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Graña-Miraglia L, Morales-Lizcano N, Wang PW, Hwang DM, Yau YCW, Waters VJ, Guttman DS. Predictive modeling of antibiotic eradication therapy success for new-onset Pseudomonas aeruginosa pulmonary infections in children with cystic fibrosis. PLoS Comput Biol 2023; 19:e1011424. [PMID: 37672526 PMCID: PMC10506723 DOI: 10.1371/journal.pcbi.1011424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 09/18/2023] [Accepted: 08/09/2023] [Indexed: 09/08/2023] Open
Abstract
Chronic Pseudomonas aeruginosa (Pa) lung infections are the leading cause of mortality among cystic fibrosis (CF) patients; therefore, the eradication of new-onset Pa lung infections is an important therapeutic goal that can have long-term health benefits. The use of early antibiotic eradication therapy (AET) has been shown to clear the majority of new-onset Pa infections, and it is hoped that identifying the underlying basis for AET failure will further improve treatment outcomes. Here we generated machine learning models to predict AET outcomes based on pathogen genomic data. We used a nested cross validation design, population structure control, and recursive feature selection to improve model performance and showed that incorporating population structure control was crucial for improving model interpretation and generalizability. Our best model, controlling for population structure and using only 30 recursively selected features, had an area under the curve of 0.87 for a holdout test dataset. The top-ranked features were generally associated with motility, adhesion, and biofilm formation.
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Affiliation(s)
- Lucía Graña-Miraglia
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nadia Morales-Lizcano
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Pauline W. Wang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - David M. Hwang
- Department of Laboratory Medicine and Pathobiology, Toronto, Ontario, Canada
- Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Yvonne C. W. Yau
- Department of Laboratory Medicine and Pathobiology, Toronto, Ontario, Canada
- Department of Paediatric Laboratory Medicine, Division of Microbiology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Valerie J. Waters
- Department of Pediatrics, Division of Infectious Diseases, The Hospital for Sick Children, Toronto, Ontario, Canada
- Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - David S. Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
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2
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Morris AJ, Yau YCW, Park S, Eisha S, McDonald N, Parsek MR, Howell PL, Hoffman LR, Nguyen D, DiGiandomenico A, Rooney AM, Coburn B, Grana-Miraglia L, Wang P, Guttman DS, Wozniak DJ, Waters VJ. Pseudomonas aeruginosa aggregation and Psl expression in sputum is associated with antibiotic eradication failure in children with cystic fibrosis. Sci Rep 2022; 12:21444. [PMID: 36509824 PMCID: PMC9744911 DOI: 10.1038/s41598-022-25889-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
We previously demonstrated that P. aeruginosa isolates that persisted in children with cystic fibrosis (CF) despite inhaled tobramycin treatment had increased anti-Psl antibody binding in vitro compared to those successfully eradicated. We aimed to validate these findings by directly visualizing P. aeruginosa in CF sputum. This was a prospective observational study of children with CF with new-onset P. aeruginosa infection who underwent inhaled tobramycin eradication treatment. Using microbial identification passive clarity technique (MiPACT), P. aeruginosa was visualized in sputum samples obtained before treatment and classified as persistent or eradicated based on outcomes. Pre-treatment isolates were also grown as biofilms in vitro. Of 11 patients enrolled, 4 developed persistent infection and 7 eradicated infection. P. aeruginosa biovolume and the number as well as size of P. aeruginosa aggregates were greater in the sputum of those with persistent compared with eradicated infections (p < 0.01). The amount of Psl antibody binding in sputum was also greater overall (p < 0.05) in samples with increased P. aeruginosa biovolume. When visualized in sputum, P. aeruginosa had a greater biovolume, with more expressed Psl, and formed more numerous, larger aggregates in CF children who failed eradication therapy compared to those who successfully cleared their infection.
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Affiliation(s)
- Amanda J Morris
- Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Yvonne C W Yau
- Division of Microbiology, Department of Pediatric Laboratory Medicine, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Subin Park
- Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Shafinaz Eisha
- Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Nancy McDonald
- Division of Respiratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Matthew R Parsek
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - P Lynne Howell
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Lucas R Hoffman
- Departments of Pediatrics and Microbiology, University of Washington, Seattle, WA, USA
| | - Dao Nguyen
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
| | - Antonio DiGiandomenico
- Vaccines and Immune Therapies, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Ashley M Rooney
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Bryan Coburn
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Lucia Grana-Miraglia
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Pauline Wang
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - David S Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Daniel J Wozniak
- Departments of Microbial Infection and Immunity, Microbiology, Ohio State University, Columbus, OH, USA
| | - Valerie J Waters
- Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada.
- Division of Infectious Diseases, Department of Pediatrics, Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada.
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3
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Blanchard AC, Waters VJ. Opportunistic Pathogens in Cystic Fibrosis: Epidemiology and Pathogenesis of Lung Infection. J Pediatric Infect Dis Soc 2022; 11:S3-S12. [PMID: 36069904 DOI: 10.1093/jpids/piac052] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022]
Abstract
Cystic fibrosis (CF) is one of the most common life-shortening genetic diseases in Caucasians. Due to abnormal accumulation of mucus, respiratory failure caused by chronic infections is the leading cause of mortality in this patient population. The microbiology of these respiratory infections includes a distinct set of opportunistic pathogens, including Pseudomonas aeruginosa, Burkholderia spp., Achromobacter spp., Stenotrophomonas maltophilia, anaerobes, nontuberculous mycobacteria, and fungi. In recent years, culture-independent methods have shown the polymicrobial nature of lung infections, and the dynamics of microbial communities. The unique environment of the CF airway predisposes to infections caused by opportunistic pathogens. In this review, we will highlight how the epidemiology and role in disease of these pathogens in CF differ from that in individuals with other medical conditions. Infectious diseases (ID) physicians should be aware of these differences and the specific characteristics of infections associated with CF.
