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Biggs SL, Jennison AV, Bergh H, Graham R, Nimmo G, Whiley D. Limited evidence of patient-to-patient transmission of Staphylococcus aureus strains between children with cystic fibrosis, Queensland, Australia. PLoS One 2022; 17:e0275256. [PMID: 36206247 PMCID: PMC9543978 DOI: 10.1371/journal.pone.0275256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES Here we used whole genome sequencing (WGS) to understand strain diversity and potential for patient-to-patient transmission of Staphylococcus aureus among children with cystic fibrosis (CF) in Queensland, Australia. METHODS S. aureus isolates (n = 401) collected between January 2018 and April 2019 from 184 patients with CF (n = 318 isolates) and 76 patients without CF (n = 83 isolates) were subjected to WGS and subsequent multilocus sequence typing (MLST), and a phylogeny was constructed from core genome single nucleotide polymorphism (SNP) analysis. The subsequent data was compared with available patient information. RESULTS WGS revealed that patients with CF were essentially colonised by the same genotypes as those seen in patients without CF. Sequence types (ST) for our patients with CF were predominantly ST5 (20.1%), ST30 (7.3%), ST15 (6.3%) and ST8 (5.3%). Two Australian clones, ST93 and ST239, typically seen in skin infections and health-care settings, respectively, were notably absent from our patients with CF. Based on a SNP distance threshold of 14 SNPs, 20 cluster types involving 50/260 patients were evident; of these, 6 clusters contained only patients found to be siblings or otherwise living in the same household. Epidemiological relationships could not be determined for a remaining 14 cluster types involving 38 patients, comprising 2-7 (median 2) patients each. Multiple S. aureus genotypes were observed in 19/73 CF patients who provided more than one sample. CONCLUSION These results show that WGS is a useful tool for surveillance of S. aureus strains in children with CF and that the strains in our CF cohort were largely consistent with those circulating in patients without CF. Overall, this confirms previous findings and indicates that S. aureus acquisition in children with CF is similar to that of other patient groups, with limited evidence of potential patient-to-patient transmission within this patient group.
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Affiliation(s)
- Sharon L. Biggs
- School of Medicine, The University of Queensland, UQ Centre for Clinical Research (UQCCR), Herston, Queensland, Australia
| | - Amy V. Jennison
- Public and Environmental Health, Forensic and Scientific Services, Coopers Plains, Queensland, Australia
| | - Haakon Bergh
- Pathology Queensland Central Laboratory, Herston, Queensland, Australia
| | - Rikki Graham
- Public and Environmental Health, Forensic and Scientific Services, Coopers Plains, Queensland, Australia
| | - Graeme Nimmo
- School of Medicine, Griffith University, Gold Coast, Queensland, Australia
| | - David Whiley
- School of Medicine, The University of Queensland, UQ Centre for Clinical Research (UQCCR), Herston, Queensland, Australia
- Pathology Queensland Central Laboratory, Herston, Queensland, Australia
- * E-mail:
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2
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Cogen JD, Nichols DP, Goss CH, Somayaji R. Drugs, Drugs, Drugs: Current Treatment Paradigms in Cystic Fibrosis Airway Infections. J Pediatric Infect Dis Soc 2022; 11:S32-S39. [PMID: 36069901 DOI: 10.1093/jpids/piac061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/23/2022] [Indexed: 12/15/2022]
Abstract
Airway infections have remained a prominent feature in persons living with cystic fibrosis (CF) despite the dramatic improvements in survival in the past decades. Antimicrobials are a cornerstone of infection management for both acute and chronic maintenance indications. Historic clinical trials of antimicrobials in CF have led to the adoption of consensus guidelines for their use in clinical care. More recently, however, there are efforts to re-think the optimal use of antimicrobials for care with the advent of novel and highly effective CF transmembrane conductance regulator modulator therapies. Encouragingly, however, drug development has remained active concurrently in this space. Our review focuses on the evidence for and perspectives regarding antimicrobial use in both acute and maintenance settings in persons with CF. The therapeutic innovations in CF and how this may affect antimicrobial approaches are also discussed.
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Affiliation(s)
- Jonathan D Cogen
- Department of Pediatrics, University of Washington , Seattle, Washington, USA
| | - David P Nichols
- Department of Pediatrics, University of Washington , Seattle, Washington, USA.,Seattle Children's Research Institute, Seattle, Washington , USA
| | - Christopher H Goss
- Department of Pediatrics, University of Washington , Seattle, Washington, USA.,Seattle Children's Research Institute, Seattle, Washington , USA.,Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Ranjani Somayaji
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
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3
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Prevalence of antibiotic resistance of Pseudomonas aeruginosa in cystic fibrosis infection: A systematic review and meta-analysis. Microb Pathog 2022; 165:105461. [DOI: 10.1016/j.micpath.2022.105461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/16/2022]
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4
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Eremwanarue OA, Nwawuba SU, Shittu OH. Characterisation of the Prevailing Multidrug Pseudomonas aeruginosa Strains from Surgical Wound Using 16S rRNA Sequencing Technique. Malays J Med Sci 2021; 28:37-49. [PMID: 34512129 PMCID: PMC8407802 DOI: 10.21315/mjms2021.28.4.5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/20/2021] [Indexed: 12/03/2022] Open
Abstract
Background Pseudomonas aeruginosa (P. aeruginosa) is prevalent in hospital-acquired surgical wound infections. It exhibits both innate and acquired resistance to a broad range of antimicrobials and remains a principal problem in clinical practice. Methods In total, 284 sterile surgical wound swabs (142 each) were collected from two government hospitals: Central Hospital Benin (CHB) and University of Benin Teaching Hospital (UBTH) in Benin City, Nigeria. Pseudomonas spp. isolated from both hospitals were screened with eight different antibiotics by way of disk diffusion method. Polymerase chain reaction (PCR) amplification of 34 multiple drug-resistant isolates was carried out using genus-specific primer set on extracted genomic DNA for the identification of Pseudomonas spp. and substituent 16S rRNA sequencing to determine the prevailing strains in the two locations. Results Sixty-two Pseudomonas spp. were isolated from the two locations (27 isolates from CHB and 35 isolates from the UBTH). Surgical wound infections screened with regularly used antibiotics revealed that 17 (62.9%) isolates from CHB and 20 (57.1%) isolates from UBTH were multiple drug resistant Pseudomonas spp. PCR identification using Pseudomonas spp. specific primer showed that 16 (94.1%) isolates from CHB and 18 (90%) isolates from UBTH were confirmed. The 16S DNA sequencing revealed that P. aeruginosa strain H25883 was dominant in both locations. Conclusion High antibiotic resistance among P. aeruginosa isolates was established in our study. PCR technique revealed a more reliable method of bacterial identification. H25883 strain of P. aeruginosa is the prevalent strain in both locations and it should be given attention in nosocomial surgical wound infections.
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Affiliation(s)
- Osagie Aibuedefe Eremwanarue
- Department of Plant Biology and Biotechnology, University of Benin, Ugbowo, Benin City, Nigeria.,Lahor Research Laboratories and Diagnostics Centre, Benin City, Nigeria
| | - Stanley Udogadi Nwawuba
- Centre for Forensic Programmes and DNA Studies, University of Benin, Ugbowo, Benin City, Nigeria
| | - Olalekan Hakeem Shittu
- Department of Plant Biology and Biotechnology, University of Benin, Ugbowo, Benin City, Nigeria
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5
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Sherrard LJ, Wee BA, Duplancic C, Ramsay KA, Dave KA, Ballard E, Wainwright CE, Grimwood K, Sidjabat HE, Whiley DM, Beatson SA, Kidd TJ, Bell SC. Emergence and impact of oprD mutations in Pseudomonas aeruginosa strains in cystic fibrosis. J Cyst Fibros 2021; 21:e35-e43. [PMID: 33775602 DOI: 10.1016/j.jcf.2021.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND Antimicrobial resistance in cystic fibrosis (CF) Pseudomonas aeruginosa airway infection is complex and often attributed to chromosomal mutations. How these mutations emerge in specific strains or whether particular gene mutations are clinically informative is unclear. This study focused on oprD, which encodes an outer membrane porin associated with carbapenem resistance when it is downregulated or inactivated. AIM Determine how mutations in oprD emerge in two prevalent Australian shared CF strains of P. aeruginosa and their clinical relevance. METHODS The two most common shared CF strains in Queensland were investigated using whole genome sequencing and their oprD sequences and antimicrobial resistance phenotypes were established. P. aeruginosa mutants with the most common oprD variants were constructed and characterised. Clinical variables were compared between people with or without evidence of infection with strains harbouring these variants. RESULTS Frequently found nonsense mutations arising from a 1-base pair substitution in oprD evolved independently in three sub-lineages, and are likely major contributors to the reduced carbapenem susceptibility observed in the clinical isolates. Lower baseline FEV1 %predicted was identified as a risk factor for infection with a sub-lineage (odds ratio=0.97; 95% confidence interval 0.96-0.99; p<0.001). However, acquiring these sub-lineage strains did not confer an accelerated decline in FEV1 nor increase the risk of death/lung transplantation. CONCLUSIONS Sub-lineages harbouring specific mutations in oprD have emerged and persisted in the shared strain populations. Infection with the sub-lineages was more likely in people with lower lung function, but this was not predictive of a worse clinical trajectory.
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Affiliation(s)
| | - Bryan A Wee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | | | - Kay A Ramsay
- QIMR Berghofer Medical Research Institute, Brisbane, Australia; Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Keyur A Dave
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Emma Ballard
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Claire E Wainwright
- Faculty of Medicine, The University of Queensland, Brisbane, Australia; Department of Respiratory and Sleep Medicine, Queensland Children's Hospital, Brisbane, Australia
| | - Keith Grimwood
- School of Medicine and Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia; Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Gold Coast, Australia
| | - Hanna E Sidjabat
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia
| | - David M Whiley
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia; Pathology Queensland Central Laboratory, Brisbane, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia; Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
| | - Timothy J Kidd
- QIMR Berghofer Medical Research Institute, Brisbane, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
| | - Scott C Bell
- QIMR Berghofer Medical Research Institute, Brisbane, Australia; Faculty of Medicine, The University of Queensland, Brisbane, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia; Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Australia.
