1
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Da Silva Cunha AL, Blanter M, Renders J, Gouwy M, Lorent N, Boon M, Struyf S, Carlon MS. Inhibiting CFTR through inh-172 in primary neutrophils reveals CFTR-specific functional defects. Sci Rep 2024; 14:31237. [PMID: 39732786 DOI: 10.1038/s41598-024-82535-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 12/05/2024] [Indexed: 12/30/2024] Open
Abstract
The lungs of people with cystic fibrosis (PwCF) are characterized by recurrent bacterial infections and inflammation. Infections in cystic fibrosis (CF) are left unresolved despite excessive neutrophil infiltration. The role of CFTR in neutrophils is not fully understood. In this study, we aimed to assess which antimicrobial functions are directly impaired by loss of CFTR function in neutrophils. In order to do so, we used a specific inhibitor of CFTR ion channel activity, inh-172. CF neutrophils from PwCF harboring severe CFTR mutations were additionally isolated to further discern CFTR-specific functional defects. We evaluated phagocytosis, reactive oxygen species (ROS) production, neutrophil elastase (NE) and myeloperoxidase (MPO) exocytosis and bacterial killing. The inh-172 model identified decreased acidification of the phagosome, increased bacterial survival and decreased ROS production upon stimulation. In PwCF neutrophils, we observed reduced degranulation of both NE and MPO. When co-culturing neutrophils with CF sputum supernatant and airway epithelial cells, the extent of phagocytosis was reduced, underscoring the importance of recreating an inflammatory environment as seen in PwCF lungs to model immune responses in vitro. Despite low CFTR expression in blood neutrophils, functional defects were found in inh-172-treated and CF neutrophils. The inh-172 model disregards donor variability and allows pinpointing neutrophil functions directly impaired by dysfunctional CFTR.
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Affiliation(s)
- Ana Lúcia Da Silva Cunha
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Center for Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Marfa Blanter
- Laboratory for Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Janne Renders
- Laboratory for Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Mieke Gouwy
- Laboratory for Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Natalie Lorent
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Department of Respiratory Diseases, UZ Leuven, Leuven, Belgium
| | - Mieke Boon
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
- Department of Development and Regeneration, Woman and Child, Leuven, Belgium
| | - Sofie Struyf
- Laboratory for Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
| | - Marianne S Carlon
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium.
- Center for Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium.
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2
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Crisan CV, Pettis ML, Goldberg JB. Antibacterial potential of Stenotrophomonas maltophilia complex cystic fibrosis isolates. mSphere 2024; 9:e0033524. [PMID: 38980073 PMCID: PMC11288042 DOI: 10.1128/msphere.00335-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/23/2024] [Indexed: 07/10/2024] Open
Abstract
Over 160,000 people worldwide suffer from cystic fibrosis (CF), a genetic condition that causes mucus to accumulate in internal organs. Lung decline is a significant health burden for people with CF (pwCF), and chronic bacterial pulmonary infections are a major cause of death. Stenotrophomonas maltophilia complex (Smc) is an emerging, multidrug-resistant CF pathogen that can cause pulmonary exacerbations and result in higher mortality. However, little is known about the antagonistic interactions that occur between Smc isolates from pwCF and competitor bacteria. We obtained 13 Smc isolates from adult and pediatric pwCF located in the United States or Australia. We co-cultured these isolates with Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia coli. We also performed whole-genome sequencing of these Smc isolates and compared their genomes using average nucleotide identity analyses. We observed that some Smc CF isolates can engage in antagonistic interactions with P. aeruginosa and S. aureus but recovered a substantial number of P. aeruginosa and S. aureus cells following co-cultures with all tested Smc isolates. By contrast, we discovered that most Smc CF isolates display strong antibacterial properties against E. coli cells and reduce recovery below detectable limits. Finally, we demonstrate that Smc CF strains from this study belong to diverse phylogenetic lineages. IMPORTANCE Antagonism toward competitor bacteria may be important for the survival of Stenotrophomonas maltophilia complex (Smc) in external environments, for the elimination of commensal species and colonization of upper respiratory tracts to enable early infections, and for competition against other pathogens after establishing chronic infections. These intermicrobial interactions could facilitate the acquisition of Smc by people with cystic fibrosis from environmental or nosocomial sources. Elucidating the mechanisms used by Smc to eliminate other bacteria could lead to new insights into the development of novel treatments.
