomic profiles, and f) presence of biofilms. RESULTS We collected 23 sputum samples (12 before antibiotic treatment and 11 after) and 77 P. aeruginosa from different CF patients. After treatment, the P. aeruginosa burden diminished but antimicrobial resistance to aztreonam, tobramycin and ceftazidime rose; non-mucoid phenotypes presented increased resistance to colistin, tobramycin, meropenem, and ciprofloxacin, and hypermutable phenotypes to ciprofloxacin. In spite of biofilm persistence, a down-regulation of genes involved in denitrification was detected. CONCLUSION A 2-week course of suppressive therapy reduces P. aeruginosa lung colonization and influences nitrogen metabolism genes, but also promotes antimicrobial resistance while P. aeruginosa persists in biofilms.
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Affiliation(s)
- Laia Fernández-Barat
- Centro de Investigación Biomedica En Red-Enfermedades Respiratorias (CibeRes, CB06/06/0028), Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CELLEX Laboratories, School of Medicine, University of Barcelona, Spain.
| | - Oana Ciofu
- Department of Immunology and Microbiology, Costerton Biofilm Center, Copenhagen, Denmark; Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Kasper N Kragh
- Department of Immunology and Microbiology, Costerton Biofilm Center, Copenhagen, Denmark; Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Tania Pressler
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark; CF Center, Rigshospitalet, Denmark
| | - Ulla Johansen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Anna Motos
- Centro de Investigación Biomedica En Red-Enfermedades Respiratorias (CibeRes, CB06/06/0028), Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CELLEX Laboratories, School of Medicine, University of Barcelona, Spain
| | - Antoni Torres
- Centro de Investigación Biomedica En Red-Enfermedades Respiratorias (CibeRes, CB06/06/0028), Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CELLEX Laboratories, School of Medicine, University of Barcelona, Spain; Pneumology Service, Clinical Thorax Institute, Hospital Clinic, Barcelona, Spain
| | - Niels Hoiby
- Department of Immunology and Microbiology, Costerton Biofilm Center, Copenhagen, Denmark; Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
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91
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Evolution of Ecological Diversity in Biofilms of Pseudomonas aeruginosa by Altered Cyclic Diguanylate Signaling. J Bacteriol 2016; 198:2608-18. [PMID: 27021563 PMCID: PMC5019052 DOI: 10.1128/jb.00048-16] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/22/2016] [Indexed: 11/29/2022] Open
Abstract
The ecological and evolutionary forces that promote and maintain diversity in biofilms are not well understood. To quantify these forces, three Pseudomonas aeruginosa populations were experimentally evolved from strain PA14 in a daily cycle of attachment, assembly, and dispersal for 600 generations. Each biofilm population evolved diverse colony morphologies and mutator genotypes defective in DNA mismatch repair. This diversity enhanced population fitness and biofilm output, owing partly to rare, early colonizing mutants that enhanced attachment of others. Evolved mutants exhibited various levels of the intracellular signal cyclic-di-GMP, which associated with their timing of adherence. Manipulating cyclic-di-GMP levels within individual mutants revealed a network of interactions in the population that depended on various attachment strategies related to this signal. Diversification in biofilms may therefore arise and be reinforced by initial colonists that enable community assembly.
IMPORTANCE How biofilm diversity assembles, evolves, and contributes to community function is largely unknown. This presents a major challenge for understanding evolution during chronic infections and during the growth of all surface-associated microbes. We used experimental evolution to probe these dynamics and found that diversity, partly related to altered cyclic-di-GMP levels, arose and persisted due to the emergence of ecological interdependencies related to attachment patterns. Clonal isolates failed to capture population attributes, which points to the need to account for diversity in infections. More broadly, this study offers an experimental framework for linking phenotypic variation to distinct ecological strategies in biofilms and for studying eco-evolutionary interactions.