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6
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Hamidian M, Lazenby J, To J, Hartstein R, Soares J, McNamara S, Whitchurch CB. Complete Genome Sequence of Stenotrophomonas maltophilia Strain CF13, Recovered from Sputum from an Australian Cystic Fibrosis Patient. Microbiol Resour Announc 2020; 9:e00628-20. [PMID: 32763931 PMCID: PMC7409848 DOI: 10.1128/mra.00628-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/11/2020] [Indexed: 11/20/2022] Open
Abstract
Stenotrophomonas maltophilia isolate CF13 is a multidrug-resistant isolate that was recovered in Sydney, Australia, in 2011, from a sputum sample from an individual with cystic fibrosis. The genome sequence of CF13 was completed using long- and short-read technologies.
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Affiliation(s)
- Mohammad Hamidian
- The ithree institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - James Lazenby
- The ithree institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Joyce To
- The ithree institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Rebecca Hartstein
- The ithree institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Jana Soares
- The ithree institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Samantha McNamara
- The ithree institute, University of Technology Sydney, Ultimo, NSW, Australia
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7
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Sala MA, Jain M. Pseudomonas aeruginosa and children with cystic fibrosis. Clin Infect Dis 2020; 73:e2529-e2530. [PMID: 32544945 DOI: 10.1093/cid/ciaa765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/12/2020] [Indexed: 11/12/2022] Open
Affiliation(s)
- Marc A Sala
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Manu Jain
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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8
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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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9
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Milczewska J, Wołkowicz T, Zacharczuk K, Mierzejewska E, Kwiatkowska M, Walicka-Serzysko K, Sands D. Clinical outcomes for cystic fibrosis patients with Pseudomonas aeruginosa cross-infections. Pediatr Pulmonol 2020; 55:161-168. [PMID: 31556252 DOI: 10.1002/ppul.24535] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 09/16/2019] [Indexed: 02/04/2023]
Abstract
INTRODUCTION Pseudomonas aeruginosa cross-infections are related to increased morbidity and mortality in cystic fibrosis (CF). OBJECTIVES The aim of the study was to evaluate the incidence of cross-infections with P. aeruginosa in children with CF. METHODOLOGY CF patients from whom at least one P. aeruginosa strain had been isolated were included in the study. The strain genotyping was performed using pulse-field gel electrophoresis. The history of contacts between patients was established based on questionnaires. RESULTS The study group consisted of 75 patients (aged 1.0-19.2 years) and the material included 170 P. aeruginosa strains. Cross-infections occurred in a group of 26 patients. In this group, the risk of the predicted occurrence of forced expiratory volume in 1 second ≤ 70% was five times greater and the risk of longer cumulative hospitalization time for intravenous antibiotic therapy (>14 days/year) was almost five times greater. In the clonal groups of strains, the multidrug-resistance rate was significantly higher than in other groups. In 2011, all tested strains were susceptible to colistin, whereas in 2012, three strains from the largest clonal group showed high levels of resistance to colistin. CONCLUSION Cross-infections with P. aeruginosa occurred in our group of patients and were associated with poor clinical outcomes. Antimicrobial resistance rate in the strains isolated from such infections was significantly higher, and this included three strains resistant to colistin.
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Affiliation(s)
- Justyna Milczewska
- Cystic Fibrosis Department, Institute of Mother and Child, Warsaw, Poland.,Cystic Fibrosis Center, Children's Hospital in Dziekanów Leśny, Warsaw, Poland
| | - Tomasz Wołkowicz
- Department of Bacteriology and Biocontamination Control, National Institute of Public Health-National Institute of Hygiene, Warsaw, Poland
| | - Katarzyna Zacharczuk
- Department of Bacteriology and Biocontamination Control, National Institute of Public Health-National Institute of Hygiene, Warsaw, Poland
| | - Ewa Mierzejewska
- Department of Epidemiology and Biostatistics, Institute of Mother and Child, Warsaw, Poland
| | - Monika Kwiatkowska
- Independent Laboratory of Microbiology, Central Laboratory, Institute of Mother and Child, Warsaw, Poland
| | - Katarzyna Walicka-Serzysko
- Cystic Fibrosis Department, Institute of Mother and Child, Warsaw, Poland.,Cystic Fibrosis Center, Children's Hospital in Dziekanów Leśny, Warsaw, Poland
| | - Dorota Sands
- Cystic Fibrosis Department, Institute of Mother and Child, Warsaw, Poland.,Cystic Fibrosis Center, Children's Hospital in Dziekanów Leśny, Warsaw, Poland
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10
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Epidemiology of Clonal Pseudomonas aeruginosa Infection in a Canadian Cystic Fibrosis Population. Ann Am Thorac Soc 2019; 15:827-836. [PMID: 29911888 DOI: 10.1513/annalsats.201801-007oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
RATIONALE The extent of the genetic relatedness among Pseudomonas aeruginosa isolates and its impact on clinical outcomes in the cystic fibrosis (CF) population is poorly understood. OBJECTIVES The objectives of this study were to determine the prevalence of clonal P. aeruginosa infection in Canada and to associate P. aeruginosa genotypes with clinical outcomes. METHODS This was an observational study of adult and pediatric patients with CF across Canada. Isolates were typed using multilocus sequence typing. A clone was defined as sharing at least six of seven alleles. Genotyping results were associated with clinical outcomes, including forced expiratory volume in 1 second, body mass index, rate of pulmonary exacerbation, and death/transplant. RESULTS A total of 1,537 P. aeruginosa isolates were genotyped to 403 unique sequence types (STs) in 402 individuals with CF. Although 39% of STs were shared, most were shared only among a small number of subjects, and the majority (79%) of the genetic diversity in P. aeruginosa isolates was observed between patients. There were no significant differences in clinical outcomes according to genotype. However, patients with a dynamic, changing ST infection pattern had both a steeper decline in forced expiratory volume in 1 second (-2.9% predicted change/yr, 95% confidence interval [CI] = -3.8 to -1.9 compared with 0.4, 95% CI = -0.3 to 1.0; P < 0.001) and body mass index (-1.0 percentile change/yr, 95% CI = -1.6 to -0.3 compared with -0.1, 95% CI = -0.7 to 0.5; P = 0.047) than those with a stable infection with the same ST. CONCLUSIONS There was no widespread sharing of dominant clones in our CF population, and the majority of the genetic diversity in P. aeruginosa was observed between patients. Changing genotypes over time within an individual was associated with worse clinical outcomes.
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11
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Sener Okur D, Yuruyen C, Gungor O, Aktas Z, Erturan Z, Akcakaya N, Camcioglu Y, Cokugras H, Koksalan K. Genotypic characterization of Pseudomonas aeruginosa isolates from Turkish children with cystic fibrosis. Infect Drug Resist 2019; 12:675-685. [PMID: 31114258 PMCID: PMC6497484 DOI: 10.2147/idr.s183151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/15/2019] [Indexed: 02/03/2023] Open
Abstract
Objective: To identify epidemic and other transmissible Pseudomonas aeruginosa strains, genotypic analyses are required. The aim of this study was to assess the distribution of P. aeruginosa strains within the Turkish pediatric cystic fibrosis (CF) clinic population. Methods: Eighteen patients attending the pediatric CF clinic of Cerrahpasa Medical Faculty were investigated in the study. Throat swab and/or sputum samples were taken from each patient at 3-month intervals. The isolates of patients were analyzed by pulsed-field gel electrophoresis (PFGE). The intra- and interpatient genotypic heterogeneity of isolates was examined to determine the clonal isolates of P. aeruginosa within the cohort. Results: A total of 108 clinical isolates of P. aeruginosa were obtained from 18 patients between May 2013 and May 2014. The pulsotypes of the first patient’s isolates could not be obtained by PFGE. From the remaining 17 patients and 101 isolates, 55 distinct pulsotypes were detected. The number of pulsotypes observed in more than one patient (minor clonal strains, cluster strains) was 8 (14.5%), and one of them colonized three patients. However, none of them was detected in more than three patients. These pulsotypes were composed of 20 isolates. In addition, with the PFGE analysis of 81 isolates, we detected 47 (85.6%) pulsotypes, which belonged to only one patient. Over different periods of this study, only 2 (11.8%) patients were colonized with the same pulsotype. Conclusion: Our study indicates that there was considerable genomic diversity among the P. aeruginosa isolates in our clinic. The presence of shared pulsotypes supports cross-transmission between patients.
