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Acosta N, Waddell B, Heirali A, Somayaji R, Surette MG, Workentine ML, Rabin HR, Parkins MD. Cystic Fibrosis Patients Infected With Epidemic Pseudomonas aeruginosa Strains Have Unique Microbial Communities. Front Cell Infect Microbiol 2020; 10:173. [PMID: 32426295 PMCID: PMC7212370 DOI: 10.3389/fcimb.2020.00173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/01/2020] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa is the archetypal cystic fibrosis (CF) pathogen. However, the clinical course experienced by infected individuals varies markedly. Understanding these differences is imperative if further improvements in outcomes are to be achieved. Multiple studies have found that patients infected with epidemic P. aeruginosa (ePA) strains may have a worse clinical prognosis than those infected with unique, non-clonal strains. Additionally, the traditionally uncultured CF lung bacterial community (i.e., CF microbiome) may further influence the outcome. We sought to identify if these two important variables, not identified through routine culture, associate and together may contribute to disease pathogenesis. Patients were classified as being infected with Prairie Epidemic ePA (PES) or a non-clonal strain, unique PA strains (uPA), through a retrospective assessment of a comprehensive strain biobank using a combination of PFGE and PES-specific PCR. Patients were matched to age, sex, time-period controls and sputum samples from equivalent time periods were identified from a sputum biobank. Bacterial 16S rRNA gene profiling and Pseudomonas qPCR was used to characterize the respiratory microbiome. We identified 31 patients infected with PES and matched them with uPA controls. Patients infected with PES at baseline have lower microbial diversity (P = 0.02) and higher P. aeruginosa relative abundance (P < 0.005). Microbial community structure was found to cluster by PA strain type, although it was not the main determinant of community structure as additional factors were also found to be drivers of CF community structure. Communities from PES infected individuals were enriched with Pseudomonas, Streptococcus and Prevotella OTUs. The disproportionate disease experienced by ePA infected CF patients may be mediated through a combination of pathogen-pathogen factors as opposed to strictly enhanced virulence of infecting P. aeruginosa strains.
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Affiliation(s)
- Nicole Acosta
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Barbara Waddell
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Alya Heirali
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Ranjani Somayaji
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.,Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Michael G Surette
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.,Departments of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | | | - Harvey R Rabin
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.,Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Michael D Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.,Department of Medicine, University of Calgary, Calgary, AB, Canada
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Murray TS, O'Rourke TK, Feinn R, Drapeau G, Collins MS. Nebulizer cleaning and disinfection practices in families with cystic fibrosis: The relationship between attitudes, practice and microbe colonization. J Cyst Fibros 2019; 18:823-828. [DOI: 10.1016/j.jcf.2019.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 01/24/2023]
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Epidemiology, Biology, and Impact of Clonal Pseudomonas aeruginosa Infections in Cystic Fibrosis. Clin Microbiol Rev 2018; 31:31/4/e00019-18. [PMID: 30158299 DOI: 10.1128/cmr.00019-18] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chronic lower airway infection with Pseudomonas aeruginosa is a major contributor to morbidity and mortality in individuals suffering from the genetic disease cystic fibrosis (CF). Whereas it was long presumed that each patient independently acquired unique strains of P. aeruginosa present in their living environment, multiple studies have since demonstrated that shared strains of P. aeruginosa exist among individuals with CF. Many of these shared strains, often referred to as clonal or epidemic strains, can be transmitted from one CF individual to another, potentially reaching epidemic status. Numerous epidemic P. aeruginosa strains have been described from different parts of the world and are often associated with an antibiotic-resistant phenotype. Importantly, infection with these strains often portends a worse prognosis than for infection with nonclonal strains, including an increased pulmonary exacerbation rate, exaggerated lung function decline, and progression to end-stage lung disease. This review describes the global epidemiology of clonal P. aeruginosa strains in CF and summarizes the current literature regarding the underlying biology and clinical impact of globally important CF clones. Mechanisms associated with patient-to-patient transmission are discussed, and best-evidence practices to prevent infections are highlighted. Preventing new infections with epidemic P. aeruginosa strains is of paramount importance in mitigating CF disease progression.