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92
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Sommer LM, Marvig RL, Luján A, Koza A, Pressler T, Molin S, Johansen HK. Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways? BMC Genomics 2016; 17:589. [PMID: 27506816 PMCID: PMC4979127 DOI: 10.1186/s12864-016-2873-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/30/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The primary cause of morbidity and mortality in cystic fibrosis (CF) patients is lung infection by Pseudomonas aeruginosa. Therefore much work has been done to understand the adaptation and evolution of P. aeruginosa in the CF lung. However, many of these studies have focused on longitudinally collected single isolates, and only few have included cross-sectional analyses of entire P. aeruginosa populations in sputum samples. To date only few studies have used the approach of metagenomic analysis for the purpose of investigating P. aeruginosa populations in CF airways. RESULTS We analysed five metagenomes together with longitudinally collected single isolates from four recently chronically infected CF patients. With this approach we were able to link the clone type and the majority of SNP profiles of the single isolates to that of the metagenome(s) for each individual patient. CONCLUSION Based on our analysis we find that when having access to comprehensive collections of longitudinal single isolates it is possible to rediscover the genotypes of the single isolates in the metagenomic samples. This suggests that information gained from genome sequencing of comprehensive collections of single isolates is satisfactory for many investigations of adaptation and evolution of P. aeruginosa to the CF airways.
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Affiliation(s)
- Lea M Sommer
- The Technical University of Denmark, Center for Biosustainability, Hørsholm, Denmark.,Rigshospitalet, Department of Clinical Microbiology, Copenhagen, Denmark
| | - Rasmus L Marvig
- Rigshospitalet, Department of Clinical Microbiology, Copenhagen, Denmark.,Rigshospitalet, Center for Genomic Medicine, Copenhagen, Denmark
| | | | - Anna Koza
- The Technical University of Denmark, Center for Biosustainability, Hørsholm, Denmark
| | | | - Søren Molin
- The Technical University of Denmark, Center for Biosustainability, Hørsholm, Denmark.,The Technical University of Denmark, Department of Systems Biology, Lyngby, Denmark
| | - Helle K Johansen
- The Technical University of Denmark, Center for Biosustainability, Hørsholm, Denmark. .,Rigshospitalet, Department of Clinical Microbiology, Copenhagen, Denmark.
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93
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Cigana C, Melotti P, Baldan R, Pedretti E, Pintani E, Iansa P, De Fino I, Favari F, Bergamini G, Tridello G, Cirillo DM, Assael BM, Bragonzi A. Genotypic and phenotypic relatedness of Pseudomonas aeruginosa isolates among the major cystic fibrosis patient cohort in Italy. BMC Microbiol 2016; 16:142. [PMID: 27400750 PMCID: PMC4940697 DOI: 10.1186/s12866-016-0760-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 07/02/2016] [Indexed: 01/06/2023] Open
Abstract
Background Pseudomonas aeruginosa is the predominant pathogen associated with the decline of pulmonary function in cystic fibrosis (CF) patients. Both environment-to-host acquisition and patient-to-patient transmission have been described for P. aeruginosa infection. Epidemic clones and bacterial phenotypic adaptation to the CF lung have been recognised as independent risk factors for disease progression. So far, there is no established link between genotypic prevalence and phenotypic traits. Here, we look at the major CF patient cohort in Italy to identify shared P. aeruginosa clones and associated common phenotypic traits. Results A comprehensive analysis of P. aeruginosa genotypes to determine the presence of high-risk shared clones and their association to specific phenotypic traits has been performed in a major Italian CF centre. Pulsed-field gel electrophoresis (PFGE) of P. aeruginosa isolates from 338 CF subjects identified 43 profiles shared by two or more patients and 214 profiles exclusive to individual patients. There was no evidence of a P. aeruginosa outbreak, but four most prevalent pulsotypes were detected. Common phenotypic traits were recorded intra-pulsotypes, but we detected heterogeneity inter-pulsotypes. Two of the four major pulsotypes included P. aeruginosa isolates with hallmarks of adaptation to the CF airways, including loss of motility, low production of siderophore, pyocyanin and proteases, and antibiotic resistance. One of these pulsotypes grouped a high percentage of hypermutable isolates. No clear correlation between epidemiological and clinical data was found. Conclusions We conclude that CF patients of this cohort shared common pulsotypes, but their phenotypic heterogeneity indicates an absence of specific traits associated to P. aeruginosa genotypic prevalence. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0760-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cristina Cigana
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132, Milan, Italy.