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Affiliation(s)
- Dicle Sener Okur
- Istanbul University Cerrahpasa, Faculty of Medicine, Department of Pediatrics, Division of Pediatric Infectious Diseases, 34098 Kocamustafapasa, Istanbul, Turkey
| | - Caner Yuruyen
- Istanbul University Istanbul, Faculty of Medicine, Department of Microbiology and Clinical Microbiology, 34390 Capa, Istanbul, Turkey
| | - Ozge Gungor
- Istanbul University Istanbul, Faculty of Medicine, Department of Microbiology and Clinical Microbiology, 34390 Capa, Istanbul, Turkey
| | - Zerrin Aktas
- Istanbul University Istanbul, Faculty of Medicine, Department of Microbiology and Clinical Microbiology, 34390 Capa, Istanbul, Turkey
| | - Zayre Erturan
- Istanbul University Istanbul, Faculty of Medicine, Department of Microbiology and Clinical Microbiology, 34390 Capa, Istanbul, Turkey
| | - Necla Akcakaya
- Istanbul University Cerrahpasa, Faculty of Medicine, Department of Pediatrics, Division of Pediatric Infectious Diseases, Clinical Immunology and Allergy, 34098 Kocamustafapasa, Istanbul, Turkey
| | - Yildiz Camcioglu
- Istanbul University Cerrahpasa, Faculty of Medicine, Department of Pediatrics, Division of Pediatric Infectious Diseases, Clinical Immunology and Allergy, 34098 Kocamustafapasa, Istanbul, Turkey
| | - Haluk Cokugras
- Istanbul University Cerrahpasa, Faculty of Medicine, Department of Pediatrics, Division of Pediatric Infectious Diseases, Clinical Immunology and Allergy, 34098 Kocamustafapasa, Istanbul, Turkey
| | - Kaya Koksalan
- Istanbul University, Institute for Medical Experimental Research (DETAE), 34390 Capa, Istanbul, Turkey
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12
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Wee BA, Tai AS, Sherrard LJ, Ben Zakour NL, Hanks KR, Kidd TJ, Ramsay KA, Lamont I, Whiley DM, Bell SC, Beatson SA. Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre. BMC Genomics 2018; 19:644. [PMID: 30165811 PMCID: PMC6117919 DOI: 10.1186/s12864-018-5018-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 08/14/2018] [Indexed: 11/18/2022] Open
Abstract
Background Chronic lung infections caused by Pseudomonas aeruginosa are a significant cause of morbidity and mortality in people with cystic fibrosis (CF). Shared P. aeruginosa strains, that can be transmitted between patients, are of concern and in Australia the AUST-02 shared strain is predominant in individuals attending CF centres in Queensland and Western Australia. M3L7 is a multidrug resistant sub-type of AUST-02 that was recently identified in a Queensland CF centre and was shown to be associated with poorer clinical outcomes. The main aim of this study was to resolve the relationship of the emergent M3L7 sub-type within the AUST-02 group of strains using whole genome sequencing. Results A whole genome core phylogeny of 63 isolates indicated that M3L7 is a monophyletic sub-lineage within the context of the broader AUST-02 group. Relatively short branch lengths connected all of the M3L7 isolates. A phylogeny based on nucleotide polymorphisms present across the genome showed that the chronological estimation of the most recent common ancestor was around 2001 (± 3 years). SNP differences between sequential non-hypermutator M3L7 isolates collected 3–4 years apart from five patients suggested both continuous infection of the same strain and cross-infection of some M3L7 variants between patients. The majority of polymorphisms that were characteristic of M3L7 (i.e. acquired after divergence from all other AUST-02 isolates sequenced) were found to produce non-synonymous mutations in virulence and antibiotic resistance genes. Conclusions M3L7 has recently diverged from a common ancestor, indicating descent from a single carrier at a CF treatment centre in Australia. Both adaptation to the lung and transmission of M3L7 between adults attending this centre may have contributed to its rapid dissemination. Further genomic investigations are required on multiple intra-sample isolates of this sub-type to decipher potential mechanisms which facilitates its epidemiological success. Electronic supplementary material The online version of this article (10.1186/s12864-018-5018-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bryan A Wee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.,Present Address: Usher Institute of Population Health Sciences & Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Anna S Tai
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia.,Department of Respiratory Medicine, Western Australia Adult Cystic Fibrosis Centre, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Laura J Sherrard
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Present Address: School of Pharmacy, Queen's University Belfast, Belfast, United Kingdom
| | - Nouri L Ben Zakour
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Kirt R Hanks
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.,Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK.,Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Kay A Ramsay
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Present Address: Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Iain Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - David M Whiley
- Faculty of Medicine, UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia.,Microbiology Department, Pathology Queensland Central Laboratory, Brisbane, QLD, Australia
| | - Scott C Bell
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia.,Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia. .,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.
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13
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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: 158] [Impact Index Per Article: 26.3] [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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14
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Sherrard LJ, Tai AS, Wee BA, Ramsay KA, Kidd TJ, Ben Zakour NL, Whiley DM, Beatson SA, Bell SC. Within-host whole genome analysis of an antibiotic resistant Pseudomonas aeruginosa strain sub-type in cystic fibrosis. PLoS One 2017; 12:e0172179. [PMID: 28273168 PMCID: PMC5342179 DOI: 10.1371/journal.pone.0172179] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/31/2017] [Indexed: 02/07/2023] Open
Abstract
A Pseudomonas aeruginosa AUST-02 strain sub-type (M3L7) has been identified in Australia, infects the lungs of some people with cystic fibrosis and is associated with antibiotic resistance. Multiple clonal lineages may emerge during treatment with mutations in chromosomally encoded antibiotic resistance genes commonly observed. Here we describe the within-host diversity and antibiotic resistance of M3L7 during and after antibiotic treatment of an acute pulmonary exacerbation using whole genome sequencing and show both variation and shared mutations in important genes. Eleven isolates from an M3L7 population (n = 134) isolated over 3 months from an individual with cystic fibrosis underwent whole genome sequencing. A phylogeny based on core genome SNPs identified three distinct phylogenetic groups comprising two groups with higher rates of mutation (hypermutators) and one non-hypermutator group. Genomes were screened for acquired antibiotic resistance genes with the result suggesting that M3L7 resistance is principally driven by chromosomal mutations as no acquired mechanisms were detected. Small genetic variations, shared by all 11 isolates, were found in 49 genes associated with antibiotic resistance including frame-shift mutations (mexA, mexT), premature stop codons (oprD, mexB) and mutations in quinolone-resistance determining regions (gyrA, parE). However, whole genome sequencing also revealed mutations in 21 genes that were acquired following divergence of groups, which may also impact the activity of antibiotics and multi-drug efflux pumps. Comparison of mutations with minimum inhibitory concentrations of anti-pseudomonal antibiotics could not easily explain all resistance profiles observed. These data further demonstrate the complexity of chronic and antibiotic resistant P. aeruginosa infection where a multitude of co-existing genotypically diverse sub-lineages might co-exist during and after intravenous antibiotic treatment.
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Affiliation(s)
- Laura J. Sherrard
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Anna S. Tai
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
- Western Australia Adult Cystic Fibrosis Centre, Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Bryan A. Wee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Kay A. Ramsay
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Timothy J. Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Centre for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Nouri L. Ben Zakour
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - David M. Whiley
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
- Pathology Queensland, Microbiology Department, Brisbane, QLD, Australia
| | - Scott A. Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Scott C. Bell
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
- * E-mail:
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15
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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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16
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Jani M, Mathee K, Azad RK. Identification of Novel Genomic Islands in Liverpool Epidemic Strain of Pseudomonas aeruginosa Using Segmentation and Clustering. Front Microbiol 2016; 7:1210. [PMID: 27536294 PMCID: PMC4971588 DOI: 10.3389/fmicb.2016.01210] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/20/2016] [Indexed: 02/03/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen implicated in a myriad of infections and a leading pathogen responsible for mortality in patients with cystic fibrosis (CF). Horizontal transfers of genes among the microorganisms living within CF patients have led to highly virulent and multi-drug resistant strains such as the Liverpool epidemic strain of P. aeruginosa, namely the LESB58 strain that has the propensity to acquire virulence and antibiotic resistance genes. Often these genes are acquired in large clusters, referred to as "genomic islands (GIs)." To decipher GIs and understand their contributions to the evolution of virulence and antibiotic resistance in P. aeruginosa LESB58, we utilized a recursive segmentation and clustering procedure, presented here as a genome-mining tool, "GEMINI." GEMINI was validated on experimentally verified islands in the LESB58 strain before examining its potential to decipher novel islands. Of the 6062 genes in P. aeruginosa LESB58, 596 genes were identified to be resident on 20 GIs of which 12 have not been previously reported. Comparative genomics provided evidence in support of our novel predictions. Furthermore, GEMINI unraveled the mosaic structure of islands that are composed of segments of likely different evolutionary origins, and demonstrated its ability to identify potential strain biomarkers. These newly found islands likely have contributed to the hyper-virulence and multidrug resistance of the Liverpool epidemic strain of P. aeruginosa.
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Affiliation(s)
- Mehul Jani
- Department of Biological Sciences, University of North Texas Denton, TX, USA
| | - Kalai Mathee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine Global Health Consortium, and Biomolecular Sciences Institute, Florida International University Miami, FL, USA
| | - Rajeev K Azad
- Department of Biological Sciences, University of North TexasDenton, TX, USA; Department of Mathematics, University of North TexasDenton, TX, USA
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17
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Tham HL, Jacob ME, Bizikova P. Molecular confirmation of shampoo as the putative source of Pseudomonas aeruginosa-induced postgrooming furunculosis in a dog. Vet Dermatol 2016; 27:320-e80. [PMID: 27237982 DOI: 10.1111/vde.12332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2016] [Indexed: 11/29/2022]
Abstract
BACKGROUND An acute onset furunculosis due to Pseudomonas aeruginosa following grooming is a well recognized entity. Although contaminated shampoos have been suspected to be the source of the infection, a molecular confirmation of this association has been missing. OBJECTIVE This case report describes a dog with postgrooming furunculosis in which Pseudomonas aeruginosa with an identical genetic fingerprint was isolated from the skin lesions as well as from the shampoo used prior to the disease onset. RESULTS The dog presented for lethargy, anorexia, pain and rapidly progressing skin lesions consistent with haemorrhagic papules, pustules, coalescing ulcers and crusts localized to the dorsal and lateral aspects of the thorax and gluteal region, which developed within 24 h after a bath. Cytology demonstrated suppurative inflammation with occasional intracellular rod-shaped bacteria. Bacterial culture from skin lesions and the shampoo bottle yielded Pseudomonas aeruginosa with an identical pulsed-field gel electrophoresis pattern. Treatment with oral ciprofloxacin and topical antimicrobial shampoo resulted in a complete resolution of skin lesions within eight weeks. CONCLUSION AND CLINICAL IMPORTANCE Our clinical investigation suggests a link between Pseudomonas-contaminated shampoo and development of postgrooming furunculosis, and underscores the need for hygienic management of shampoos to help limit this disease.