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Affiliation(s)
- Ana C Blanchard
- Department of Pediatrics, Division of Infectious Diseases, CHU Sainte-Justine, Université de Montréal, 3175 Chemin de la Côte-Sainte-Catherine, Montreal, Quebec, H3T 1C5, Canada
| | - Valerie J Waters
- Department of Pediatrics, Division of Infectious Diseases, The Hospital for Sick Children, University of Toronto, 555 University Avenue, Toronto, Ontario, M5G 1X8, Canada
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4
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Waters VJ, LiPuma JJ. Airway Infection in Cystic Fibrosis: Microbiology and Management. J Pediatric Infect Dis Soc 2022; 11:S1-S2. [PMID: 36069897 DOI: 10.1093/jpids/piac077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 07/07/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Valerie J Waters
- Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - John J LiPuma
- Division of Infectious Diseases, Department of Pediatrics, C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan, USA
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5
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Morris AJ, Jackson L, Cw Yau Y, Reichhardt C, Beaudoin T, Uwumarenogie S, Guttman KM, Lynne Howell P, Parsek MR, Hoffman LR, Nguyen D, DiGiandomenico A, Guttman DS, Wozniak DJ, Waters VJ. The role of Psl in the failure to eradicate Pseudomonas aeruginosa biofilms in children with cystic fibrosis. NPJ Biofilms Microbiomes 2021; 7:63. [PMID: 34349133 PMCID: PMC8338932 DOI: 10.1038/s41522-021-00234-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/01/2021] [Indexed: 11/09/2022] Open
Abstract
The exopolysaccharide Psl contributes to biofilm structure and antibiotic tolerance and may play a role in the failure to eradicate Pseudomonas aeruginosa from cystic fibrosis (CF) airways. The study objective was to determine whether there were any differences in Psl in P. aeruginosa isolates that were successfully eradicated compared to those that persisted, despite inhaled tobramycin treatment, in children with CF. Initial P. aeruginosa isolates were collected from children with CF undergoing eradication treatment, grown as biofilms and labeled with 3 anti-Psl monoclonal antibodies (Cam003/Psl0096, WapR001, WapR016) before confocal microscopy visualization. When grown as biofilms, P. aeruginosa isolates from children who failed antibiotic eradication therapy, had significantly increased Psl0096 binding compared to isolates from those who cleared P. aeruginosa. This was confirmed in P. aeruginosa isolates from the SickKids Eradication Cohort as well as the Early Pseudomonas Infection Control (EPIC) trial. Increased anti-Psl antibody binding was associated with bacterial aggregation and tobramycin tolerance. The biofilm matrix represents a potential therapeutic target to improve P. aeruginosa eradication treatment.
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Affiliation(s)
- Amanda J Morris
- Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Lindsay Jackson
- Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Yvonne Cw Yau
- Division of Microbiology, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | | | - Trevor Beaudoin
- Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Stephanie Uwumarenogie
- Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Kevin M Guttman
- Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - P Lynne Howell
- Program in Molecular Medicine, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Matthew R Parsek
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Lucas R Hoffman
- Departments of Pediatrics and Microbiology, University of Washington, Seattle, WA, USA
| | - Dao Nguyen
- Department of Medicine, McGill University, Montreal, QC, Canada
| | - Antonio DiGiandomenico
- Discovery Microbiome, Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, USA
| | - David S Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Daniel J Wozniak
- Departments of Microbial Infection and Immunity, Microbiology, Ohio State University, Columbus, OH, USA
| | - Valerie J Waters
- Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada. .,Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, Toronto, Canada. .,Department of Pediatrics, University of Toronto, Toronto, ON, Canada.
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6
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Waters VJ, Baertschiger RM, Kitai I. Inguinal mass in a 4-month-old boy. CMAJ 2021; 192:E845. [PMID: 32690560 DOI: 10.1503/cmaj.200056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Affiliation(s)
- Valerie J Waters
- Divisions of Infectious Diseases, Department of Pediatrics (Waters, Kitai), and of General Surgery, Department of Surgery (Baertschiger), The Hospital for Sick Children, University of Toronto, Toronto, Ont.
| | - Reto M Baertschiger
- Divisions of Infectious Diseases, Department of Pediatrics (Waters, Kitai), and of General Surgery, Department of Surgery (Baertschiger), The Hospital for Sick Children, University of Toronto, Toronto, Ont
| | - Ian Kitai
- Divisions of Infectious Diseases, Department of Pediatrics (Waters, Kitai), and of General Surgery, Department of Surgery (Baertschiger), The Hospital for Sick Children, University of Toronto, Toronto, Ont
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7
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Clark ST, Stapleton PJ, Wang PW, Yau YCW, Waters VJ, Hwang DM, Guttman DS. Evaluation of digital dispense-assisted broth microdilution antimicrobial susceptibility testing for Pseudomonas aeruginosa isolates. Sci Rep 2021; 11:9157. [PMID: 33911107 PMCID: PMC8080699 DOI: 10.1038/s41598-021-88423-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/09/2021] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial susceptibility testing (AST) is essential for detecting resistance in Pseudomonas aeruginosa and other bacterial pathogens. Here we evaluated the performance of broth microdilution (BMD) panels created using a semi-automated liquid handler, the D300e Digital Dispenser (Tecan Group Ltd., CH) that relies on inkjet printing technology. Microtitre panels (96-well) containing nine twofold dilutions of 12 antimicrobials from five classes (β-lactams, β-lactam/β-lactamase inhibitors, aminoglycosides, fluoroquinolones, polymyxins) were prepared in parallel using the D300e Digital Dispenser and standard methods described by CLSI/ISO. To assess performance, panels were challenged with three well characterized quality control organisms and 100 clinical P. aeruginosa isolates. Traditional agreement and error measures were used for evaluation. Essential (EA) and categorical (CA) agreements were 92.7% and 98.0% respectively for P. aeruginosa isolates with evaluable on-scale results. The majority of minor errors that fell outside acceptable EA parameters (≥ ± 1 dilution, 1.9%) were seen with aztreonam (5%) and ceftazidime (4%), however all antimicrobials displayed acceptable performance in this situation. Differences in MIC were often log2 dilution lower for D300e dispensed panels. Major and very major errors were noted for aztreonam (2.6%) and cefepime (1.7%) respectively. The variable performance of D300e panels suggests that further testing is required to confirm their diagnostic utility for P. aeruginosa.