| | - Paola Melotti
- Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Integrata di Verona, piazzale Stefani 1, 37126, Verona, Italy
| | - Rossella Baldan
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132, Milan, Italy
| | - Elisa Pedretti
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132, Milan, Italy
| | - Emily Pintani
- Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Integrata di Verona, piazzale Stefani 1, 37126, Verona, Italy
| | - Patrizia Iansa
- Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Integrata di Verona, piazzale Stefani 1, 37126, Verona, Italy
| | - Ida De Fino
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132, Milan, Italy
| | - Flavio Favari
- Microbiology and Virology Unit, Department of Pathology, Azienda Ospedaliera Universitaria Integrata di Verona, piazzale Stefani 1, 37126, Verona, Italy
| | - Gabriella Bergamini
- Department of Pathology and Diagnostics, University of Verona, Strada le Grazie 8, 37134, Verona, Italy
| | - Gloria Tridello
- Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Integrata di Verona, piazzale Stefani 1, 37126, Verona, Italy
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132, Milan, Italy
| | - Baroukh M Assael
- Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Integrata di Verona, piazzale Stefani 1, 37126, Verona, Italy
| | - Alessandra Bragonzi
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132, Milan, Italy.
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94
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Temperate phages both mediate and drive adaptive evolution in pathogen biofilms. Proc Natl Acad Sci U S A 2016; 113:8266-71. [PMID: 27382184 DOI: 10.1073/pnas.1520056113] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Temperate phages drive genomic diversification in bacterial pathogens. Phage-derived sequences are more common in pathogenic than nonpathogenic taxa and are associated with changes in pathogen virulence. High abundance and mobilization of temperate phages within hosts suggests that temperate phages could promote within-host evolution of bacterial pathogens. However, their role in pathogen evolution has not been experimentally tested. We experimentally evolved replicate populations of Pseudomonas aeruginosa with or without a community of three temperate phages active in cystic fibrosis (CF) lung infections, including the transposable phage, ɸ4, which is closely related to phage D3112. Populations grew as free-floating biofilms in artificial sputum medium, mimicking sputum of CF lungs where P. aeruginosa is an important pathogen and undergoes evolutionary adaptation and diversification during chronic infection. Although bacterial populations adapted to the biofilm environment in both treatments, population genomic analysis revealed that phages altered both the trajectory and mode of evolution. Populations evolving with phages exhibited a greater degree of parallel evolution and faster selective sweeps than populations without phages. Phage ɸ4 integrated randomly into the bacterial chromosome, but integrations into motility-associated genes and regulators of quorum sensing systems essential for virulence were selected in parallel, strongly suggesting that these insertional inactivation mutations were adaptive. Temperate phages, and in particular transposable phages, are therefore likely to facilitate adaptive evolution of bacterial pathogens within hosts.
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95
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Maldonado RF, Sá-Correia I, Valvano MA. Lipopolysaccharide modification in Gram-negative bacteria during chronic infection. FEMS Microbiol Rev 2016; 40:480-93. [PMID: 27075488 PMCID: PMC4931227 DOI: 10.1093/femsre/fuw007] [Citation(s) in RCA: 372] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/23/2015] [Accepted: 03/10/2016] [Indexed: 12/16/2022] Open
Abstract
The Gram-negative bacterial lipopolysaccharide (LPS) is a major component of the outer membrane that plays a key role in host-pathogen interactions with the innate immune system. During infection, bacteria are exposed to a host environment that is typically dominated by inflammatory cells and soluble factors, including antibiotics, which provide cues about regulation of gene expression. Bacterial adaptive changes including modulation of LPS synthesis and structure are a conserved theme in infections, irrespective of the type or bacteria or the site of infection. In general, these changes result in immune system evasion, persisting inflammation and increased antimicrobial resistance. Here, we review the modifications of LPS structure and biosynthetic pathways that occur upon adaptation of model opportunistic pathogens (Pseudomonas aeruginosa, Burkholderia cepacia complex bacteria, Helicobacter pylori and Salmonella enterica) to chronic infection in respiratory and gastrointestinal sites. We also discuss the molecular mechanisms of these variations and their role in the host-pathogen interaction.