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Affiliation(s)
- Cristian V. Crisan
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory+Children’s Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Joanna B. Goldberg
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory+Children’s Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, Georgia, USA
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3
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Sanmukh SG, Admella J, Moya-Andérico L, Fehér T, Arévalo-Jaimes BV, Blanco-Cabra N, Torrents E. Accessing the In Vivo Efficiency of Clinically Isolated Phages against Uropathogenic and Invasive Biofilm-Forming Escherichia coli Strains for Phage Therapy. Cells 2023; 12:cells12030344. [PMID: 36766686 PMCID: PMC9913540 DOI: 10.3390/cells12030344] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/09/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Escherichia coli is one of the most common members of the intestinal microbiota. Many of its strains are associated with various inflammatory infections, including urinary or gut infections, especially when displaying antibiotic resistance or in patients with suppressed immune systems. According to recent reports, the biofilm-forming potential of E. coli is a crucial factor for its increased resistance against antibiotics. To overcome the limitations of using antibiotics against resistant E. coli strains, the world is turning once more towards bacteriophage therapy, which is becoming a promising candidate amongst the current personalized approaches to target different bacterial infections. Although matured and persistent biofilms pose a serious challenge to phage therapy, they can still become an effective alternative to antibiotic treatment. Here, we assess the efficiency of clinically isolated phages in phage therapy against representative clinical uropathogenic and invasive biofilm-forming E. coli strains. Our results demonstrate that irrespective of host specificity, bacteriophages producing clear plaques with a high burst size, and exhibiting depolymerizing activity, are good candidates against biofilm-producing E. coli pathogens as verified from our in vitro and in vivo experiments using Galleria mellonella where survival was significantly increased for phage-therapy-treated larvae.
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Affiliation(s)
- Swapnil Ganesh Sanmukh
- Bacterial Infections: Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 15-21, 08028 Barcelona, Spain
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Eötvös Lóránd Research Network, H-6726 Szeged, Hungary
- Correspondence: or (S.G.S.); or (E.T.)
| | - Joana Admella
- Bacterial Infections: Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 15-21, 08028 Barcelona, Spain
| | - Laura Moya-Andérico
- Bacterial Infections: Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 15-21, 08028 Barcelona, Spain
| | - Tamás Fehér
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Eötvös Lóránd Research Network, H-6726 Szeged, Hungary
| | - Betsy Verónica Arévalo-Jaimes
- Bacterial Infections: Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 15-21, 08028 Barcelona, Spain
| | - Núria Blanco-Cabra
- Bacterial Infections: Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 15-21, 08028 Barcelona, Spain
- Microbiology Section, Department of Genetics, Microbiology, and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Eduard Torrents
- Bacterial Infections: Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 15-21, 08028 Barcelona, Spain
- Microbiology Section, Department of Genetics, Microbiology, and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
- Correspondence: or (S.G.S.); or (E.T.)
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4
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Muggeo A, Perotin JM, Brisebarre A, Dury S, Dormoy V, Launois C, Ancel J, Mulette P, de Champs C, Deslée G, Guillard T. Extended Bacteria Culture-Based Clustering Identifies a Phenotype Associating Increased Cough and Enterobacterales in Stable Chronic Obstructive Pulmonary Disease. Front Microbiol 2022; 12:781797. [PMID: 34970242 PMCID: PMC8712763 DOI: 10.3389/fmicb.2021.781797] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/11/2021] [Indexed: 11/13/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory lung disease characterized by airflow limitation. This chronic respiratory disease represents the third leading cause of death worldwide. Alteration of the airway microbiota has been reported to be associated with exacerbation frequency in COPD, but its role on the symptoms in patients at stable state is still incompletely described. This study aimed to determine whether bacteria isolated in sputum can be associated with the clinical features of COPD patients within stable state. Our study highlights, for the first time, that altered microbiota with Enterobacterales is associated with pejorative clinical symptoms in stable COPD patients. The airway microbiota of 38 patients was analyzed using an extended culture approach and mass spectrometry identification. Cluster analysis by principal coordinate analysis of the bacterial communities showed that the patients could be classified into three distinct clusters in our cohort. The clusters showed no differences in proportions of the phylum, but one of them was associated with a high prevalence of Enterobacterales (71.4% in cluster 1 vs. 0% in cluster 3), loss of microbiota diversity, and higher bacterial load (107 vs. 105 CFU/ml, respectively) and characterized by predominant cough and impact on mental health. These novel findings, supported by further studies, could lead to modifying the processing of COPD sputum in the everyday practice of clinical microbiology laboratories.