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Affiliation(s)
- Shawn T Clark
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
| | - Patrick J Stapleton
- Department of Pediatric Laboratory Medicine, Division of Microbiology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Pauline W Wang
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Yvonne C W Yau
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Pediatric Laboratory Medicine, Division of Microbiology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Valerie J Waters
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Pediatrics, Division of Infectious Diseases, The Hospital for Sick Children, Toronto, ON, Canada
| | - David M Hwang
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Laboratory Medicine & Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
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8
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Waters VJ, Kidd TJ, Canton R, Ekkelenkamp MB, Johansen HK, LiPuma JJ, Bell SC, Elborn JS, Flume PA, VanDevanter DR, Gilligan P. Reconciling Antimicrobial Susceptibility Testing and Clinical Response in Antimicrobial Treatment of Chronic Cystic Fibrosis Lung Infections. Clin Infect Dis 2020; 69:1812-1816. [PMID: 31056660 DOI: 10.1093/cid/ciz364] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/29/2019] [Indexed: 01/28/2023] Open
Abstract
Median cystic fibrosis (CF) survival has increased dramatically over time due to several factors, including greater availability and use of antimicrobial therapies. During the progression of CF lung disease, however, the emergence of multidrug antimicrobial resistance can limit treatment effectiveness, threatening patient longevity. Current planktonic-based antimicrobial susceptibility testing lacks the ability to predict clinical response to antimicrobial treatment of chronic CF lung infections. There are numerous reasons for these limitations including bacterial phenotypic and genotypic diversity, polymicrobial interactions, and impaired antibiotic efficacy within the CF lung environment. The parallels to other chronic diseases such as non-CF bronchiectasis are discussed as well as research priorities for moving forward.
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Affiliation(s)
- Valerie J Waters
- Division of Infectious Diseases, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Canada
| | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Rafael Canton
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Miquel B Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
| | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet, Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor
| | - Scott C Bell
- Department of Thoracic Medicine, Prince Charles Hospital and QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - J Stuart Elborn
- Imperial College Hospital, Queen's University Belfast, Northern Ireland
| | - Patrick A Flume
- Departments of Medicine and Pediatrics, Medical University of South Carolina, Charleston
| | - Donald R VanDevanter
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Peter Gilligan
- Department of Pathology-Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill
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9
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Bullington W, Hempstead S, Smyth AR, Drevinek P, Saiman L, Waters VJ, Bell SC, VanDevanter DR, Flume PA, Elborn S, Muhlebach MS. Antimicrobial resistance: Concerns of healthcare providers and people with CF. J Cyst Fibros 2020; 20:407-412. [PMID: 32563724 DOI: 10.1016/j.jcf.2020.05.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND Chronic lung infections and their treatment pose risks for the development of antimicrobial resistance (AMR) in people with cystic fibrosis (PWCF). In this study, we evaluated the attitudes of healthcare providers' (HCP) and PWCF or their parents' toward AMR within the international CF community. METHODS HCP and PWCF identified through listservs and CF-related organizations were asked to complete an AMR centered survey, with additional questions on antimicrobial stewardship (AMS) for HCP. Descriptive analyses are reported. RESULTS The responding 443 HCP and 464 PWCF/Parents were from 30 and 25 countries, respectively. Sixty-two percent of HCP and 56% of PWCF stated they were "very concerned" about AMR, with Pseudomonas spp. and Burkholderia spp. considered the most concerning organisms for both HCP and PWCF/Parents. Non-tuberculous mycobacteria were of greater concern to HCP compared to PWCF/Parents. There was a discrepancy regarding AMR education to PWCF, with 80% of HCP stating having discussed this with PWCF/Parents, but only 50% of PWCF recalling such discussions. CONCLUSION These results highlight that AMR is relevant to CF HCP and PWCF internationally, indicating that educational tools and research are warranted.
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Affiliation(s)
- Wendy Bullington
- Department of Pharmacy Services, Medical University of South Carolina, Charleston, SC, USA.
| | | | - Alan R Smyth
- Division of Child Health, Obstetrics & Gynaecology, University of Nottingham, Nottingham, United Kingdom.
| | - Pavel Drevinek
- Departments of Medical Microbiology Motol University Hospital and 2nd Faculty of Medicine, Charles University, Prague, Czech Republic.
| | - Lisa Saiman
- Department of Pediatrics, Columbia University, New York, New York, USA.
| | - Valerie J Waters
- Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada.
| | - Scott C Bell
- Department of Thoracic Medicine, The Prince Charles Hospital and QIMR Berghofer Medical Research Institute, Brisbane, Australia.
| | - Donald R VanDevanter
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
| | - Patrick A Flume
- Departments of Medicine and Pediatrics, Medical University of South Carolina, Charleston, SC, USA.
| | - Stuart Elborn
- Imperial College and Royal Brompton Hospital, London and Queen's University Belfast, United Kingdom.
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10
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Abstract
Although survival of individuals with cystic fibrosis (CF) has been continuously improving for the past 40 years, respiratory failure secondary to recurrent pulmonary infections remains the leading cause of mortality in this patient population. Certain pathogens such as Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus, and species of the Burkholderia cepacia complex continue to be associated with poorer clinical outcomes including accelerated lung function decline and increased mortality. In addition, other organisms such as anaerobes, viruses, and fungi are increasingly recognized as potential contributors to disease progression. Culture-independent molecular methods are also being used for diagnostic purposes and to examine the interaction of microorganisms in the CF airway. Given the importance of CF airway infections, ongoing initiatives to promote understanding of the epidemiology, clinical course, and treatment options for these infections are needed.