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Affiliation(s)
- Heng L Tham
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - Megan E Jacob
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - Petra Bizikova
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA.,Comparative Medicine Institute, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
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18
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Within-Host Evolution of the Dutch High-Prevalent Pseudomonas aeruginosa Clone ST406 during Chronic Colonization of a Patient with Cystic Fibrosis. PLoS One 2016; 11:e0158106. [PMID: 27337151 PMCID: PMC4918941 DOI: 10.1371/journal.pone.0158106] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/12/2016] [Indexed: 01/01/2023] Open
Abstract
This study investigates adaptation of ST406, a prevalent P. aeruginosa clone, present in 15% of chronically infected cystic fibrosis (CF) patients in the Netherlands, in a newly infected CF patient during three years using whole genome sequencing (WGS), transcriptomics, and phenotypic assays, including biofilm formation. WGS-based phylogeny demonstrates that ST406 is genetically distinct from other reported CF related strains or epidemic clones. Comparative genomic analysis of the early (S1) and late (S2) isolate yielded 42 single nucleotide polymorphisms (SNPs) and 10 indels and a single 7 kb genomic fragment only found in S2. Most SNPs and differentially expressed genes encoded proteins involved in metabolism, secretion and signal transduction or transcription. SNPs were identified in regulator genes mexT and exsA and coincided with differential gene expression of mexE and mexF, encoding the MexE/F efflux pump, genes encoding the type six secretion system (T6SS) and type three secretion system (T3SS), which have also been previously implicated in adaptation of other P. aeruginosa strains during chronic infection of CF lungs. The observation that genetically different strains from different patients have accumulated similar genetic adaptations supports the concept of adaptive parallel evolution of P. aeruginosa in chronically infected CF patients. Phenotypically, there was loss of biofilm maturation coinciding with a significant lower level of transcription of both bfmR and bfmS during chronic colonization. These data suggest that the high-prevalent Dutch CF clone ST406 displays adaptation to the CF lung niche, which involves a limited number of mutations affecting regulators controlling biofilm formation and secretion and genes involved in metabolism. These genes could provide good targets for anti-pseudomonal therapy.
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19
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Saiman L, Siegel JD, LiPuma JJ, Brown RF, Bryson EA, Chambers MJ, Downer VS, Fliege J, Hazle LA, Jain M, Marshall BC, O’Malley C, Pattee SR, Potter-Bynoe G, Reid S, Robinson KA, Sabadosa KA, Schmidt HJ, Tullis E, Webber J, Weber DJ. Infection Prevention and Control Guideline for Cystic Fibrosis: 2013 Update. Infect Control Hosp Epidemiol 2016; 35 Suppl 1:S1-S67. [DOI: 10.1086/676882] [Citation(s) in RCA: 270] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The 2013 Infection Prevention and Control (IP&C) Guideline for Cystic Fibrosis (CF) was commissioned by the CF Foundation as an update of the 2003 Infection Control Guideline for CF. During the past decade, new knowledge and new challenges provided the following rationale to develop updated IP&C strategies for this unique population:1.The need to integrate relevant recommendations from evidence-based guidelines published since 2003 into IP&C practices for CF. These included guidelines from the Centers for Disease Control and Prevention (CDC)/Healthcare Infection Control Practices Advisory Committee (HICPAC), the World Health Organization (WHO), and key professional societies, including the Infectious Diseases Society of America (IDSA) and the Society for Healthcare Epidemiology of America (SHEA). During the past decade, new evidence has led to a renewed emphasis on source containment of potential pathogens and the role played by the contaminated healthcare environment in the transmission of infectious agents. Furthermore, an increased understanding of the importance of the application of implementation science, monitoring adherence, and feedback principles has been shown to increase the effectiveness of IP&C guideline recommendations.2.Experience with emerging pathogens in the non-CF population has expanded our understanding of droplet transmission of respiratory pathogens and can inform IP&C strategies for CF. These pathogens include severe acute respiratory syndrome coronavirus and the 2009 influenza A H1N1. Lessons learned about preventing transmission of methicillin-resistantStaphylococcus aureus(MRSA) and multidrug-resistant gram-negative pathogens in non-CF patient populations also can inform IP&C strategies for CF.
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20
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Streeter K, Neuman C, Thompson J, Hatje E, Katouli M. The characteristics of genetically related Pseudomonas aeruginosa from diverse sources and their interaction with human cell lines. Can J Microbiol 2016; 62:233-40. [DOI: 10.1139/cjm-2015-0536] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We investigated a collection of Pseudomonas aeruginosa strains from hospitalised patients (n = 20) and various environmental sources (n = 214) for their genetic relatedness; virulence properties; antibiotic resistance; and interaction with intestinal (Caco-2), renal (A-498), and lung (Calu-3) cell lines. Using RAPD–PCR, we found high diversity among the strains irrespective of their sources, with only 6 common (C) types containing strains from both a clinical and environmental source. Environmental strains belonging to these C-types showed greater adhesion to A-498 cells than did clinical strains (17 ± 13 bacteria/cell versus 13 ± 11 bacteria/cell; p < 0.001), whereas clinical strains showed significantly greater adhesion to Calu-3 and Caco-2 cells than did environmental strains (p < 0.001 for both). The virulence genes and antibiotic resistance profiles of the strains were similar; however, the prevalence of environmental strains carrying both exoS and exoU was significantly (p < 0.0368) higher than clinical strains. While all strains were resistant to ticarcillin and ticarcillin–clavulanic acid, resistance against aztreonam, gentamicin, amikacin, piperacillin, and ceftazidime varied among environmental and clinical strains. These results suggest that environmental strains of P. aeruginosa carry virulence properties similar to clinical strains, including adhesion to various human cell lines, with some strains showing a higher adhesion to specific cell lines, indicating they may have a better ability to cause infection in those sites under predisposing conditions of the host.
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Affiliation(s)
- Klrissa Streeter
- Genecology Research Centre, School of Health and Sport Sciences, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, 4558, Queensland, Australia
- Genecology Research Centre, School of Health and Sport Sciences, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, 4558, Queensland, Australia
| | - Christina Neuman
- Genecology Research Centre, School of Health and Sport Sciences, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, 4558, Queensland, Australia
- Genecology Research Centre, School of Health and Sport Sciences, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, 4558, Queensland, Australia
| | - Jasmin Thompson
- Genecology Research Centre, School of Health and Sport Sciences, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, 4558, Queensland, Australia
- Genecology Research Centre, School of Health and Sport Sciences, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, 4558, Queensland, Australia
| | - Eva Hatje
- Genecology Research Centre, School of Health and Sport Sciences, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, 4558, Queensland, Australia
- Genecology Research Centre, School of Health and Sport Sciences, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, 4558, Queensland, Australia
| | - Mohammad Katouli
- Genecology Research Centre, School of Health and Sport Sciences, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, 4558, Queensland, Australia
- Genecology Research Centre, School of Health and Sport Sciences, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, 4558, Queensland, Australia
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21
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Genotypic Diversity within a Single Pseudomonas aeruginosa Strain Commonly Shared by Australian Patients with Cystic Fibrosis. PLoS One 2015; 10:e0144022. [PMID: 26633539 PMCID: PMC4669131 DOI: 10.1371/journal.pone.0144022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/12/2015] [Indexed: 12/12/2022] Open
Abstract
In cystic fibrosis (CF), Pseudomonas aeruginosa undergoes intra-strain genotypic and phenotypic diversification while establishing and maintaining chronic lung infections. As the clinical significance of these changes is uncertain, we investigated intra-strain diversity in commonly shared strains from CF patients to determine if specific gene mutations were associated with increased antibiotic resistance and worse clinical outcomes. Two-hundred-and-one P. aeruginosa isolates (163 represented a dominant Australian shared strain, AUST-02) from two Queensland CF centres over two distinct time-periods (2001–2002 and 2007–2009) underwent mexZ and lasR sequencing. Broth microdilution antibiotic susceptibility testing in a subset of isolates was also performed. We identified a novel AUST-02 subtype (M3L7) in adults attending a single Queensland CF centre. This M3L7 subtype was multi-drug resistant and had significantly higher antibiotic minimum inhibitory concentrations than other AUST-02 subtypes. Prospective molecular surveillance using polymerase chain reaction assays determined the prevalence of the ‘M3L7’ subtype at this centre during 2007–2009 (170 patients) and 2011 (173 patients). Three-year clinical outcomes of patients harbouring different strains and subtypes were compared. MexZ and LasR sequences from AUST-02 isolates were more likely in 2007–2009 than 2001–2002 to exhibit mutations (mexZ: odds ratio (OR) = 3.8; 95% confidence interval (CI): 1.1–13.5 and LasR: OR = 2.5; 95%CI: 1.3–5.0). Surveillance at the adult centre in 2007–2009 identified M3L7 in 28/509 (5.5%) P. aeruginosa isolates from 13/170 (7.6%) patients. A repeat survey in 2011 identified M3L7 in 21/519 (4.0%) P. aeruginosa isolates from 11/173 (6.4%) patients. The M3L7 subtype was associated with greater intravenous antibiotic and hospitalisation requirements, and a higher 3-year risk of death/lung transplantation, than other AUST-02 subtypes (adjusted hazard ratio [HR] = 9.4; 95%CI: 2.2–39.2) and non-AUST-02 strains (adjusted HR = 4.8; 95%CI: 1.4–16.2). This suggests ongoing microevolution of the shared CF strain, AUST-02, was associated with an emerging multi-drug resistant subtype and possibly poorer clinical outcomes.