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Affiliation(s)
- Anaëlle Muggeo
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Laboratory of Bacteriology-Virology-Hospital Hygiene-Parasitology-Mycology, Reims University Hospital, Reims, France
| | - Jeanne-Marie Perotin
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Department of Respiratory Diseases, Reims University Hospital, Reims, France
| | - Audrey Brisebarre
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France
| | - Sandra Dury
- Department of Respiratory Diseases, Reims University Hospital, Reims, France
| | - Valérian Dormoy
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France
| | - Claire Launois
- Department of Respiratory Diseases, Reims University Hospital, Reims, France
| | - Julien Ancel
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Department of Respiratory Diseases, Reims University Hospital, Reims, France
| | - Pauline Mulette
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Department of Respiratory Diseases, Reims University Hospital, Reims, France
| | - Christophe de Champs
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Laboratory of Bacteriology-Virology-Hospital Hygiene-Parasitology-Mycology, Reims University Hospital, Reims, France
| | - Gaëtan Deslée
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Department of Respiratory Diseases, Reims University Hospital, Reims, France
| | - Thomas Guillard
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Laboratory of Bacteriology-Virology-Hospital Hygiene-Parasitology-Mycology, Reims University Hospital, Reims, France
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5
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Felton E, Burrell A, Chaney H, Sami I, Koumbourlis AC, Freishtat RJ, Crandall KA, Hahn A. Inflammation in children with cystic fibrosis: contribution of bacterial production of long-chain fatty acids. Pediatr Res 2021; 90:99-108. [PMID: 33654282 PMCID: PMC8370878 DOI: 10.1038/s41390-021-01419-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 02/02/2021] [Indexed: 01/12/2023]
Abstract
BACKGROUND Cystic fibrosis (CF) affects >70,000 people worldwide, yet the microbiologic trigger for pulmonary exacerbations (PExs) remains unknown. The objective of this study was to identify changes in bacterial metabolic pathways associated with clinical status. METHODS Respiratory samples were collected at hospital admission for PEx, end of intravenous (IV) antibiotic treatment, and follow-up from 27 hospitalized children with CF. Bacterial DNA was extracted and shotgun DNA sequencing was performed. MetaPhlAn2 and HUMAnN2 were used to evaluate bacterial taxonomic and pathway relative abundance, while DESeq2 was used to evaluate differential abundance based on clinical status. RESULTS The mean age of study participants was 10 years; 85% received combination IV antibiotic therapy (beta-lactam plus a second agent). Long-chain fatty acid (LCFA) biosynthesis pathways were upregulated in follow-up samples compared to end of treatment: gondoate (p = 0.012), oleate (p = 0.048), palmitoleate (p = 0.043), and pathways of fatty acid elongation (p = 0.012). Achromobacter xylosoxidans and Escherichia sp. were also more prevalent in follow-up compared to PEx (p < 0.001). CONCLUSIONS LCFAs may be associated with persistent infection of opportunistic pathogens. Future studies should more closely investigate the role of LCFA production by lung bacteria in the transition from baseline wellness to PEx in persons with CF. IMPACT Increased levels of LCFAs are found after IV antibiotic treatment in persons with CF. LCFAs have previously been associated with increased lung inflammation in asthma. This is the first report of LCFAs in the airway of persons with CF. This research provides support that bacterial production of LCFAs may be a contributor to inflammation in persons with CF. Future studies should evaluate LCFAs as predictors of future PExs.
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Affiliation(s)
- Erin Felton
- grid.253615.60000 0004 1936 9510School of Medicine and Health Sciences, George Washington University, Washington, DC USA
| | - Aszia Burrell
- grid.239560.b0000 0004 0482 1586Center for Genetic Medicine Research, Children’s National Research Institute, Washington, DC USA
| | - Hollis Chaney
- grid.253615.60000 0004 1936 9510Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC USA ,grid.239560.b0000 0004 0482 1586Division of Pulmonary and Sleep Medicine, Children’s National Hospital, Washington, DC USA
| | - Iman Sami
- grid.253615.60000 0004 1936 9510Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC USA ,grid.239560.b0000 0004 0482 1586Division of Pulmonary and Sleep Medicine, Children’s National Hospital, Washington, DC USA
| | - Anastassios C. Koumbourlis
- grid.253615.60000 0004 1936 9510Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC USA ,grid.239560.b0000 0004 0482 1586Division of Pulmonary and Sleep Medicine, Children’s National Hospital, Washington, DC USA
| | - Robert J. Freishtat
- grid.239560.b0000 0004 0482 1586Center for Genetic Medicine Research, Children’s National Research Institute, Washington, DC USA ,grid.253615.60000 0004 1936 9510Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC USA ,grid.239560.b0000 0004 0482 1586Division of Emergency Medicine, Children’s National Hospital, Washington, DC USA
| | - Keith A. Crandall
- grid.253615.60000 0004 1936 9510Department of Biostatistics and Bioinformatics, Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC USA
| | - Andrea Hahn
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA. .,Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA. .,Division of Infectious Disease, Children's National Hospital, Washington, DC, USA.
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6
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Synthesis and Antimicrobial Activity of Phosphonopeptide Derivatives Incorporating Single and Dual Inhibitors. Molecules 2020; 25:molecules25071557. [PMID: 32231126 PMCID: PMC7180716 DOI: 10.3390/molecules25071557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/16/2020] [Accepted: 03/20/2020] [Indexed: 11/22/2022] Open
Abstract
In diagnostic microbiology, culture media are widely used for detection of pathogenic bacteria. Such media employ various ingredients to optimize detection of specific pathogens such as chromogenic enzyme substrates and selective inhibitors to reduce the presence of commensal bacteria. Despite this, it is rarely possible to inhibit the growth of all commensal bacteria, and thus pathogens can be overgrown and remain undetected. One approach to attempt to remedy this is the use of “suicide substrates” that can target specific bacterial enzymes and selectively inhibit unwanted bacterial species. With the purpose of identifying novel selective inhibitors, six novel phosphonopeptide derivatives based on d/l-fosfalin and β-chloro-l-alanine were synthesized and tested on 19 different strains of clinically relevant bacteria. Several compounds show potential as useful selective agents that could be exploited in the recovery of several bacterial pathogens including Salmonella, Pseudomonas aeruginosa, and Listeria.