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Affiliation(s)
- Ana C Blanchard
- Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Valerie J Waters
- Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
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11
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Blanchard AC, Tang L, Tadros M, Muller M, Spilker T, Waters VJ, LiPuma JJ, Tullis E. Burkholderia cenocepacia ET12 transmission in adults with cystic fibrosis. Thorax 2019; 75:88-90. [PMID: 31732688 DOI: 10.1136/thoraxjnl-2019-214098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/15/2019] [Indexed: 12/14/2022]
Abstract
This report describes transmission of a Burkholderia cenocepacia ET12 strain (ET12-Bc) at the Toronto Adult Cystic Fibrosis (CF) Centre occurring from 2008 to 2017. Epidemiological and genomic data from 11 patients with CF were evaluated. Isolates were analysed using whole genome sequencing (WGS). Epidemiological investigation and WGS analysis suggested nosocomial transmission, despite enhanced infection control precautions. This was associated with subsequent deaths in 10 patients. ET12-Bc positive patients are no longer cared for on the same unit as ET12-Bc negative patients.
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Affiliation(s)
- Ana C Blanchard
- Pediatrics, Infectious Diseases, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lin Tang
- Infection Prevention and Control, St Michael's Hospital, Toronto, Ontario, Canada
| | - Manal Tadros
- Laboratory Medicine, St Michael's Hospital, Toronto, Ontario, Canada
| | - Matthew Muller
- Internal Medicine, Infectious Diseases/Infection Prevention and Control, St Michael's Hospital, Toronto, Ontario, Canada
| | - Theodore Spilker
- Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Valerie J Waters
- Pediatrics, Infectious Diseases, Hospital for Sick Children, Toronto, Ontario, Canada
| | - John J LiPuma
- Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Elizabeth Tullis
- Internal Medicine, Respirology, St Michael's Hospital, Toronto, Ontario, Canada
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12
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Zemanick E, Burgel PR, Taccetti G, Holmes A, Ratjen F, Byrnes CA, Waters VJ, Bell SC, VanDevanter DR, Stuart Elborn J, Flume PA. Antimicrobial resistance in cystic fibrosis: A Delphi approach to defining best practices. J Cyst Fibros 2019; 19:370-375. [PMID: 31680041 DOI: 10.1016/j.jcf.2019.10.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 08/10/2019] [Accepted: 10/02/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND Antimicrobial susceptibility testing (AST) is a cornerstone of infection management in cystic fibrosis. However, there is little evidence that AST predicts the clinical outcome of CF antimicrobial treatment. It has been suggested there is a need for careful consideration of current AST use by the CF community. METHODS We engaged a group of experts consisting of pulmonary (adult and pediatric) and infectious disease clinicians, microbiologists, and pharmacists representing a broad international experience. We conducted an iterative systematic survey (Delphi) to determine and quantify consensus regarding key questions facing CF clinicians in the use of respiratory culture results including what tests to order, when to obtain them, and how to act upon the results of the testing. RESULTS Consensus was reached for many questions but there was not universal agreement to the questions that were addressed. There were some differences with respect to cultures obtained for surveillance compared to when there is clinical worsening. Areas of general consensus include when and how respiratory cultures should be performed, what information should be reported, and when AST should be performed. A key finding is that clinical response to treatment is used to guide treatment decisions rather than AST results. CONCLUSIONS Recommendations are presented regarding questions related to microbiology testing for patients with CF. We have also offered recommendations for priority research questions.
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Affiliation(s)
- Edith Zemanick
- Department of Pediatrics, University of Colorado, Anschutz Medical Campus, Aurora, CO, United States.
| | - Pierre-Régis Burgel
- Division of Respiratory Medicine and Adult Cystic Fibrosis Center, Assistance Publique Hôpitaux de Paris and University Paris Descartes, Paris, France; ERN-Lung cystic fibrosis network.
| | - Giovanni Taccetti
- Cystic Fibrosis Center, Department of Pediatrics, University of Florence, Italy.
| | - Alison Holmes
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London. United Kingdom.
| | - Felix Ratjen
- Division of Respiratory Medicine, Department of Pediatrics, Translational Medicine,Research Institute, The Hospital for Sick Children, University of Toronto, Toronto, Canada.
| | - Catherine A Byrnes
- Department of Paediatrics, University of Auckland & Respiratory Department, Starship Children's Health, Auckland, New Zealand
| | - Valerie J Waters
- Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada.
| | - Scott C Bell
- Department of Thoracic Medicine, The Prince Charles Hospital and QIMR Berghofer Medical Research Institute, Brisbane, Australia.
| | - Donald R VanDevanter
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH, United States.
| | - J Stuart Elborn
- Imperial College and Royal Brompton Hospital, London and Queen's University Belfast, United Kingdom.
| | - Patrick A Flume
- Departments of Medicine and Pediatrics, Medical University of South Carolina, Charleston, SC, United States.
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Ho SSC, Nashid N, Waters VJ, LiPuma JJ, Zlosnik JEA, Otley A, Somers GR, Kamath BM, Yau YCW. Burkholderia multivorans septicemia in a pediatric liver transplant patient. Am J Transplant 2019; 19:933-938. [PMID: 30091842 DOI: 10.1111/ajt.15065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/16/2018] [Accepted: 07/31/2018] [Indexed: 01/25/2023]
Abstract
"Cepacia syndrome", caused by Burkholderia cepacia complex and often associated with cystic fibrosis, carries a high mortality rate. It is rare for Burkholderia multivorans, a species within the B. cepacia complex, to cause cepacia syndrome even among patients with cystic fibrosis. This is the first reported fatal case of cepacia syndrome caused by B. multivorans occurring in a pediatric liver transplant recipient who does not have cystic fibrosis. We describe the unique characteristics of this pathogen among the non-cystic fibrosis population and the importance of early recognition and treatment.