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22
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Duong J, Booth SC, McCartney NK, Rabin HR, Parkins MD, Storey DG. Phenotypic and Genotypic Comparison of Epidemic and Non-Epidemic Strains of Pseudomonas aeruginosa from Individuals with Cystic Fibrosis. PLoS One 2015; 10:e0143466. [PMID: 26599104 PMCID: PMC4657914 DOI: 10.1371/journal.pone.0143466] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/05/2015] [Indexed: 11/18/2022] Open
Abstract
Epidemic strains of Pseudomonas aeruginosa have been found worldwide among the cystic fibrosis (CF) patient population. Using pulse-field gel electrophoresis, the Prairie Epidemic Strain (PES) has recently been found in one-third of patients attending the Calgary Adult CF Clinic in Canada. Using multi-locus sequence typing, PES isolates from unrelated patients were found to consistently have ST192. Though most patients acquired PES prior to enrolling in the clinic, some patients were observed to experience strain replacement upon transitioning to the clinic whereby local non-epidemic P. aeruginosa isolates were displaced by PES. Here we genotypically and phenotypically compared PES to other P. aeruginosa epidemic strains (OES) found around the world as well as local non-epidemic CF P. aeruginosa isolates in order to characterize PES. Since some epidemic strains are associated with worse clinical outcomes, we assessed the pathogenic potential of PES to determine if these isolates are virulent, shared properties with OES, and if its phenotypic properties may offer a competitive advantage in displacing local non-epidemic isolates during strain replacement. As such, we conducted a comparative analysis using fourteen phenotypic traits, including virulence factor production, biofilm formation, planktonic growth, mucoidy, and antibiotic susceptibility to characterize PES, OES, and local non-epidemic isolates. We observed that PES and OES could be differentiated from local non-epidemic isolates based on biofilm growth with PES isolates being more mucoid. Pairwise comparisons indicated that PES produced significantly higher levels of proteases and formed better biofilms than OES but were more susceptible to antibiotic treatment. Amongst five patients experiencing strain replacement, we found that super-infecting PES produced lower levels of proteases and elastases but were more resistant to antibiotics compared to the displaced non-epidemic isolates. This comparative analysis is the first to be completed on a large scale between groups of epidemic and non-epidemic CF P. aeruginosa isolates.
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Affiliation(s)
- Jessica Duong
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Sean C. Booth
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Nathan K. McCartney
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Harvey R. Rabin
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Michael D. Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Douglas G. Storey
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
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23
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Infection control knowledge, beliefs and behaviours amongst cystic fibrosis patients with epidemic Pseudomonas aeruginosa. BMC Pulm Med 2015; 15:138. [PMID: 26542115 PMCID: PMC4635525 DOI: 10.1186/s12890-015-0116-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/01/2015] [Indexed: 01/26/2023] Open
Abstract
Background Epidemic P. aeruginosa (ePA) infections are common in cystic fibrosis (CF) and have been associated with accelerated clinical decline. Factors associated with ePA are unclear, and evidence based infection control interventions are lacking. Methods We prospectively collect all bacterial pathogens from adult CF patients. We performed PA strain typing on retrospectively collected enrolment samples and recent isolates to identify patients infected with ePA. All patients attending our clinic were approached to complete a survey on infection control knowledge, beliefs and exposures. We analyzed responses of those with ePA relative to the entire cohort without ePA as well as those infected with unique strains of P. aeruginosa to assess for risk factors for ePA and differences in infection control knowledge, beliefs or behaviours. Results Of 144 participants, 30 patients had ePA (two Liverpool epidemic strain, 28 Prairie epidemic strain), 83 % of which had established infection prior to transition to the adult clinic. Risk of concomitant infecting pathogens was no different between groups although, Staphylococcus aureus and non-tuberculous mycobacteria were less common in those with ePA. Patients with ePA were more likely to have attended CF-camp and have a history of CF fundraising. Patients with ePA did not differ with respect to beliefs regarding pathogens or transmission risk, except they believed indirect contact posed little risk. Furthermore, patients with ePA were more likely to continue to associate with others with CF despite extensive counselling. Use of peer-peer online networking was minimal in both groups. Conclusion Infections with ePA are closely linked to past exposures, now routinely discouraged. As socialization is the greatest risk factor for ePA, infection control strategies for ePA must focus on discouraging face-to-face interactions amongst CF patients. As peer support remains a desire amongst patients, investment in technologies and strategies that enable indirect communication and support are required.
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24
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Molecular surveillance for carbapenemase genes in carbapenem-resistant Pseudomonas aeruginosa in Australian patients with cystic fibrosis. Pathology 2015; 47:156-60. [PMID: 25551306 DOI: 10.1097/pat.0000000000000216] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The aim of this study was to assess the prevalence of acquired carbapenemase genes amongst carbapenem non-susceptible Pseudomonas aeruginosa isolates in Australian patients with cystic fibrosis (CF). Cross-sectional molecular surveillance for acquired carbapenemase genes was performed on CF P. aeruginosa isolates from two isolate banks comprising: (i) 662 carbapenem resistant P. aeruginosa isolates from 227 patients attending 10 geographically diverse Australian CF centres (2007-2009), and (ii) 519 P. aeruginosa isolates from a cohort of 173 adult patients attending one Queensland CF clinic in 2011. All 1189 P. aeruginosa isolates were tested by polymerase chain reaction (PCR) protocols targeting ten common carbapenemase genes, as well the Class 1 integron intI1 gene and the aadB aminoglycoside resistance gene. No carbapenemase genes were identified among all isolates tested. The intI1 and aadB genes were frequently detected and were significantly associated with the AUST-02 strain (OR 24.6, 95% CI 9.3-65.6; p < 0.0001) predominantly from Queensland patients. Despite the high prevalence of carbapenem resistance in P. aeruginosa in Australian patients with CF, no acquired carbapenemase genes were detected in the study, suggesting chromosomal mutations remain the key resistance mechanism in CF isolates. Systematic surveillance for carbapenemase-producing P. aeruginosa in CF by molecular surveillance is ongoing.
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Goeminne PC, Nawrot TS, De Boeck K, Nemery B, Dupont LJ. Proximity to blue spaces and risk of infection with Pseudomonas aeruginosa in cystic fibrosis: A case-control analysis. J Cyst Fibros 2015; 14:741-7. [PMID: 25940953 DOI: 10.1016/j.jcf.2015.04.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 04/11/2015] [Accepted: 04/13/2015] [Indexed: 01/12/2023]
Abstract
BACKGROUND The acquisition of Pseudomonas aeruginosa in cystic fibrosis (CF) is associated with lower survival, decreased lung function, worse radiological scores, increased exacerbations and reduced nutritional status. Open water is a known reservoir and a potential source of exposure to P. aeruginosa. METHODS Twenty eight adult CF patients who had no history of P. aeruginosa and had negative P. aeruginosa IgG antibody levels, were matched by age and sex with 28 CF patients with chronic P. aeruginosa colonization. Straight line and closest walking distance from patient's residence to the nearest "blue space", i.e. surface water as determined by Google Earth, were compared between the two groups, and odds ratios (OR) were estimated using conditional logistic regression. RESULTS Patients who were never infected with P. aeruginosa lived significantly further away from a natural water source than P. aeruginosa colonized patients, both when considering shortest walking distance (mean 487 m vs 308 m, p=0.014) and beeline (mean 324 m vs 202 m, p=0.021). Conditional logistic regression (correcting for FEV1%) revealed ORs for chronic P. aeruginosa colonization of 0.35 (95% CI 0.13-0.98; p=0.045) and 0.12 (95% CI 0.02-0.81; p=0.028) for each doubling in the beeline or walking distance, respectively, between residence and open water. CONCLUSION We discovered that adult CF patients without P. aeruginosa infection live significantly further from blue space than CF patients with chronic P. aeruginosa colonization. Within the limitations of a case-control study, this may indicate that natural open water represents a source of infection by P. aeruginosa in CF. REGISTRATION The study was approved by the local ethical committee of the UZ Leuven, Belgium (ML-5028).
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Affiliation(s)
- Pieter C Goeminne
- Department of Respiratory Disease, University Hospital of Leuven, Belgium.
| | - Tim S Nawrot
- Center for Environmental Sciences, Hasselt University, Hasselt, Belgium; Centre for Environment and health, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Kris De Boeck
- Department of Paediatrics, University Hospital of Leuven, Belgium
| | - Ben Nemery
- Centre for Environment and health, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Lieven J Dupont
- Department of Respiratory Disease, University Hospital of Leuven, Belgium
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Kidd TJ, Ramsay KA, Vidmar S, Carlin JB, Bell SC, Wainwright CE, Grimwood K. Pseudomonas aeruginosa genotypes acquired by children with cystic fibrosis by age 5-years. J Cyst Fibros 2015; 14:361-9. [PMID: 25563522 DOI: 10.1016/j.jcf.2014.12.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 10/22/2014] [Accepted: 12/15/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND We describe Pseudomonas aeruginosa acquisitions in children with cystic fibrosis (CF) aged ≤5-years, eradication treatment efficacy, and genotypic relationships between upper and lower airway isolates and strains from non-CF sources. METHODS Of 168 CF children aged ≤5-years in a bronchoalveolar lavage (BAL)-directed therapy trial, 155 had detailed microbiological results. Overall, 201/271 (74%) P. aeruginosa isolates from BAL and oropharyngeal cultures were available for genotyping, including those collected before and after eradication therapy. RESULTS Eighty-two (53%) subjects acquired P. aeruginosa, of which most were unique strains. Initial eradication success rate was 90%, but 36 (44%) reacquired P. aeruginosa, with genotypic substitutions more common in BAL (12/14) than oropharyngeal (3/11) cultures. Moreover, oropharyngeal cultures did not predict BAL genotypes reliably. CONCLUSIONS CF children acquire environmental P. aeruginosa strains frequently. However, discordance between BAL and oropharyngeal strains raises questions over upper airway reservoirs and how to best determine eradication in non-expectorating children.