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7
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Izydorczyk C, Waddell B, Edwards BD, Greysson-Wong J, Surette MG, Somayaji R, Rabin HR, Conly JM, Church DL, Parkins MD. Epidemiology of E. coli in Cystic Fibrosis Airways Demonstrates the Capacity for Persistent Infection but Not Patient-Patient Transmission. Front Microbiol 2020; 11:475. [PMID: 32265892 PMCID: PMC7100150 DOI: 10.3389/fmicb.2020.00475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/04/2020] [Indexed: 11/16/2022] Open
Abstract
Escherichia coli is frequently isolated from the respiratory secretions of cystic fibrosis (CF) patients yet is not considered a classical CF pathogen. Accordingly, little is known about the natural history of this organism in the CF airways, as well as the potential for patient-to-patient transmission. Patients attending the Calgary Adult CF Clinic (CACFC) between January 1983 and December 2016 with at least one E. coli-positive sputum culture were identified by retrospective review. Annual E. coli isolates from the CACFC biobank from each patient were typed by pulsed-field gel electrophoresis (PFGE) and isolates belonging to shared pulsotypes were sequenced. Single nucleotide polymorphism (SNP) and phylogenetic analysis were used to investigate the natural history of E. coli infection and identify potential transmission events. Forty-five patients with E. coli-positive sputum cultures were identified. Most patients had a single infection episode with a single pulsotype, while replacement of an initial pulsotype with a second was observed in three patients. Twenty-four had E. coli recovered from their sputum more than once and 18 patients had persistent infections (E. coli carriage >6 months with ≥3 positive cultures). Shared pulsotypes corresponded to known extraintestinal pathogenic E. coli strains: ST-131, ST-73, and ST-1193. Phylogenetic relationships and SNP distances among isolates within shared pulsotypes were consistent with independent acquisition of E. coli by individual patients. Most recent common ancestor date estimates of isolates between patients were inconsistent with patient-to-patient transmission. E. coli infection in CF is a dynamic process that appears to be characterized by independent acquisition within our patient population and carriage of unique sets of strains over time by individual patients.
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Affiliation(s)
- Conrad Izydorczyk
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Barbara Waddell
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Brett D. Edwards
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jasper Greysson-Wong
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Michael G. Surette
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Ranjani Somayaji
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Harvey R. Rabin
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - John M. Conly
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Health Services, Calgary, AB, Canada
| | - Deirdre L. Church
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Health Services, Calgary, AB, Canada
| | - Michael D. Parkins
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Health Services, Calgary, AB, Canada
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8
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Schneer S, Khoury J, Adir Y, Stein N, Shaked Mishan P, Ken-Dror S, Weber G, Meler R, Khateeb A, Shteinberg M. Clinical characteristics and outcomes of patients with Escherichia coli in airway samples. CLINICAL RESPIRATORY JOURNAL 2019; 14:205-213. [PMID: 31799802 DOI: 10.1111/crj.13116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/10/2019] [Accepted: 11/25/2019] [Indexed: 01/23/2023]
Abstract
PURPOSES Escherichia coli is one of the most common pathogens in nosocomial and community-acquired infections, but is an uncommon respiratory pathogen. However, this pathogen may at times be seen in respiratory secretions. The study aims to determine the clinical and prognostic value of E. coli in respiratory secretions. METHODS Cultures of respiratory secretions from hospitalized and outpatients between 2009 and 2016 were screened for isolation of E. coli. We defined three groups of patients: "Sensitive (S)"-growth of E. coli sensitive to all antimicrobials tested; Intermediate (I)-resistant to 1-2 antimicrobial classes; and "Resistant (R)"-resistant to at least three antibiotic classes. We compared factors associated with resistant strains and outcomes between the groups. RESULTS Eighty patients with E. coli isolates from respiratory secretions were identified while screening 177 712 (4.5: 10 000 samples). Of the E. Coli-positive cultures, 11 were from ambulatory patients, 31 patients were hospitalized and 37 were hospitalized and intubated. Ten people had bronchiectasis and 29 had COPD. Patients with resistant E. coli had significantly more hospitalization days prior to positive culture (S = 1.2 ± 1.89 days, I = 1.23 ± 1.5 days and R = 3.7 ± 5.4 days, respectively; P = 0.002). Mortality was higher in patients with a resistant strain (R) versus (I) or (S) (76.7%, 31.8% and 26.7%, respectively; P < 0.0001) and remained significantly elevated after correction for prior hospital days. CONCLUSIONS Pulmonary infection due to E. coli is uncommon. Isolation of resistant E. coli is associated with length of previous hospitalization, elevated mortality and may be viewed as a nosocomial pathogen.