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Affiliation(s)
- Rita F. Maldonado
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon 1049-001, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon 1049-001, Portugal
| | - Miguel A. Valvano
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5C1, Canada
- Centre for Infection and Immunity, Queen's University Belfast, Belfast BT9 7BL, UK
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96
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Within-Host Evolution of the Dutch High-Prevalent Pseudomonas aeruginosa Clone ST406 during Chronic Colonization of a Patient with Cystic Fibrosis. PLoS One 2016; 11:e0158106. [PMID: 27337151 PMCID: PMC4918941 DOI: 10.1371/journal.pone.0158106] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/12/2016] [Indexed: 01/01/2023] Open
Abstract
This study investigates adaptation of ST406, a prevalent P. aeruginosa clone, present in 15% of chronically infected cystic fibrosis (CF) patients in the Netherlands, in a newly infected CF patient during three years using whole genome sequencing (WGS), transcriptomics, and phenotypic assays, including biofilm formation. WGS-based phylogeny demonstrates that ST406 is genetically distinct from other reported CF related strains or epidemic clones. Comparative genomic analysis of the early (S1) and late (S2) isolate yielded 42 single nucleotide polymorphisms (SNPs) and 10 indels and a single 7 kb genomic fragment only found in S2. Most SNPs and differentially expressed genes encoded proteins involved in metabolism, secretion and signal transduction or transcription. SNPs were identified in regulator genes mexT and exsA and coincided with differential gene expression of mexE and mexF, encoding the MexE/F efflux pump, genes encoding the type six secretion system (T6SS) and type three secretion system (T3SS), which have also been previously implicated in adaptation of other P. aeruginosa strains during chronic infection of CF lungs. The observation that genetically different strains from different patients have accumulated similar genetic adaptations supports the concept of adaptive parallel evolution of P. aeruginosa in chronically infected CF patients. Phenotypically, there was loss of biofilm maturation coinciding with a significant lower level of transcription of both bfmR and bfmS during chronic colonization. These data suggest that the high-prevalent Dutch CF clone ST406 displays adaptation to the CF lung niche, which involves a limited number of mutations affecting regulators controlling biofilm formation and secretion and genes involved in metabolism. These genes could provide good targets for anti-pseudomonal therapy.
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97
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Abstract
In cystic fibrosis, statistical models have been more successful in predicting mortality than the time course of clinical status. We develop a system of partial differential equations that simultaneously track mortality and patient status, with all model parameters estimated from the extensive and carefully maintained database from the Cystic Fibrosis Foundation. Cystic fibrosis is an autosomal recessive disease that leads to loss of lung function, most commonly assessed using the Forced Expiratory Volume in 1 second (FEV1%). This loss results from inflammation secondary to chronic bacterial infections, particularly Pseudomonas aeruginosa, methicillin-sensitive Staphylococcus aureus (MSSA) and members of the virulent Burkholderia complex. The model tracks FEV1% and carriage of these three bacteria over the course of a patient’s life. Analysis of patient state changes from year to year reveals four feedback loops: a damaging positive feedback loop between P. aeruginosa carriage and lower FEV1%, negative feedback loops between P. aeruginosa and MSSA and between P. aeruginosa and Burkholderia, and a protective positive feedback loop between MSSA carriage and higher FEV1%. The partial differential equations built from this data analysis accurately capture the life-long progression of the disease, quantify the key role of high annual FEV1% variability in reducing survivorship, the relative unimportance of short-term bacterial interactions for long-term survival, and the potential benefits of eradicating the most harmful bacteria.
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98
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Bernier SP, Workentine ML, Li X, Magarvey NA, O'Toole GA, Surette MG. Cyanide Toxicity to Burkholderia cenocepacia Is Modulated by Polymicrobial Communities and Environmental Factors. Front Microbiol 2016; 7:725. [PMID: 27242743 PMCID: PMC4870242 DOI: 10.3389/fmicb.2016.00725] [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: 01/16/2016] [Accepted: 05/02/2016] [Indexed: 12/31/2022] Open
Abstract
Microbes within polymicrobial communities can establish positive and negative interactions that have the potential to influence the overall behavior of the community. Pseudomonas aeruginosa and species of the Burkholderia cepacia complex (Bcc) can co-exist in the lower airways, however several studies have shown that P. aeruginosa can effectively kill the Bcc in vitro, for which hydrogen cyanide (HCN) was recently proposed to play a critical role. Here we show that modification of the environment (i.e., culture medium), long-term genetic adaptation of P. aeruginosa to the cystic fibrosis (CF) lung, or the addition of another bacterial species to the community can alter the sensitivity of Burkholderia cenocepacia to P. aeruginosa toxins. We specifically demonstrate that undefined rich media leads to higher susceptibility of B. cenocepacia to P. aeruginosa toxins like cyanide as compared to a synthetic medium (SCFM), that mimics the CF lung nutritional content. Overall, our study shows that the polymicrobial environment can have profound effects on negative interactions mediated by P. aeruginosa against B. cenocepacia. In fact, evolved P. aeruginosa or the presence of other species such as Staphylococcus aureus can directly abolish the direct competition mediated by cyanide and consequently maintaining a higher level of species diversity within the community.