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Affiliation(s)
- Timothy J Kidd
- Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Herston, QLD 4029, Australia.
| | - Kay A Ramsay
- Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Herston, QLD 4029, Australia
| | - Suzanna Vidmar
- Clinical Epidemiology and Biostatistics Unit, Murdoch Childrens Research Institute and Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - John B Carlin
- Clinical Epidemiology and Biostatistics Unit, Murdoch Childrens Research Institute and Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - Scott C Bell
- Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Herston, QLD 4029, Australia; Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, QLD 4032, Australia
| | - Claire E Wainwright
- Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Herston, QLD 4029, Australia; Queensland Children's Respiratory Centre, Royal Children's Hospital, Herston, QLD 4029, Australia
| | - Keith Grimwood
- Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Herston, QLD 4029, Australia; Griffith Health Institute, Griffith University and Gold Coast University Hospital, Southport, QLD 4222, Australia
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AbdulWahab A, Taj-Aldeen SJ, Ibrahim E, Abdulla SH, Muhammed R, Ahmed I, Abdeen Y, Sadek O, Abu-Madi M. Genetic relatedness and host specificity of Pseudomonas aeruginosa isolates from cystic fibrosis and non-cystic fibrosis patients. Infect Drug Resist 2014; 7:309-16. [PMID: 25429232 PMCID: PMC4242404 DOI: 10.2147/idr.s72112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Pseudomonas aeruginosa is one of the primary pathogens isolated more frequently in cystic fibrosis (CF) and it exhibits innate resistance to a wide range of antibiotics. PURPOSE We sought to determine whether the highly prevalent genotypes of P. aeruginosa are specifically linked to CF patients and have any related multidrug antibiotic resistance. Isolates from hospitalized non-CF patients and from environmental sources were also genotypically analyzed. METHODS Collections of P. aeruginosa from lower respiratory secretions (n=45) were genotyped using pulsed-field gel electrophoresis (PFGE). Phenotypic screening for antibiotic susceptibility was performed for the common antimicrobial agents by E-test and automated Phoenix method. RESULTS P. aeruginosa isolates from CF (n=32), hospitalized non-CF patients (n=13), and environment sources (n=5) were analyzed. The population structure of P. aeruginosa is highly diverse and population-specific. All PFGE results of P. aeruginosa isolates fall among four major clusters. Cluster 1 contained 16 P. aeruginosa isolates from CF patients and two from environmental sources; cluster 2 contained 11 P. aeruginosa isolates from CF and one each from non-CF and environmental sources; cluster 3 contained 12 P. aeruginosa isolates from hospitalized non-CF patients and two P. aeruginosa isolates from one CF patient and one environmental source; and cluster 4 consisted of three isolates from CF patients and one from the environment. The majority of multidrug-resistant P. aeruginosa isolates were in clusters 3 and 4. P. aeruginosa isolates from CF patients were resistant to ciprofloxacin (34.4%) followed by resistance to amikacin and gentamicin (each 28%), whereas the majority of isolates from non-CF patients were resistant to meropenem (69%) and were grouped in cluster 3. CONCLUSION PFGE of P. aeruginosa isolates from CF patients shows a high degree of similarity, suggesting specific adaptation of these clones to CF-affected lungs. The hospitalized non-CF cluster has a different clonal origin, indicating specific clustering in a specific location, suggesting hospital-acquired P. aeruginosa infections.
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Affiliation(s)
- Atqah AbdulWahab
- Department of Pediatrics, Hamad Medical Corporation, Qatar University, Doha, Qatar
| | - Saad J Taj-Aldeen
- Microbiology Division, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Qatar University, Doha, Qatar
| | - Emad Ibrahim
- Microbiology Division, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Qatar University, Doha, Qatar
| | - Shaikha H Abdulla
- Molecular Biology Unit, Central Food Laboratories, Supreme Council of Health, Qatar University, Doha, Qatar
| | - Ramees Muhammed
- Molecular Biology Unit, Central Food Laboratories, Supreme Council of Health, Qatar University, Doha, Qatar
| | - Irshad Ahmed
- Molecular Biology Unit, Central Food Laboratories, Supreme Council of Health, Qatar University, Doha, Qatar
| | - Yasmine Abdeen
- Department of Health Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Omnia Sadek
- Department of Health Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Marawan Abu-Madi
- Department of Health Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
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Fothergill JL, Winstanley C, James CE. Novel therapeutic strategies to counterPseudomonas aeruginosainfections. Expert Rev Anti Infect Ther 2014; 10:219-35. [DOI: 10.1586/eri.11.168] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Clifton IJ, Peckham DG. Defining routes of airborne transmission ofPseudomonas aeruginosain people with cystic fibrosis. Expert Rev Respir Med 2014; 4:519-29. [DOI: 10.1586/ers.10.42] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Conway SP, Peckham DG, Denton M, Brownlee KG. Optimizing treatment policies and improving care: impact on outcome in patients with cystic fibrosis. Expert Rev Pharmacoecon Outcomes Res 2014; 5:791-806. [DOI: 10.1586/14737167.5.6.791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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De Soyza A, Hall AJ, Mahenthiralingam E, Drevinek P, Kaca W, Drulis-Kawa Z, Stoitsova SR, Toth V, Coenye T, Zlosnik JEA, Burns JL, Sá-Correia I, De Vos D, Pirnay JP, Kidd TJ, Reid D, Manos J, Klockgether J, Wiehlmann L, Tümmler B, McClean S, Winstanley C. Developing an international Pseudomonas aeruginosa reference panel. Microbiologyopen 2013; 2:1010-23. [PMID: 24214409 PMCID: PMC3892346 DOI: 10.1002/mbo3.141] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 09/27/2013] [Accepted: 10/07/2013] [Indexed: 01/22/2023] Open
Abstract
Pseudomonas aeruginosa is a major opportunistic pathogen in cystic fibrosis (CF) patients and causes a wide range of infections among other susceptible populations. Its inherent resistance to many antimicrobials also makes it difficult to treat infections with this pathogen. Recent evidence has highlighted the diversity of this species, yet despite this, the majority of studies on virulence and pathogenesis focus on a small number of strains. There is a pressing need for a P. aeruginosa reference panel to harmonize and coordinate the collective efforts of the P. aeruginosa research community. We have collated a panel of 43 P. aeruginosa strains that reflects the organism's diversity. In addition to the commonly studied clones, this panel includes transmissible strains, sequential CF isolates, strains with specific virulence characteristics, and strains that represent serotype, genotype or geographic diversity. This focussed panel of P. aeruginosa isolates will help accelerate and consolidate the discovery of virulence determinants, improve our understanding of the pathogenesis of infections caused by this pathogen, and provide the community with a valuable resource for the testing of novel therapeutic agents.
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Affiliation(s)
- Anthony De Soyza
- Institute of Cellular Medicine, Newcastle University, Newcastle, U.K
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Scott NE, Hare NJ, White MY, Manos J, Cordwell SJ. Secretome of transmissible Pseudomonas aeruginosa AES-1R grown in a cystic fibrosis lung-like environment. J Proteome Res 2013; 12:5357-69. [PMID: 23991618 DOI: 10.1021/pr4007365] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Pseudomonas aeruginosa is the predominant cause of mortality in patients with cystic fibrosis (CF). We examined the secretome of an acute, transmissible CF P. aeruginosa (Australian epidemic strain 1-R; AES-1R) compared with laboratory-adapted PAO1. Culture supernatant proteins from rich (LB) and minimal (M9) media were compared using 2-DE and 2DLC-MS/MS, which revealed elevated abundance of PasP protease and absence of AprA protease in AES-1R. CF lung-like artificial sputum medium (ASMDM) contains serum and mucin that generally preclude proteomics of secreted proteins. ASMDM culture supernatants were subjected to 2DLC-MS/MS, which allowed the identification of 57 P. aeruginosa proteins, and qualitative spectral counting was used to estimate relative abundance. AES-1R-specific AES_7139 and PasP were more abundant in AES-1R ASMDM culture supernatants, while AprA could only be identified in PAO1. Relative quantitation was performed using selected reaction monitoring. Significantly elevated levels of PasP, LasB, chitin-binding protein (CbpD), and PA4495 were identified in AES-1R ASMDM supernatants. Quantitative PCR showed elevated pasP in AES-1R during early (18 h) ASMDM growth, while no evidence of aprA expression could be observed. Genomic screening of CF isolates revealed aes_7139 was present in all AES-1 and one pair of sequential nonepidemic isolates. Secreted proteins may be crucial in aiding CF-associated P. aeruginosa to establish infection and for adaptation to the CF lung.
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Affiliation(s)
- Nichollas E Scott
- School of Molecular Bioscience, The University of Sydney , Building GO8, Maze Crescent, Sydney, New South Wales 2006, Australia
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Syrmis MW, Moser RJ, Kidd TJ, Hunt P, Ramsay KA, Bell SC, Wainwright CE, Grimwood K, Nissen MD, Sloots TP, Whiley DM. High-throughput single-nucleotide polymorphism-based typing of shared Pseudomonas aeruginosa strains in cystic fibrosis patients using the Sequenom iPLEX platform. J Med Microbiol 2013; 62:734-740. [PMID: 23412772 DOI: 10.1099/jmm.0.055905-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Shared strains of Pseudomonas aeruginosa are now well recognized in people with cystic fibrosis (CF), and suitable P. aeruginosa laboratory typing tools are pivotal to understanding their clinical significance and guiding infection control policies in CF clinics. We therefore compared a single-nucleotide polymorphism (SNP)-based typing method using Sequenom iPLEX matrix-assisted laser desorption ionization with time-of-flight mass spectrometry (MALDI-TOF MS) with typing methods used routinely by our laboratory. We analysed 617 P. aeruginosa isolates that included 561 isolates from CF patients collected between 2001 and 2009 in two Brisbane CF clinics and typed previously by enterobacterial repetitive intergenic consensus (ERIC)-PCR, as well as 56 isolates from non-CF patients analysed previously by multilocus sequence typing (MLST). The isolates were tested using a P. aeruginosa Sequenom iPLEX MALDI-TOF (PA iPLEX) method comprising two multiplex reactions, a 13-plex and an 8-plex, to characterize 20 SNPs from the P. aeruginosa housekeeping genes acsA, aroE, guaA, mutL, nuoD, ppsA and trpE. These 20 SNPs were employed previously in a real-time format involving 20 separate assays in our laboratory. The SNP analysis revealed 121 different SNP profiles for the 561 CF isolates. Overall, there was at least 96% agreement between the ERIC-PCR and SNP analyses for all predominant shared strains among patients attending our CF clinics: AUST-01, AUST-02 and AUST-06. For the less frequently encountered shared strain AUST-07, 6/25 (24%) ERIC-PCR profiles were misidentified initially as AUST-02 or as unique, illustrating the difficulty of gel-based analyses. SNP results for the 56 non-CF isolates were consistent with previous MLST data. Thus, the PA iPLEX format provides an attractive high-throughput alternative to ERIC-PCR for large-scale investigations of shared P. aeruginosa strains.