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Affiliation(s)
- Sonia Schneer
- Pulmonary Division, Lady Davis-Carmel Medical Center, Haifa, Israel.,The B. Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Johad Khoury
- Pulmonary Division, Lady Davis-Carmel Medical Center, Haifa, Israel.,The B. Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Yochai Adir
- Pulmonary Division, Lady Davis-Carmel Medical Center, Haifa, Israel.,The B. Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Nili Stein
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel
| | | | - Shifra Ken-Dror
- Clinical Microbiological Laboratory, Central Laboratories Haifa & Western Galilee, Clalit Health Services, Haifa, Israel
| | - Gabriel Weber
- The B. Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel.,Clinical Microbiological Laboratory, Central Laboratories Haifa & Western Galilee, Clalit Health Services, Haifa, Israel.,Infectious Disease and Infection Control Unit, Carmel Medical Center, Haifa, Israel
| | - Ruth Meler
- Pulmonary Division, Lady Davis-Carmel Medical Center, Haifa, Israel
| | - Aysha Khateeb
- The B. Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Michal Shteinberg
- Pulmonary Division, Lady Davis-Carmel Medical Center, Haifa, Israel.,The B. Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
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9
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Edwards BD, Somayaji R, Greysson-Wong J, Izydorczyk C, Waddell B, Storey DG, Rabin HR, Surette MG, Parkins MD. Clinical Outcomes Associated With Escherichia coli Infections in Adults With Cystic Fibrosis: A Cohort Study. Open Forum Infect Dis 2019; 7:ofz476. [PMID: 31976352 PMCID: PMC6966422 DOI: 10.1093/ofid/ofz476] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 11/14/2019] [Indexed: 11/13/2022] Open
Abstract
Background Analysis of “emerging” pathogens in cystic fibrosis (CF) lung disease has focused on unique pathogens that are rare in other human diseases or are drug resistant. Escherichia coli is recovered in the sputum of up to 25% of patients with CF, yet little is known about the epidemiology or clinical impact of infection. Methods We studied patients attending a Canadian adult CF clinic who had positive sputum cultures for E coli from 1978 to 2016. Infection was categorized as transient or persistent (≥3 positive sputum cultures, spanning >6 months). Those with persistent infection were matched 2:1 with age, sex, and time-period controls without history of E coli infection, and mixed-effects models were used to assess pulmonary exacerbation (PEx) frequency, lung function decline, hospitalization, and intravenous antibiotic days. Results Forty-five patients (12.3%) had E coli recovered from sputum samples between 1978 and 2016, and 18 patients (40%) developed persistent infection. Nine patients (24%) had PEx at incident infection, and increased bioburden was predictive of exacerbation (P = .03). Risk factors for persistent infection included lower nutritional status (P < .001) and lower lung function (P = .009), but chronic infection with Pseudomonas aeruginosa was protective. There was no difference in annual lung function decline, need for hospitalization or intravenous antibiotics, or risk of PEx in patients with persistent infection. Conclusions Persistent E coli infection was frequent and was more common in CF patients with low nutritional status and lung function. However, this does not predict clinical decline. Multicenter studies would allow better characterization of the epidemiology and clinical impact of E coli infection.
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Affiliation(s)
- B D Edwards
- Department of Medicine, University of Calgary
| | - R Somayaji
- Department of Medicine, University of Calgary.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary.,Department of Community Health Sciences, University of Calgary
| | - J Greysson-Wong
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary
| | - C Izydorczyk
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary
| | - B Waddell
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary
| | - D G Storey
- Department of Biological Sciences, University of Calgary
| | - H R Rabin
- Department of Medicine, University of Calgary.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary
| | - M G Surette
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary.,Department of Medicine, McMaster University.,Biochemistry and Biomedical Sciences, the Farncombe Family Digestive Health Research Institute, McMaster University
| | - M D Parkins
- Department of Medicine, University of Calgary.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary
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10
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Vermeulen F, Proesmans M, Vermaelen M, Boon M, De Boeck K. Isolation of Enterobacteriaceae in airway samples is associated with worse outcome in preschool children with cystic fibrosis. J Cyst Fibros 2019; 19:365-369. [PMID: 31690526 DOI: 10.1016/j.jcf.2019.10.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND Increased abundance of Enterobacteriaceae(EB) in the respiratory microbiome of young CF patients was reported to precede Pseudomonas aeruginosa(PA) colonisation. We explored whether impending PA colonisation can be predicted by growth of EB in routine airway cultures and whether EB contribute to CF lung disease severity. METHODS We retrospectively studied the records of 62 children with CF for growth of EB and PA during the first 5 years of life and subsequent best lung function at ages 5-7 and 9-11 years. RESULTS At least one EB positive month occurred in 36/62 (58%) patients. Median (IQR) age at first EB isolation was 0.4 (0.2-0.8) years. PA isolation before age 5 was more frequent in the EB positive (23/36, 54%) than in EB negative children (10/26, 38%; p = 0.048). EB isolation preceded PA isolation in 19/23 (83%) cases (p = 0.003). Median (IQRf) FEV1 at age 5 to 7 years was 105% (94-117) in the EB positive group and 108% (102-115) in the EB negative group (p = 0.154). At age 9-11, FEV1 was lower in EB positive children (99%(88-105) vs 105%(96-110); p = 0.035). Only PA isolation (p = 0.002) before age 5 years was a significant predictor of FEV1 at age 5-7 years. Both EB isolation (p = 0.033) and PA isolation (p = 0.023) were predictors of the FEV1 at age 9-11 years. CONCLUSION In preschool children with CF, EB were isolated in just over half of the children. In that subgroup PA isolation was more common. Both EB and PA isolation are associated with worse lung function at later age.