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Affiliation(s)
- Shaun S C Ho
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Nancy Nashid
- Division of Infectious Diseases, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Valerie J Waters
- Division of Infectious Diseases, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - John J LiPuma
- Department of Pediatrics and Communicable Disease, University of Michigan Medical School, Ann Arbor, MI, USA
| | - James E A Zlosnik
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anthony Otley
- Division of Gastroenterology & Nutrition, IWK Health Centre, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Gino R Somers
- Division of Pathology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Binita M Kamath
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Yvonne C W Yau
- Division of Microbiology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
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14
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Somayaji R, Parkins MD, Shah A, Martiniano SL, Tunney MM, Kahle JS, Waters VJ, Elborn JS, Bell SC, Flume PA, VanDevanter DR. Antimicrobial susceptibility testing (AST) and associated clinical outcomes in individuals with cystic fibrosis: A systematic review. J Cyst Fibros 2019; 18:236-243. [PMID: 30709744 DOI: 10.1016/j.jcf.2019.01.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/14/2019] [Accepted: 01/21/2019] [Indexed: 02/02/2023]
Abstract
BACKGROUND Antimicrobial susceptibility testing (AST) is a cornerstone of infection management. Cystic fibrosis (CF) treatment guidelines recommend AST to select antimicrobial treatments for CF airway infection but its utility in this setting has never been objectively demonstrated. METHODS We conducted a systematic review of primary published articles designed to address two PICO (patient, intervention, comparator, outcome) questions: 1) "For individuals with CF, is clinical response to antimicrobial treatment of bacterial airways infection predictable from AST results available at treatment initiation?" and 2) "For individuals with CF, is clinical response to antimicrobial treatment of bacterial airways infection affected by the method used to guide antimicrobial selection?" Relationships between AST results and clinical response (changes in pulmonary function, weight, signs and symptoms of respiratory tract infection, and time to next event) were assessed for each article and results were compared across articles when possible. RESULTS Twenty-five articles describing the results of 20 separate studies, most of which described Pseudomonas aeruginosa treatment, were identified. Thirteen studies described pulmonary exacerbation (PEx) treatment and seven described 'maintenance' of chronic bacterial airways infection. In only three of 16 studies addressing PICO question #1 was there a suggestion that baseline bacterial isolate antimicrobial susceptibility was associated with clinical response to treatment. None of the four studies addressing PICO question #2 suggested that antimicrobial selection methods influenced clinical outcomes. CONCLUSIONS There is little evidence that AST predicts the clinical outcome of CF antimicrobial treatment, suggesting a need for careful consideration of current AST use by the CF community.
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Affiliation(s)
| | | | - Anand Shah
- Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom; Imperial College London, United Kingdom
| | | | | | | | | | | | - Scott C Bell
- The Prince Charles Hospital and QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
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15
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Clark ST, Sinha U, Zhang Y, Wang PW, Donaldson SL, Coburn B, Waters VJ, Yau YCW, Tullis DE, Guttman DS, Hwang DM. Penicillin-binding protein 3 is a common adaptive target among Pseudomonas aeruginosa isolates from adult cystic fibrosis patients treated with β-lactams. Int J Antimicrob Agents 2019; 53:620-628. [PMID: 30664925 DOI: 10.1016/j.ijantimicag.2019.01.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 12/03/2018] [Accepted: 01/16/2019] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Determining the mechanisms that modulate β-lactam resistance in clinical Pseudomonas aeruginosa (P. aeruginosa) isolates can be challenging, as the molecular profiles identified in mutation-based or expression-based resistance determinant screens may not correlate with in vitro phenotypes. One of the lesser studied resistance mechanisms in P. aeruginosa is the modification of penicillin-binding protein 3 (pbpB/ftsI). This study reported that nonsynonymous polymorphisms within pbpB frequently occur among β-lactam resistant sputum isolates, and are associated with unique antibiotic susceptibility patterns. METHODS Longitudinally collected isolates (n = 126) from cystic fibrosis (CF) patients with or without recent β-lactam therapy or of non-clinical origin were tested for susceptibility to six β-lactams (aztreonam, ceftazidime, cefsulodin, cefepime, meropenem, and piperacillin). Known β-lactam resistance mechanisms were characterised by polymerase chain reaction (PCR)-based methods, and polymorphisms in the transpeptidase-encoding domain of pbpB identified by sequencing. RESULTS Twelve nonsynonymous polymorphisms were detected among 86 isolates (67%) from five CF patients with a history of β-lactam therapy, compared with one polymorphism in 30 (3.3%) from three patients who had not received β-lactam treatments. No nonsynonymous polymorphisms were found in ten environmental isolates. Multiple pbpB alleles, often with different combinations of polymorphisms, were detected within the population of strains from each CF patient for up to 2.6 years. Traditional patterns of ampC or mexA de-repression reduced expression of oprD or the presence of extended-spectrum β-lactamases were not observed in resistant isolates with nonsynonymous polymorphisms in pbpB. CONCLUSION This study's findings suggest that pbpB is a common adaptive target, and may contribute to the development of β-lactam resistance in P. aeruginosa.
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Affiliation(s)
- Shawn T Clark
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Utkarshna Sinha
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
| | - Yu Zhang
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
| | - Pauline W Wang
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - Sylva L Donaldson
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - Bryan Coburn
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Valerie J Waters
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pediatrics, Division of Infectious Diseases, The Hospital for Sick Children, Toronto, Canada
| | - Yvonne C W Yau
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pediatric Laboratory Medicine, Division of Microbiology, The Hospital for Sick Children, Toronto, Canada
| | - D Elizabeth Tullis
- Toronto Adult Cystic Fibrosis Centre, St Michael's Hospital, Toronto, Canada
| | - David S Guttman
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada; Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - David M Hwang
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Laboratory Medicine & Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, Canada.