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Affiliation(s)
- Melanie W Syrmis
- Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Paediatric Infectious Diseases Laboratory, Royal Children's Hospital, Brisbane, Queensland, Australia
| | - Ralf J Moser
- Sequenom Inc., Sequenom Asia Pacific, Herston, Queensland, Australia
| | - Timothy J Kidd
- Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Paediatric Infectious Diseases Laboratory, Royal Children's Hospital, Brisbane, Queensland, Australia
| | - Priscilla Hunt
- Sequenom Inc., Sequenom Asia Pacific, Herston, Queensland, Australia
| | - Kay A Ramsay
- Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Paediatric Infectious Diseases Laboratory, Royal Children's Hospital, Brisbane, Queensland, Australia
| | - Scott C Bell
- Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Queensland, Australia.,Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Brisbane, Queensland, Australia
| | - Claire E Wainwright
- Queensland Children's Respiratory Centre, Royal Children's Hospital, Brisbane, Australia.,Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Brisbane, Queensland, Australia
| | - Keith Grimwood
- Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Paediatric Infectious Diseases Laboratory, Royal Children's Hospital, Brisbane, Queensland, Australia
| | - Michael D Nissen
- Microbiology Division, Pathology Queensland Central Laboratory, Herston, Queensland, Australia.,Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Paediatric Infectious Diseases Laboratory, Royal Children's Hospital, Brisbane, Queensland, Australia
| | - Theo P Sloots
- Microbiology Division, Pathology Queensland Central Laboratory, Herston, Queensland, Australia.,Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Paediatric Infectious Diseases Laboratory, Royal Children's Hospital, Brisbane, Queensland, Australia
| | - David M Whiley
- Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Paediatric Infectious Diseases Laboratory, Royal Children's Hospital, Brisbane, Queensland, Australia
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Ashish A, Shaw M, Winstanley C, Humphreys L, Walshaw MJ. Halting the spread of epidemic pseudomonas aeruginosa in an adult cystic fibrosis centre: a prospective cohort study. JRSM SHORT REPORTS 2013; 4:1. [PMID: 23413403 PMCID: PMC3572656 DOI: 10.1258/shorts.2012.012018] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Objectives To assess if cohort segregation policies are effective in preventing cross-infection in cystic fibrosis (CF) clinics. Design A prospective cohort study. Setting A large adult CF centre in Northwest England. Participants All CF patients cared for at the Liverpool adult CF centre 2003–2009. Methods Regular sputum sampling with genotyping of pseudomonas aeruginosa (Psa) isolates led to a policy of inpatient and outpatient segregation by microbiological group. Main outcome measures Prevalence and cross-infection/super-infection rates of a transmissible Psa strain, i.e. the Liverpool epidemic strain (LES) in adult CF patients at the Liverpool adult CF centre from 2003 to 2009. Results There was a decline in the proportion of patients with LES (71–53%) and an increase in those with unique strains (23–31%) and without Psa infection (6–17%) from 2003 to 2009. There were two cases of LES super-infection and one case of new chronic Psa infection (with a unique strain). There were no cases of transmissible strain infection in patients previously uninfected by Psa. Conclusions Our segregation policy has halted the spread of the commonest highly transmissible strain in the UK (LES) in our clinic, without endangering patients who were not previously infected with Psa. It confirms that if genotypic surveillance is used, it is unnecessary to segregate patients infected with unique strains from those without Psa infection.
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Affiliation(s)
- Abdul Ashish
- Liverpool Heart and Chest Hospital , Liverpool L14 3PE , UK
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Molecular epidemiological surveillance of multidrug-resistant Pseudomonas aeruginosa isolates in a pediatric population of patients with cystic fibrosis and determination of risk factors for infection with the Houston-1 strain. J Clin Microbiol 2013; 51:1237-40. [PMID: 23303498 DOI: 10.1128/jcm.02157-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multiyear molecular epidemiological surveillance of multidrug-resistant Pseudomonas aeruginosa (MRPA) in a pediatric cystic fibrosis care center identified an endemic MRPA strain (Houston-1). Recent hospitalization was found to be a statistically significant risk factor for acquisition of the endemic strain. Multiple infection control improvements led to the reduced incidence of the Houston-1 strain in the CF population.
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Infection control in cystic fibrosis: barriers to implementation and ideas for improvement. Curr Opin Pulm Med 2012; 15:626-31. [PMID: 19644375 DOI: 10.1097/mcp.0b013e328330d974] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW This review will focus on recent research documenting baseline adherence to infection control recommendations and barriers to their implementation as experienced by multidisciplinary cystic fibrosis (CF) care providers. In addition, controversies regarding optimal infection control will be discussed. Finally, suggestions to improve infection control in CF will be proposed. RECENT FINDINGS Compliance with recent guidelines was assessed for clinical microbiology laboratories and for infection control policies at CF care centers in the United States. Unlike earlier reports, the vast majority of laboratories used selective media for Burkholderia cepacia complex and identified all species of nonlactose fermenting Gram-negative bacilli. Fewer used selective media for Staphylococcus aureus or used agar-based susceptibility testing assays for Pseudomonas aeruginosa. Only 103 (65%) of 158 CF care centers provided written infection control policies for review and these were more likely to address inpatient than outpatient settings. Surveys of healthcare professionals showed that access to a copy of the CF infection control guidelines reduced barriers to adherence to selected infection control practices. SUMMARY These data suggest that access to national infection control guidelines and written local policies are critically important to improving infection control for CF.
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Conway SP, Lee TW. Prevention of chronic Pseudomonas aeruginosa infection in people with cystic fibrosis. Expert Rev Respir Med 2012; 3:349-61. [PMID: 20477327 DOI: 10.1586/ers.09.26] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cystic fibrosis is the most common genetically inherited disease in the Caucasian population, with approximately 30,000 patients in the USA and more than 50,000 patients worldwide. The primary defect in the cystic fibrosis transmembrane regulator gene affects the production and/or function of the cystic fibrosis transmembrane regulator protein. Depending on the severity of the genetic defect, patients may have minimal disease expression (e.g., male infertility) or multisystem involvement, including recurrent respiratory infection progressing to respiratory failure, hepatobiliary disease, exocrine pancreatic insufficiency, diabetes mellitus and gastrointestinal tract motility problems. Pseudomonas aeruginosa is commonly isolated from the lower respiratory tract in early childhood. Chronic infection is associated with increased morbidity and mortality. P. aeruginosa infection may be acquired from the environment or by person-to-person contact. Clinicians should adopt a proactive protocol to prevent chronic infection. The cornerstones of such a policy are microbiological surveillance, infection control and antibiotic-based eradication regimens.
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Affiliation(s)
- Steven P Conway
- CF Services, Leeds Regional Paediatric Cystic Fibrosis Centre, Childrens' Day Hospital, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK.
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Keating D, Crowe MJ, Kennedy B, Salmon A, Britton D, Gallagher CG, McKone EF, Schaffer K. Molecular detection of an atypical, highly resistant, clonal Pseudomonas aeruginosa isolate in cystic fibrosis patients. J Cyst Fibros 2012; 12:141-6. [PMID: 22902869 DOI: 10.1016/j.jcf.2012.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 07/19/2012] [Accepted: 07/20/2012] [Indexed: 10/28/2022]
Abstract
BACKGROUND The identification of Pseudomonas aeruginosa (P. aeruginosa) isolates in sputum from cystic fibrosis (CF) patients can be challenging due to the multitude of phenotypic changes isolates undergo during adaptation to the microenvironment of the CF lung. METHODS We report the occurrence of shared P. aeruginosa isolates which failed identification by phenotypic methodologies and required species specific polymerase chain reaction. P. aeruginosa isolates were genotyped by macrorestriction analysis. RESULTS Analysis of atypical isolates revealed one clonal P. aeruginosa isolate and three smaller clusters. In contrast molecular typing of phenotypically characteristic P. aeruginosa isolates revealed only small clusters. Despite exhibiting higher levels of antimicrobial resistance, acquisition of atypical strains was not associated with significant changes in clinical decline. CONCLUSIONS Our experience highlights the importance of accurate identification of bacterial isolates in CF lung disease to detect clonal spread of atypical isolates.
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Affiliation(s)
- Deirdre Keating
- Department of Medical Microbiology, St. Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - Mary J Crowe
- Department of Medical Microbiology, St. Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - Barry Kennedy
- Department of Respiratory Medicine, St. Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - Abigail Salmon
- Department of Medical Microbiology, St. Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - David Britton
- Department of Medical Microbiology, St. Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - Charles G Gallagher
- Department of Respiratory Medicine, St. Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - Edward F McKone
- Department of Respiratory Medicine, St. Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - Kirsten Schaffer
- Department of Medical Microbiology, St. Vincent's University Hospital, Elm Park, Dublin 4, Ireland.