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Affiliation(s)
- Francois Vermeulen
- Pediatric Pulmonology, Department of Pediatrics, University of Leuven, Leuven, Belgium.
| | - Marijke Proesmans
- Pediatric Pulmonology, Department of Pediatrics, University of Leuven, Leuven, Belgium
| | - Mathias Vermaelen
- Pediatric Pulmonology, Department of Pediatrics, University of Leuven, Leuven, Belgium
| | - Mieke Boon
- Pediatric Pulmonology, Department of Pediatrics, University of Leuven, Leuven, Belgium
| | - Kris De Boeck
- Pediatric Pulmonology, Department of Pediatrics, University of Leuven, Leuven, Belgium
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11
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Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) strains are responsible for a majority of human extraintestinal infections globally, resulting in enormous direct medical and social costs. ExPEC strains are comprised of many lineages, but only a subset is responsible for the vast majority of infections. Few systematic surveillance systems exist for ExPEC. To address this gap, we systematically reviewed and meta-analyzed 217 studies (1995 to 2018) that performed multilocus sequence typing or whole-genome sequencing to genotype E. coli recovered from extraintestinal infections or the gut. Twenty major ExPEC sequence types (STs) accounted for 85% of E. coli isolates from the included studies. ST131 was the most common ST from 2000 onwards, covering all geographic regions. Antimicrobial resistance-based isolate study inclusion criteria likely led to an overestimation and underestimation of some lineages. European and North American studies showed similar distributions of ExPEC STs, but Asian and African studies diverged. Epidemiology and population dynamics of ExPEC are complex; summary proportion for some STs varied over time (e.g., ST95), while other STs were constant (e.g., ST10). Persistence, adaptation, and predominance in the intestinal reservoir may drive ExPEC success. Systematic, unbiased tracking of predominant ExPEC lineages will direct research toward better treatment and prevention strategies for extraintestinal infections.
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12
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Rutter WC, Burgess DR, Burgess DS. Increasing Incidence of Multidrug Resistance Among Cystic Fibrosis Respiratory Bacterial Isolates. Microb Drug Resist 2017; 23:51-55. [DOI: 10.1089/mdr.2016.0048] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- W. Cliff Rutter
- University of Kentucky College of Pharmacy, Lexington, Kentucky
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, Kentucky
| | - Donna R. Burgess
- University of Kentucky College of Pharmacy, Lexington, Kentucky
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, Kentucky
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13
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Different next generation sequencing platforms produce different microbial profiles and diversity in cystic fibrosis sputum. J Microbiol Methods 2016; 130:95-99. [PMID: 27609714 DOI: 10.1016/j.mimet.2016.09.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/02/2016] [Accepted: 09/02/2016] [Indexed: 11/20/2022]
Abstract
BACKGROUND Cystic fibrosis (CF) is an autosomal recessive disease characterized by recurrent lung infections. Studies of the lung microbiome have shown an association between decreasing diversity and progressive disease. 454 pyrosequencing has frequently been used to study the lung microbiome in CF, but will no longer be supported. We sought to identify the benefits and drawbacks of using two state-of-the-art next generation sequencing (NGS) platforms, MiSeq and PacBio RSII, to characterize the CF lung microbiome. Each has its advantages and limitations. METHODS Twelve samples of extracted bacterial DNA were sequenced on both MiSeq and PacBio NGS platforms. DNA was amplified for the V4 region of the 16S rRNA gene and libraries were sequenced on the MiSeq sequencing platform, while the full 16S rRNA gene was sequenced on the PacBio RSII sequencing platform. Raw FASTQ files generated by the MiSeq and PacBio platforms were processed in mothur v1.35.1. RESULTS There was extreme discordance in alpha-diversity of the CF lung microbiome when using the two platforms. Because of its depth of coverage, sequencing of the 16S rRNA V4 gene region using MiSeq allowed for the observation of many more operational taxonomic units (OTUs) and higher Chao1 and Shannon indices than the PacBio RSII. Interestingly, several patients in our cohort had Escherichia, an unusual pathogen in CF. Also, likely because of its coverage of the complete 16S rRNA gene, only PacBio RSII was able to identify Burkholderia, an important CF pathogen. CONCLUSION When comparing microbiome diversity in clinical samples from CF patients using 16S sequences, MiSeq and PacBio NGS platforms may generate different results in microbial community composition and structure. It may be necessary to use different platforms when trying to correctly identify dominant pathogens versus measuring alpha-diversity estimates, and it would be important to use the same platform for comparisons to minimize errors in interpretation.