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Woo TE, Lim R, Surette MG, Waddell B, Bowron JC, Somayaji R, Duong J, Mody CH, Rabin HR, Storey DG, Parkins MD. Epidemiology and natural history of Pseudomonas aeruginosa airway infections in non-cystic fibrosis bronchiectasis. ERJ Open Res 2018; 4:00162-2017. [PMID: 29930949 PMCID: PMC6004520 DOI: 10.1183/23120541.00162-2017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 04/13/2018] [Indexed: 01/20/2023] Open
Abstract
The natural history and epidemiology of Pseudomonas aeruginosa infections in non-cystic fibrosis (non-CF) bronchiectasis is not well understood. As such it was our intention to determine the evolution of airway infection and the transmission potential of P. aeruginosa in patients with non-CF bronchiectasis. A longitudinal cohort study was conducted from 1986-2011 using a biobank of prospectively collected isolates from patients with non-CF bronchiectasis. Patients included were ≥18 years old and had ≥2 positive P. aeruginosa cultures over a minimum 6-month period. All isolates obtained at first and most recent clinical encounters, as well as during exacerbations, that were morphologically distinct on MacConkey agar were genotyped by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). A total of 203 isolates from 39 patients were analysed. These were compared to a large collection of globally epidemic and local CF strains, as well as non-CF isolates. We identified four patterns of infection in non-CF bronchiectasis including: 1) persistence of a single strain (n=26; 67%); 2) strain displacement (n=8; 20%); 3) temporary disruption (n=3; 8%); and 4) chaotic airway infection (n=2; 5%). Patterns of infection were not significant predictors of rates of lung function decline or progression to end-stage disease and acquisition of new strains did not associate with the occurrence of exacerbations. Rarely, non-CF bronchiectasis strains with similar pulsotypes were observed in CF and non-CF controls, but no CF epidemic strains were observed. While rare shared strains were observed in non-CF bronchiectasis, whole-genome sequencing refuted patient-patient transmission. We observed a higher incidence of strain-displacement in our patient cohort compared to those observed in CF studies, although this did not impact on outcomes.
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Affiliation(s)
- Taylor E. Woo
- Dept of Biological Sciences, University of Calgary, Calgary, Canada
- Dept of Medicine, University of Calgary, Calgary, Canada
| | - Rachel Lim
- Dept of Medicine, University of Calgary, Calgary, Canada
| | - Michael G. Surette
- Dept of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
- Dept of Medicine and Dept of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Barbara Waddell
- Dept of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Joel C. Bowron
- Dept of Biological Sciences, University of Calgary, Calgary, Canada
| | - Ranjani Somayaji
- Dept of Medicine, University of Calgary, Calgary, Canada
- Dept of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Jessica Duong
- Dept of Biological Sciences, University of Calgary, Calgary, Canada
| | - Christopher H. Mody
- Dept of Medicine, University of Calgary, Calgary, Canada
- Dept of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Harvey R. Rabin
- Dept of Medicine, University of Calgary, Calgary, Canada
- Dept of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Douglas G. Storey
- Dept of Biological Sciences, University of Calgary, Calgary, Canada
- Dept of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Michael D. Parkins
- Dept of Medicine, University of Calgary, Calgary, Canada
- Dept of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
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Prevalence and Outcomes of Achromobacter Species Infections in Adults with Cystic Fibrosis: a North American Cohort Study. J Clin Microbiol 2017; 55:2074-2085. [PMID: 28446570 DOI: 10.1128/jcm.02556-16] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 03/20/2017] [Indexed: 02/07/2023] Open
Abstract