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16
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Diaz Caballero J, Clark ST, Wang PW, Donaldson SL, Coburn B, Tullis DE, Yau YCW, Waters VJ, Hwang DM, Guttman DS. A genome-wide association analysis reveals a potential role for recombination in the evolution of antimicrobial resistance in Burkholderia multivorans. PLoS Pathog 2018; 14:e1007453. [PMID: 30532201 PMCID: PMC6300292 DOI: 10.1371/journal.ppat.1007453] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 12/19/2018] [Accepted: 11/02/2018] [Indexed: 01/05/2023] Open
Abstract
Cystic fibrosis (CF) lung infections caused by members of the Burkholderia cepacia complex, such as Burkholderia multivorans, are associated with high rates of mortality and morbidity. We performed a population genomics study of 111 B. multivorans sputum isolates from one CF patient through three stages of infection including an early incident isolate, deep sampling of a one-year period of chronic infection occurring weeks before a lung transplant, and deep sampling of a post-transplant infection. We reconstructed the evolutionary history of the population and used a lineage-controlled genome-wide association study (GWAS) approach to identify genetic variants associated with antibiotic resistance. We found the incident isolate was basally related to the rest of the strains and more susceptible to antibiotics from three classes (β-lactams, aminoglycosides, quinolones). The chronic infection isolates diversified into multiple, distinct genetic lineages and showed reduced antimicrobial susceptibility to the same antibiotics. The post-transplant reinfection isolates derived from the same source as the incident isolate and were genetically distinct from the chronic isolates. They also had a level of susceptibility in between that of the incident and chronic isolates. We identified numerous examples of potential parallel pathoadaptation, in which multiple mutations were found in the same locus or even codon. The set of parallel pathoadaptive loci was enriched for functions associated with virulence and resistance. Our GWAS analysis identified statistical associations between a polymorphism in the ampD locus with resistance to β-lactams, and polymorphisms in an araC transcriptional regulator and an outer membrane porin with resistance to both aminoglycosides and quinolones. Additionally, these three loci were independently mutated four, three and two times, respectively, providing further support for parallel pathoadaptation. Finally, we identified a minimum of 14 recombination events, and observed that loci carrying putative parallel pathoadaptations and polymorphisms statistically associated with β-lactam resistance were over-represented in these recombinogenic regions. Cystic fibrosis (CF) is the most common lethal genetic disorder affecting individuals of European descent. Most CF patients die at a young age due to chronic lung infections. Among the organisms involved in these infections are bacteria from the Burkholderia cepacia complex (BCC), which are strongly associated with poor clinical prognosis. This study examines how the most prevalent BCC species among CF patients, B. multivorans, evolves within a single CF patient by studying the first B. multivorans isolate recovered from the patient, one hundred isolates recovered over a one year period during the chronic infection phase, and an additional ten isolates recovered after the reinfection of the transplanted lungs. We found that B. multivorans diversify phenotypically and genetically within the CF lung over the course of the infection, and evolves into a complex population during the chronic infection phase. We found that isolates collected from the post-transplant reinfection were more closely related to descendants of the original isolate rather than those recovered in the chronic infection. We identify genetic variants statistically associated with resistance to the antibiotics, and showed that some of these variants were found in regions that show patterns of recombination (genetic exchange) between strains. We also found that genes which were mutated multiple times during overall infection were more likely to be found in regions showing signals consistent with recombination. The presence of multiple independent mutations in a gene is a very strong signal that the gene helps bacteria adapt to their environment. Overall, this study provides insight into how pathogens adapt to the host during long-term infections, specific genes associated with antibiotic resistance, and the origin of new and recurrent infections.
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Affiliation(s)
- Julio Diaz Caballero
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Shawn T. Clark
- Latner Thoracic Surgery Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Pauline W. Wang
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Sylva L. Donaldson
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Bryan Coburn
- Division of Infectious Diseases, Department of Medicine, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - D. Elizabeth Tullis
- Adult Cystic Fibrosis Clinic, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Yvonne C. W. Yau
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Pediatric Laboratory Medicine, Division of Microbiology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Valerie J. Waters
- Department of Pediatrics, Division of Infectious Diseases, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - David M. Hwang
- Latner Thoracic Surgery Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - David S. Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Flume PA, Waters VJ, Bell SC, Van Devanter DR, Stuart Elborn J. Antimicrobial resistance in cystic fibrosis: Does it matter? J Cyst Fibros 2018; 17:687-689. [PMID: 30270113 DOI: 10.1016/j.jcf.2018.08.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/31/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Patrick A Flume
- Departments of Medicine and Pediatrics, Medical University of South Carolina, Charleston, SC, USA.
| | - Valerie J Waters
- Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada.
| | - Scott C Bell
- Department of Thoracic Medicine, The Prince Charles Hospital, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
| | - Donald R Van Devanter
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
| | - J Stuart Elborn
- Imperial College and Royal Brompton Hospital, London, Queen's University Belfast, Ireland.
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18
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Kidd TJ, Canton R, Ekkelenkamp M, Johansen HK, Gilligan P, LiPuma JJ, Bell SC, Elborn JS, Flume PA, VanDevanter DR, Waters VJ. Defining antimicrobial resistance in cystic fibrosis. J Cyst Fibros 2018; 17:696-704. [PMID: 30266518 DOI: 10.1016/j.jcf.2018.08.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/21/2018] [Accepted: 08/31/2018] [Indexed: 12/31/2022]
Abstract
Antimicrobial resistance (AMR) can present significant challenges in the treatment of cystic fibrosis (CF) lung infections. In CF and other chronic diseases, AMR has a different profile and clinical consequences compared to acute infections and this requires different diagnostic and treatment approaches. This review defines AMR, explains how it occurs, describes the methods used to measure AMR as well as their limitations, and concludes with future directions for research and development in the area of AMR in CF.
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Affiliation(s)
- Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
| | - Rafael Canton
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.
| | - Miquel Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet, Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
| | - Peter Gilligan
- Clinical Microbiology-Immunology Laboratories, UNC HealthCare, Chapel Hill, NC, USA.
| | - John J LiPuma
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Scott C Bell
- Department of Thoracic Medicine, The Prince Charles Hospital and QIMR Berghofer Medical Researhc Institute, Brisbane, Australia.
| | - J Stuart Elborn
- Imperial College and Royal Brompton Hospital, London, Queen's University Belfast, United Kingdom.
| | - Patrick A Flume
- Departments of Medicine and Pediatrics, Medical University of South Carolina, Charleston, SC, USA.
| | - Donald R VanDevanter
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
| | - Valerie J Waters
- Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, USA.