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14
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Skolnik K, Nguyen A, Somayaji R, Thornton CS, Waddell B, Surette MG, Rabin HR, Parkins MD. Clinical implications and characterization of Group A Streptoccoccus infections in adults with cystic fibrosis. BMC Pulm Med 2015; 15:161. [PMID: 26651825 PMCID: PMC4676819 DOI: 10.1186/s12890-015-0157-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 12/08/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Persistent airway infection is a hallmark feature of cystic fibrosis (CF). However, increasingly it has been observed that non-classical pathogens may transiently infect CF lower airways. Streptococcus pyogenes (Group A Streptococcus; (GAS)) is an uncommon but potentially dangerous cause of community-acquired pneumonia. Our aim was to determine the incidence, natural history, and clinical impact of GAS infections in CF and phenotypically and genotypically characterize the isolates. METHODS We retrospectively evaluated the Calgary Adult CF Clinic biobank to identify adults with at least one GAS isolate. Patient demographics, medical and pulmonary exacerbation (PEx) histories were evaluated. The primary outcome was PEx occurrence at incident GAS culture. Secondary outcomes evaluated were changes in lung function and PEx frequency following GAS isolation. Isolates were assessed for extra-cellular virulence factor production capacity and ability to produce quorum sensing (AI-2). Isolates were genotyped using pulse-field gel electrophoresis (PFGE). RESULTS Fifteen individuals who cultured GAS twenty times were identified. At the time of GAS isolation, 47% (7/15) of subjects experienced a PEx and half of these (4/7) were severe. Individuals were more likely to have a PEx at the time of the index GAS isolate compared to the preceding visit (RR = 6.0, 95% CI 0.82-43.0, p = 0.08), particularly if GAS was the numerically dominant sputum pathogen (RR = 6.5, 95% CI 1.00-43.0, p = 0.009). There were no changes in PEx frequency or rate of lung function decline following GAS. None of the patients developed chronic airways infection, bacteremia, necrotizing pneumonia or empyema. Susceptibility was universal to common anti-Streptococcal antibiotics and anti-Pseudomonal antibiotics commonly used in CF, with the exception of azithromycin. GAS isolates varied in their production of protease, DNase, and AI-2 but these did not correlate with PEx, and none produced elastase, chrondrotin sulfatase or H202. One patient had prolonged carriage with the same isolate and two patients had isolates with similar PFGE patterns. CONCLUSIONS GAS was an uncommon lower respiratory pathogen of adults with CF. Identification of GAS in sputum was frequently associated with PEx, particularly when numerically dominant. However, transient GAS infection did not result in chronic infection nor appreciably change long-term disease trajectory.
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Affiliation(s)
- Kate Skolnik
- Departments of Medicine, The University of Calgary, Calgary, AB, Canada.
| | - Austin Nguyen
- Departments of Microbiology, Immunology and Infectious Diseases, The University of Calgary, 3330 Hospital Drive, NW, Calgary, AB, Canada.
| | - Ranjani Somayaji
- Departments of Medicine, The University of Calgary, Calgary, AB, Canada. .,Departments of Microbiology, Immunology and Infectious Diseases, The University of Calgary, 3330 Hospital Drive, NW, Calgary, AB, Canada.
| | - Christina S Thornton
- Departments of Microbiology, Immunology and Infectious Diseases, The University of Calgary, 3330 Hospital Drive, NW, Calgary, AB, Canada.
| | - Barbara Waddell
- Departments of Microbiology, Immunology and Infectious Diseases, The University of Calgary, 3330 Hospital Drive, NW, Calgary, AB, Canada.
| | - Michael G Surette
- Department of Medicine, McMaster University, Hamilton, ON, Canada. .,Department of Biochemistry, McMaster University, Hamilton, ON, Canada. .,The Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada.
| | - Harvey R Rabin
- Departments of Medicine, The University of Calgary, Calgary, AB, Canada. .,Departments of Microbiology, Immunology and Infectious Diseases, The University of Calgary, 3330 Hospital Drive, NW, Calgary, AB, Canada.
| | - Michael D Parkins
- Departments of Medicine, The University of Calgary, Calgary, AB, Canada. .,Departments of Microbiology, Immunology and Infectious Diseases, The University of Calgary, 3330 Hospital Drive, NW, Calgary, AB, Canada.
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15
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Chibabhai V, Lowman W. Epidemiology of cystic fibrosis respiratory pathogens isolated at a South African Hospital, 2006–2010. S Afr J Infect Dis 2015. [DOI: 10.1080/23120053.2016.1156864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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16
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Assessment of airway microbiota and inflammation in cystic fibrosis using multiple sampling methods. Ann Am Thorac Soc 2015; 12:221-9. [PMID: 25474078 DOI: 10.1513/annalsats.201407-310oc] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
RATIONALE Oropharyngeal (OP) swabs and induced sputum (IS) are used for airway bacteria surveillance in nonexpectorating children with cystic fibrosis (CF). Molecular analyses of these airway samples detect complex microbial communities. However, the optimal noninvasive sampling approach for microbiota analyses and the clinical relevance of microbiota, particularly its relationship to airway inflammation, is not well characterized. OBJECTIVES The goals of this study were to compare molecular analyses of concurrently collected saliva, OP swabs, IS, and expectorated sputum (ES) from children with CF and to determine the association between microbiota, lung function, and airway inflammation. METHODS Saliva, OP swabs, IS, and ES were collected from 16 children with CF. Spirometry was performed. MEASUREMENTS AND MAIN RESULTS Respiratory and saliva samples (n = 61) were sequenced for bacterial microbial communities, and total and CF-specific bacterial quantitative PCR assays were performed. Airway samples underwent conventional culture for CF-specific pathogens. Neutrophil elastase, IL-1β, IL-1ra, IL-6, Il-8, TNF-α, and vascular endothelial growth factor were measured in ES and IS. Sequencing results from individual subjects were similar across samples, with greater between-subject than within-subject variation. However, Pseudomonas and Staphylococcus were detected in higher relative abundance from lower airways (ES and IS) compared with paired upper airway samples (OP and saliva). Pseudomonas, Staphylococcus, and Enterobacteriaceae correlated with increased airway inflammation. Divergence between microbiota in upper airway compared with lower airway samples, indicating greater differences between communities, was associated with increased sputum neutrophil elastase. CONCLUSIONS Bacteria detected in IS samples resemble ES samples, whereas OP samples may underrepresent bacteria associated with airway inflammation. Divergence of lower airway communities from upper airway was associated with airway inflammation and may portend disease progression.