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Affiliation(s)
- Steve P Bernier
- Department of Medicine, Faculty of Health Sciences, Farncombe Family Digestive Health Research Institute, McMaster University Hamilton, ON, Canada
| | - Matthew L Workentine
- Department of Medicine, Faculty of Health Sciences, Farncombe Family Digestive Health Research Institute, McMaster University Hamilton, ON, Canada
| | - Xiang Li
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University Hamilton, ON, Canada
| | - Nathan A Magarvey
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University Hamilton, ON, Canada
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth Hanover, NH, USA
| | - Michael G Surette
- Department of Medicine, Faculty of Health Sciences, Farncombe Family Digestive Health Research Institute, McMaster UniversityHamilton, ON, Canada; Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster UniversityHamilton, ON, Canada
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99
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Temperate phages enhance pathogen fitness in chronic lung infection. ISME JOURNAL 2016; 10:2553-5. [PMID: 27070941 PMCID: PMC4950967 DOI: 10.1038/ismej.2016.51] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/19/2016] [Accepted: 03/04/2016] [Indexed: 11/08/2022]
Abstract
The Liverpool Epidemic Strain (LES) is a polylysogenic, transmissible strain of Pseudomonas aeruginosa, capable of superinfecting existing P. aeruginosa respiratory infections in individuals with cystic fibrosis (CF). The LES phages are highly active in the CF lung and may have a role in the competitiveness of the LES in vivo. In this study, we tested this by competing isogenic PAO1 strains that differed only by the presence or absence of LES prophages in a rat model of chronic lung infection. Lysogens invaded phage-susceptible populations, both in head-to-head competition and when invading from rare, in the spatially structured, heterogeneous lung environment. Appreciable densities of free phages in lung tissue confirmed active phage lysis in vivo. Moreover, we observed lysogenic conversion of the phage-susceptible competitor. These results suggest that temperate phages may have an important role in the competitiveness of the LES in chronic lung infection by acting as anti-competitor weapons.
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100
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Tetz G, Vikina D, Tetz V. Antimicrobial activity of mul-1867, a novel antimicrobial compound, against multidrug-resistant Pseudomonas aeruginosa. Ann Clin Microbiol Antimicrob 2016; 15:19. [PMID: 27001074 PMCID: PMC4802586 DOI: 10.1186/s12941-016-0134-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/14/2016] [Indexed: 02/07/2023] Open
Abstract
Background There is an urgent need for new antimicrobial compounds to treat various lung infections caused by multidrug-resistant Pseudomonas aeruginosa (MDR-PA). Methods We studied the potency of Mul-1867 against MDR-PA isolates from patients with cystic fibrosis, chronic obstructive pulmonary disease, and ventilator-associated pneumonia. The minimal inhibitory concentrations (MICs) and minimum biofilm eliminating concentrations (MBECs), defined as the concentrations of drug that kill 50 % (MBEC50), 90 % (MBEC90), and 100 % (MBEC100) of the bacteria in preformed biofilms, were determined by using the broth macrodilution method. Results Mul-1867 exhibited significant activity against MDR-PA and susceptible control strains, with MICs ranging from 1.0 to 8.0 µg/mL. Mul-1867 also possesses anti-biofilm activity against mucoid and non-mucoid 24-h-old MDR-PA biofilms. The MBEC50 value was equal to onefold the MIC. The MBEC90 value ranged from two to fourfold the MIC. Moreover, Mul-1867 completely eradicated mature biofilms at the concentrations tested, with MBEC100 values ranging between 16- and 32-fold the MIC. Mul-1867 was non-toxic to Madin-Darby canine kidney (MDCK) cells at concentrations up to 256 µg/mL. Conclusion Overall, these data indicate that Mul-1867 is a promising locally acting antimicrobial for the treatment and prevention of P. aeruginosa infections.
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Affiliation(s)
- George Tetz
- TGV-Laboratories LLC, 303 5th avenue, # 2012, New York, NY, 10016, USA.
| | - Daria Vikina
- Institute of Human Microbiology, New York, NY, 10016, USA
| | - Victor Tetz
- Institute of Human Microbiology, New York, NY, 10016, USA
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