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19
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Chuong KH, Hwang DM, Tullis DE, Waters VJ, Yau YCW, Guttman DS, O'Doherty KC. Navigating social and ethical challenges of biobanking for human microbiome research. BMC Med Ethics 2017; 18:1. [PMID: 28077127 PMCID: PMC5225618 DOI: 10.1186/s12910-016-0160-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 12/16/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Biobanks are considered to be key infrastructures for research development and have generated a lot of debate about their ethical, legal and social implications (ELSI). While the focus has been on human genomic research, rapid advances in human microbiome research further complicate the debate. DISCUSSION We draw on two cystic fibrosis biobanks in Toronto, Canada, to illustrate our points. The biobanks have been established to facilitate sample and data sharing for research into the link between disease progression and microbial dynamics in the lungs of pediatric and adult patients. We begin by providing an overview of some of the ELSI associated with human microbiome research, particularly on the implications for the broader society. We then discuss ethical considerations regarding the identifiability of samples biobanked for human microbiome research, and examine the issue of return of results and incidental findings. We argue that, for the purposes of research ethics oversight, human microbiome research samples should be treated with the same privacy considerations as human tissues samples. We also suggest that returning individual microbiome-related findings could provide a powerful clinical tool for care management, but highlight the need for a more grounded understanding of contextual factors that may be unique to human microbiome research. CONCLUSIONS We revisit the ELSI of biobanking and consider the impact that human microbiome research might have. Our discussion focuses on identifiability of human microbiome research samples, and return of research results and incidental findings for clinical management.
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Affiliation(s)
- Kim H Chuong
- Department of Psychology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - David M Hwang
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Canada.,University Health Network, Toronto, Canada
| | - D Elizabeth Tullis
- Adult Cystic Fibrosis, University of Toronto, Toronto, Canada.,Toronto Adult Cystic Fibrosis Centre, St Michael's Hospital, Toronto, Canada
| | - Valerie J Waters
- Department of Paediatrics, University of Toronto, Toronto, Canada.,Division of Infectious Diseases, Hospital for Sick Children, Toronto, Canada
| | - Yvonne C W Yau
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Canada.,Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Canada
| | - David S Guttman
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Canada
| | - Kieran C O'Doherty
- Department of Psychology, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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20
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Clark ST, Diaz Caballero J, Cheang M, Coburn B, Wang PW, Donaldson SL, Zhang Y, Liu M, Keshavjee S, Yau YC, Waters VJ, Elizabeth Tullis D, Guttman DS, Hwang DM. Phenotypic diversity within a Pseudomonas aeruginosa population infecting an adult with cystic fibrosis. Sci Rep 2015; 5:10932. [PMID: 26047320 PMCID: PMC4456944 DOI: 10.1038/srep10932] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/05/2015] [Indexed: 01/05/2023] Open
Abstract
Chronic airway infections caused by Pseudomonas aeruginosa contribute to the progression of pulmonary disease in individuals with cystic fibrosis (CF). In the setting of CF, within-patient adaptation of a P. aeruginosa strain generates phenotypic diversity that can complicate microbiological analysis of patient samples. We investigated within- and between- sample diversity of 34 phenotypes among 235 P. aeruginosa isolates cultured from sputum samples collected from a single CF patient over the span of one year, and assessed colony morphology as a screening tool for predicting phenotypes, including antimicrobial susceptibilities. We identified 15 distinct colony morphotypes that varied significantly in abundance both within and between sputum samples. Substantial within sample phenotypic heterogeneity was also noted in other phenotypes, with morphotypes being unreliable predictors of antimicrobial susceptibility and other phenotypes. Emergence of isolates with reduced susceptibility to β-lactams was observed during periods of clinical therapy with aztreonam. Our findings confirm that the P. aeruginosa population in chronic CF lung infections is highly dynamic, and that intra-sample phenotypic diversity is underestimated if only one or few colonies are analyzed per sample.
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Affiliation(s)
- Shawn T. Clark
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Latner Thoracic Surgery Research Laboratories, University Health Network, Toronto, Canada
| | | | - Mary Cheang
- Latner Thoracic Surgery Research Laboratories, University Health Network, Toronto, Canada
| | - Bryan Coburn
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - Pauline W. Wang
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Canada
| | - Sylva L. Donaldson
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Canada
| | - Yu Zhang
- Latner Thoracic Surgery Research Laboratories, University Health Network, Toronto, Canada
| | - Mingyao Liu
- Latner Thoracic Surgery Research Laboratories, University Health Network, Toronto, Canada
| | - Shaf Keshavjee
- Latner Thoracic Surgery Research Laboratories, University Health Network, Toronto, Canada
| | - Yvonne C.W. Yau
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Pediatric Laboratory Medicine, Division of Microbiology, The Hospital for Sick Children, Toronto, Canada
| | - Valerie J. Waters
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Pediatrics, Division of Infectious Diseases, The Hospital for Sick Children, Toronto, Canada
| | - D. Elizabeth Tullis
- Department of Medicine, Division of Respirology, St. Michael’s Hospital, Toronto, Canada
| | - David S. Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Canada
| | - David M. Hwang
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Latner Thoracic Surgery Research Laboratories, University Health Network, Toronto, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Canada
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21
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Waters VJ, Stanojevic S, Sonneveld N, Klingel M, Grasemann H, Yau YCW, Tullis E, Wilcox P, Freitag A, Chilvers M, Ratjen FA. Factors associated with response to treatment of pulmonary exacerbations in cystic fibrosis patients. J Cyst Fibros 2015; 14:755-62. [PMID: 25690407 DOI: 10.1016/j.jcf.2015.01.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/23/2015] [Accepted: 01/23/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND Pulmonary exacerbations are associated with significant lung function decline from baseline in cystic fibrosis (CF) and it is not well understood why some patients do not respond to antibiotic therapy. The objective of this study was to identify factors associated with lung function response to antibiotic treatment of pulmonary exacerbations. METHODS As a secondary analysis of a randomized, controlled trial of intravenous antibiotic treatment for pulmonary exacerbations in CF patients, we investigated whether baseline factors and changes in sputum bacterial density, serum or sputum inflammatory markers were associated with recovery of lung function and risk of subsequent exacerbation. RESULTS In 36 of the 70 exacerbations (51%), patients' lung function returned to >100% of their baseline at day 14 of antibiotic treatment; 34 exacerbations were classified as non-responders. Baseline characteristics were not significantly different between responders and non-responders. Less of a drop in FEV1 from baseline to exacerbation (OR 1.09, 95% CI 1.0, 1.18, p=0.04) as well as a greater decrease in sputum neutrophil elastase (OR 2.94, 95% CI 1.07, 8.06, p=0.04) were associated with response to antibiotic treatment at day 14. In addition, higher CRP (HR 1.35 (95% CI: 1.01, 1.78), p=0.04) and sputum neutrophil elastase (HR 1.71 (95% CI: 1.02, 2.88), p=0.04) at day 14 of antibiotic therapy were associated with an increased risk of subsequent exacerbation. CONCLUSIONS Inadequate reduction of inflammation during an exacerbation is associated with failure to recover lung function and increased risk of subsequent re-exacerbation in CF patients.