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17
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Hosseinkhan N, Zarrineh P, Rokni-Zadeh H, Ashouri MR, Masoudi-Nejad A. Co-expressional conservation in virulence and stress related genes of three Gammaproteobacterial species: Escherichia coli, Salmonella enterica and Pseudomonas aeruginosa. MOLECULAR BIOSYSTEMS 2015; 11:3137-48. [PMID: 26387845 DOI: 10.1039/c5mb00353a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Gene co-expression analysis is one of the main aspects of systems biology that uses high-throughput gene expression data. In the present study we applied cross-species co-expressional analysis on a module of biofilm and stress response associated genes. We addressed different kinds of stresses in three most intensively studied members of Gammaproteobacteria including Escherichia coli K12, Pseudomonas aeruginosa PAO1 and Salmonella enterica for which large sets of gene expression data are available. Our aim was to evaluate the presence of common stress response strategies adopted by these microorganisms that may be assigned to the other members of Gammaproteobacteria. Results of functional annotation analysis revealed distinct categories among co-expressed genes, most of which concerned biological processes associated with virulence and stress response. Transcriptional regulatory analysis of genes present in co-expressed modules showed that the global stress sigma factor, RpoS, besides several local transcription factors accounts for the observed co-expressional response, and that several cases of feed-forward loops exist between global regulators, local transcription factors and their targets. Our results lend partial support to our underlying assumption of the conservation of core biological processes and regulatory interactions among these related Gammaproteobacteria members. This has led to the implementation of transferring gene function annotations from well-studied Gammaproteobacterial species to less-characterized members. These findings can shed light on the discovery of new drug targets capable of controlling severe infections caused by these groups of bacteria.
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Affiliation(s)
- Nazanin Hosseinkhan
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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18
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Parkins MD, Floto RA. Emerging bacterial pathogens and changing concepts of bacterial pathogenesis in cystic fibrosis. J Cyst Fibros 2015; 14:293-304. [PMID: 25881770 DOI: 10.1016/j.jcf.2015.03.012] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/21/2015] [Accepted: 03/22/2015] [Indexed: 12/22/2022]
Abstract
Chronic suppurative lower airway infection is a hallmark feature of cystic fibrosis (CF). Decades of experience in clinical microbiology have enabled the development of improved technologies and approaches for the cultivation and identification of microorganisms from sputum. It is increasingly apparent that the microbial constituents of the lower airways in CF exist in a dynamic state. Indeed, while changes in prevalence of various pathogens occur through ageing, differences exist in successive cohorts of patients and between clinics, regions and countries. Classical pathogens such as Pseudomonas aeruginosa, Burkholderia cepacia complex and Staphylococcus aureus are increasingly being supplemented with new and emerging organisms rarely observed in other areas of medicine. Moreover, it is now recognized that common oropharyngeal organisms, previously presumed to be benign colonizers may contribute to disease progression. As infection remains the leading cause of morbidity and mortality in CF, an understanding of the epidemiology, risk factors for acquisition and natural history of infection including interactions between colonizing bacteria is required. Unified approaches to the study and determination of pathogen status are similarly needed. Furthermore, experienced and evidence-based treatment data is necessary to optimize outcomes for individuals with CF.
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Affiliation(s)
- Michael D Parkins
- Department of Medicine, The University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Microbiology, Immunology and Infectious Diseases, The University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada.
| | - R Andres Floto
- Cambridge Institute for Medical Research, University of Cambridge, Papworth Hospital, Cambridge CB23 3RE, UK; Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge CB23 3RE, UK.
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First report of chronic pulmonary infection by KPC-3-producing and colistin-resistant Klebsiella pneumoniae sequence type 258 (ST258) in an adult patient with cystic fibrosis. J Clin Microbiol 2015; 53:1442-4. [PMID: 25653395 DOI: 10.1128/jcm.03199-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The spread of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae continues to increase, and the possible development of KPC-producing K. pneumoniae infections in cystic fibrosis (CF) patients is a matter of concern. Here, we describe the establishment of a chronic lung infection due to a colistin-resistant KPC-producing K. pneumoniae isolate in an Italian CF patient.
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