Achromobacter species are increasingly being detected in cystic fibrosis (CF) patients, with an unclear epidemiology and impact. We studied a cohort of patients attending a Canadian adult CF clinic who had positive sputum cultures for Achromobacter species in the period from 1984 to 2013. Infection was categorized as transient or persistent (≥50% positive cultures for 1 year). Those with persistent infection were matched 2:1 with age-, sex-, and time-matched controls without a history of Achromobacter infection, and mixed-effects models were used to assess pulmonary exacerbation (PEx) frequency and lung function decline. Isolates from a biobank were retrospectively assessed, identified to the species level by nrdA sequencing, and genotyped using pulsed-field gel electrophoresis (PFGE). Thirty-four patients (11% of those in our clinic), with a median age of 24 years (interquartile range [IQR], 20.3 to 29.8 years), developed Achromobacter infection. Ten patients (29%) developed persistent infection. Persistence did not denote permanence, as most patients ultimately cleared infection, often after years. Patients were more likely to experience PEx at incident isolation than at prior or subsequent visits (odds ratio [OR], 2.7 [95% confidence interval {CI}, 1.2 to 6.7]; P = 0.03). Following persistent infection, there was no difference in annual lung function decline (-1.08% [95% CI, -2.73 to 0.57%] versus -2.74% [95% CI, -4.02 to 1.46%]; P = 0.12) or the odds of PEx (OR, 1.21 [95% CI, 0.45 to 3.28]; P = 0.70). Differential virulence among Achromobacter species was not observed, and no cases of transmission occurred. We demonstrated that incident Achromobacter infection was associated with a greater risk of PEx; however, neither transient nor chronic infection was associated with a worsened long-term prognosis. Large, multicenter studies are needed to clarify the clinical impact, natural history, and transmissibility of Achromobacter.
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Somayaji R, Lam JC, Surette MG, Waddell B, Rabin HR, Sibley CD, Purighalla S, Parkins MD. Long-term clinical outcomes of 'Prairie Epidemic Strain' Pseudomonas aeruginosa infection in adults with cystic fibrosis. Thorax 2016; 72:333-339. [PMID: 27682327 DOI: 10.1136/thoraxjnl-2015-208083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 08/10/2016] [Accepted: 08/31/2016] [Indexed: 01/21/2023]
Abstract
RATIONALE Epidemic Pseudomonas aeruginosa (PA) plays an important role in cystic fibrosis (CF) lung disease. A novel strain, the 'Prairie Epidemic Strain' (PES), has been identified in up to 30% of patients in Prairie-based Canadian CF centres. OBJECTIVE To determine the incidence, prevalence and long-term clinical impact of PES infection. METHODS A cohort of adults with CF was followed from 1980 to 2014 where bacteria isolated from clinical encounters were prospectively collected. Strain typing was performed using pulse-field gel electrophoresis and multilocus sequence typing. Patients were divided into one of four cohorts: no PA, transient PA, chronic PA with unique strains and chronic PES. Proportional Cox hazard and linear mixed models were used to assess for CF-associated respiratory death or transplantation, and rates of %FEV1 and body mass index (BMI) decline. RESULTS 274 patients (51.7% male) were analysed: 44--no PA, 29--transient PA, 137--unique PA, 64--PES. A total of 92 patients (33.6%) died or underwent lung transplantation (2423.0 patient-years). PES infection was associated with greater risk of respiratory death or lung transplant compared with the no PA group (aHR, 3.94 (95% CI 1.18 to 13.1); p=0.03) and unique PA group (aHR, 1.75 (95% CI 1.05 to 2.92) p=0.03). Rate of lung function decline (%FEV1 predicted) was greatest in the PES group (1.73%/year (95% CI 1.63% to 1.82%); p<0.001). BMI improved over time but at an attenuated rate in the PES group (p=0.001). CONCLUSIONS Infection with PES was associated with increased patient morbidity through three decades and manifested in an increased risk of respiratory death and/or lung transplantation.
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Affiliation(s)
- Ranjani Somayaji
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - John C Lam
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Michael G Surette
- Departments of Medicine, and Biochemistry and Biomedical Sciences, The Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Barbara Waddell
- Department of Microbiology, Immunology & Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Harvey R Rabin
- Departments of Medicine, and Microbiology, Immunology & Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | | | - Swathi Purighalla
- Department of Microbiology, Immunology & Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Michael D Parkins
- Departments of Medicine, and Microbiology, Immunology & Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
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