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Affiliation(s)
- Valerie J Waters
- Division of Infectious Diseases, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto.
| | - Sanja Stanojevic
- Division of Respiratory Medicine, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto.
| | - Nicole Sonneveld
- Division of Respiratory Medicine, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto.
| | - Michelle Klingel
- Division of Respiratory Medicine, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto.
| | - Hartmut Grasemann
- Division of Respiratory Medicine, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto.
| | - Yvonne C W Yau
- Division of Microbiology, Department of Pediatric Laboratory Medicine, Hospital for Sick Children, University of Toronto, Toronto.
| | - Elizabeth Tullis
- Division of Respirology and Keenan Research Centre of Li Ka Shing Knowledge Institute, Department of Medicine, St. Michael's Hospital, University of Toronto, Toronto.
| | - Pearce Wilcox
- Division of Respiratory Medicine, Department of Medicine, St Paul's Hospital, University of British Columbia, Vancouver.
| | - Andreas Freitag
- Division of Respiratory Medicine, Department of Medicine, Hamilton Health Sciences Center, McMaster University, Hamilton.
| | - Mark Chilvers
- Division of Respiratory Medicine, Department of Pediatrics, British Columbia Children's Hospital, Vancouver.
| | - Felix A Ratjen
- Division of Respiratory Medicine, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto.
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Maughan H, Wang PW, Diaz Caballero J, Fung P, Gong Y, Donaldson SL, Yuan L, Keshavjee S, Zhang Y, Yau YCW, Waters VJ, Tullis DE, Hwang DM, Guttman DS. Analysis of the cystic fibrosis lung microbiota via serial Illumina sequencing of bacterial 16S rRNA hypervariable regions. PLoS One 2012; 7:e45791. [PMID: 23056217 PMCID: PMC3462755 DOI: 10.1371/journal.pone.0045791] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 08/24/2012] [Indexed: 12/26/2022] Open
Abstract
The characterization of bacterial communities using DNA sequencing has revolutionized our ability to study microbes in nature and discover the ways in which microbial communities affect ecosystem functioning and human health. Here we describe Serial Illumina Sequencing (SI-Seq): a method for deep sequencing of the bacterial 16S rRNA gene using next-generation sequencing technology. SI-Seq serially sequences portions of the V5, V6 and V7 hypervariable regions from barcoded 16S rRNA amplicons using an Illumina short-read genome analyzer. SI-Seq obtains taxonomic resolution similar to 454 pyrosequencing for a fraction of the cost, and can produce hundreds of thousands of reads per sample even with very high multiplexing. We validated SI-Seq using single species and mock community controls, and via a comparison to cystic fibrosis lung microbiota sequenced using 454 FLX Titanium. Our control runs show that SI-Seq has a dynamic range of at least five orders of magnitude, can classify >96% of sequences to the genus level, and performs just as well as 454 and paired-end Illumina methods in estimation of standard microbial ecology diversity measurements. We illustrate the utility of SI-Seq in a pilot sample of central airway secretion samples from cystic fibrosis patients.
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Affiliation(s)
- Heather Maughan
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (HM); (DG)
| | - Pauline W. Wang
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Julio Diaz Caballero
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Pauline Fung
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Yunchen Gong
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Sylva L. Donaldson
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Lijie Yuan
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Shaf Keshavjee
- Latner Thoracic Surgery Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Yu Zhang
- Latner Thoracic Surgery Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Yvonne C. W. Yau
- Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Valerie J. Waters
- Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - David M. Hwang
- Latner Thoracic Surgery Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - David S. Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (HM); (DG)
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Abstract
Stenotrophomonas maltophilia is a multiple-antibiotic-resistant opportunistic pathogen that is being isolated with increasing frequency from patients with health-care-associated infections and especially from patients with cystic fibrosis (CF). While clinicians feel compelled to treat infections involving this organism, its potential for virulence is not well established. We evaluated the immunostimulatory properties and overall virulence of clinical isolates of S. maltophilia using the well-characterized opportunistic pathogen Pseudomonas aeruginosa PAO1 as a control. The properties of CF isolates were examined specifically to see if they have a common phenotype. The immunostimulatory properties of S. maltophilia were studied in vitro by stimulating airway epithelial and macrophage cell lines. A neonatal mouse model of pneumonia was used to determine the rates of pneumonia, bacteremia, and mortality, as well as the inflammatory response elicited by S. maltophilia infection. Respiratory and nonrespiratory S. maltophilia isolates were highly immunostimulatory and elicited significant interleukin-8 expression by airway epithelial cells, as well as tumor necrosis factor alpha (TNF-alpha) expression by macrophages. TNF-alpha signaling appears to be important in the pathogenesis of S. maltophilia infection as less than 20% of TNFR1 null mice (compared with 100% of wild-type mice) developed pneumonia and bacteremia following intranasal inoculation. The S. maltophilia isolates were weakly invasive, and low-level bacteremia with no mortality was observed. Despite the lack of invasiveness of S. maltophilia, the immunostimulatory properties of this organism and its induction of TNF-alpha expression specifically indicate that it is likely to contribute significantly to airway inflammation.
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Affiliation(s)
- Valerie J Waters
- College of Physicians and Surgeons, Columbia University, 650 W. 168th Street, BB 4-416, New York, NY 10032, USA
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