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Waters V, Zlosnik JEA, Yau YCW, Speert DP, Aaron SD, Guttman DS. Comparison of three typing methods for Pseudomonas aeruginosa isolates from patients with cystic fibrosis. Eur J Clin Microbiol Infect Dis 2012; 31:3341-50. [PMID: 22843295 DOI: 10.1007/s10096-012-1701-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 07/10/2012] [Indexed: 10/28/2022]
Abstract
The aim of this study was to compare two traditional pattern matching techniques, pulsed-field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD), with the more reproducible technique of multilocus sequence typing (MLST) to genotype a blinded sample of Pseudomonas aeruginosa isolates from cystic fibrosis (CF) patients. A blinded sample of 48 well-characterized CF P. aeruginosa isolates was genotyped by PFGE, RAPD, and MLST, each performed in a different laboratory. The discriminatory power and congruence between the methods were compared using the Simpson's index, Rand index, and Wallace coefficient. PFGE and MLST had the greatest congruence with the highest Rand index (0.697). The discriminatory power of PFGE, RAPD, and MLST were comparable, with high Simpson's indices (range 0.973-0.980). MLST identified the most clonal relationships. When clonality was defined as agreement between two or more methods, MLST had the greatest predictive value (100 %) in labeling strains as unique, while PFGE had the greatest predictive value (96 %) in labeling strains as clonal. This study demonstrated the highest level of agreement between PFGE and MLST in genotyping P. aeruginosa isolates from CF patients. MLST had the greatest predictive value in identifying strains as unique and, thus, has the potential to be a cost-efficient, high-throughput, first-pass typing method.
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Affiliation(s)
- V Waters
- Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, 555 University Avenue, Toronto, Ontario, M5G 1X8, Canada.
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Hu H, Harmer C, Anuj S, Wainwright CE, Manos J, Cheney J, Harbour C, Zablotska I, Turnbull L, Whitchurch CB, Grimwood K, Rose B. Type 3 secretion system effector genotype and secretion phenotype of longitudinally collected Pseudomonas aeruginosa isolates from young children diagnosed with cystic fibrosis following newborn screening. Clin Microbiol Infect 2012; 19:266-72. [PMID: 22329595 DOI: 10.1111/j.1469-0691.2012.03770.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Studies of the type 3 secretion system (T3SS) in Pseudomonas aeruginosa isolates from chronically infected older children and adults with cystic fibrosis (CF) show a predominantly exoS+/exoU- (exoS+) genotype and loss of T3SS effector secretion over time. Relatively little is known about the role of the T3SS in the pathogenesis of early P. aeruginosa infection in the CF airway. In this longitudinal study, 168 P. aeruginosa isolates from 58 children diagnosed with CF following newborn screening and 47 isolates from homes of families with or without children with CF were genotyped by pulsed-field gel electrophoresis (PFGE) and T3SS genotype and phenotype determined using multiplex PCR and western blotting. Associations were sought between T3SS data and clinical variables and comparisons made between T3SS data of clinical and environmental PFGE genotypes. Seventy-seven of the 92 clinical strains were exoS+ (71% secretors (ExoS+)) and 15 were exoU+ (93% secretors (ExoU+)). Initial exoS+ strains were five times more likely to secrete ExoS than subsequent exoS+ strains at first isolation. The proportion of ExoS+ strains declined with increasing age at acquisition. No associations were found between T3SS characteristics and gender, site of isolation, exacerbation, a persistent strain or pulmonary outcomes. Fourteen of the 23 environmental strains were exoS+ (79% ExoS+) and nine were exoU+ (33% ExoU+). The exoU+ environmental strains were significantly less likely to secrete ExoU than clinical strains. This study provides new insight into the T3SS characteristics of P. aeruginosa isolated from the CF airway early in life.
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Affiliation(s)
- H Hu
- Department of Infectious Diseases and Immunology, Central Clinical School, University of Sydney, NSW 2006, Australia
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Hare NJ, Solis N, Harmer C, Marzook NB, Rose B, Harbour C, Crossett B, Manos J, Cordwell SJ. Proteomic profiling of Pseudomonas aeruginosa AES-1R, PAO1 and PA14 reveals potential virulence determinants associated with a transmissible cystic fibrosis-associated strain. BMC Microbiol 2012; 12:16. [PMID: 22264352 PMCID: PMC3398322 DOI: 10.1186/1471-2180-12-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 01/22/2012] [Indexed: 11/15/2022] Open
Abstract
Background Pseudomonas aeruginosa is an opportunistic pathogen that is the major cause of morbidity and mortality in patients with cystic fibrosis (CF). While most CF patients are thought to acquire P. aeruginosa from the environment, person-person transmissible strains have been identified in CF clinics worldwide. The molecular basis for transmissibility and colonization of the CF lung remains poorly understood. Results A dual proteomics approach consisting of gel-based and gel-free comparisons were undertaken to analyse protein profiles in a transmissible, early (acute) isolate of the Australian epidemic strain 1 (AES-1R), the virulent burns/wound isolate PA14, and the poorly virulent, laboratory-associated strain PAO1. Over 1700 P. aeruginosa proteins were confidently identified. AES-1R protein profiles revealed elevated abundance of proteins associated with virulence and siderophore biosynthesis and acquisition, antibiotic resistance and lipopolysaccharide and fatty acid biosynthesis. The most abundant protein in AES-1R was confirmed as a previously hypothetical protein with sequence similarity to carbohydrate-binding proteins and database search revealed this gene is only found in the CF-associated strain PA2192. The link with CF infection may suggest that transmissible strains have acquired an ability to rapidly interact with host mucosal glycoproteins. Conclusions Our data suggest that AES-1R expresses higher levels of proteins, such as those involved in antibiotic resistance, iron acquisition and virulence that may provide a competitive advantage during early infection in the CF lung. Identification of novel proteins associated with transmissibility and acute infection may aid in deciphering new strategies for intervention to limit P. aeruginosa infections in CF patients.
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Affiliation(s)
- Nathan J Hare
- School of Molecular Bioscience, The University of Sydney, Sydney 2006, Australia
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42
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Lee JY, Ko KS. Antimicrobial Resistance and Clones ofAcinetobacterSpecies andPseudomonas aeruginosa. ACTA ACUST UNITED AC 2012. [DOI: 10.4167/jbv.2012.42.1.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Ji-Young Lee
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Kwan Soo Ko
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
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43
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Hare NJ, Soe CZ, Rose B, Harbour C, Codd R, Manos J, Cordwell SJ. Proteomics of Pseudomonas aeruginosa Australian Epidemic Strain 1 (AES-1) Cultured under Conditions Mimicking the Cystic Fibrosis Lung Reveals Increased Iron Acquisition via the Siderophore Pyochelin. J Proteome Res 2011; 11:776-95. [DOI: 10.1021/pr200659h] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Nathan J. Hare
- School of Molecular Bioscience, The University of Sydney, 2006 Australia
| | | | | | | | | | | | - Stuart J. Cordwell
- School of Molecular Bioscience, The University of Sydney, 2006 Australia
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Ashish A, Shaw M, Winstanley C, Ledson MJ, Walshaw MJ. Increasing resistance of the Liverpool Epidemic Strain (LES) of Pseudomonas aeruginosa (Psa) to antibiotics in cystic fibrosis (CF)--a cause for concern? J Cyst Fibros 2011; 11:173-9. [PMID: 22146482 DOI: 10.1016/j.jcf.2011.11.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 11/10/2011] [Accepted: 11/14/2011] [Indexed: 12/01/2022]
Abstract
BACKGROUND Transmissible Pseudomonas aeruginosa (Psa) strains such as the Liverpool Epidemic Strain (LES) are now widespread throughout UK CF clinics: their susceptibility to antibiotics is therefore important. To study this, we compared antibiogram patterns of Psa strains in our CF clinic over 5 years, looking at differences in resistance patterns between strains and changes to these over time. METHODS The antibiograms of sputum samples between 2004 and 2008 from patients attending our centre were included. We compared Psa isolate antibiotic resistance (to six anti-pseudomonal antibiotics) patterns for patients infected with LES with those infected with other Psa strains, both in the total population in 2004 (125 patients) and 2008 (166 patients) and also longitudinally from annual review samples 2004 to 2008 in matched and unmatched patient groups. RESULTS LES exhibited significantly more resistant isolates in 2004 (p<0.0001). There was an increase in antibiotic resistance in both LES and other Psa strains over time (p<0.001). Cox proportional hazards analysis of both unmatched (n=125) and matched (n=56) patients in 2004 revealed that LES infected patients were more likely to develop antibiotic resistant isolates over time (hazard ratio 8.1, p<0.001). Fewer LES isolates were classed as fully sensitive in both matched and unmatched groups at the end of study period (p<0.001). CONCLUSION This study shows a worrying trend in antibiotic resistance in the Psa isolates amongst patients chronically infected with LES. This highlights the need to prevent cross infection through segregation and also the need to develop new strategies to treat these organisms.
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Affiliation(s)
- Abdul Ashish
- Liverpool Heart and Chest Hospital, Thomas Drive, Liverpool L14 3PE, United Kingdom
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45
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Logan C, Habington A, Lennon G, Grogan J, Byrne M, O'Leary J, O'Sullivan N. Genetic relatedness of Pseudomonas aeruginosa isolates among a paediatric cystic fibrosis patient cohort in Ireland. J Med Microbiol 2011; 61:64-70. [PMID: 21921114 DOI: 10.1099/jmm.0.035642-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosa is one of the primary pathogens in the cystic fibrosis (CF) lung and a significant cause of morbidity and mortality. Reports of the spread of epidemic or transmissible strains of P. aeruginosa within and across CF centres in Europe have raised concern regarding the possibility of clonal spread among and within CF centres in Ireland. P. aeruginosa isolates (313 isolates from 142 sputum samples and 53 throat swabs) from 68 CF patients were examined using PFGE to explore the diversity of P. aeruginosa isolates among CF patients in a Dublin paediatric hospital. Only 57 different P. aeruginosa genotypes were identified among the 313 isolates. Forty-three of the genotypes were observed only in individual patients (distinct genotypes) while 13 cluster strains (present in two to four patients) were observed. Typing of P. aeruginosa isolates identified one indistinguishable clonal isolate of P. aeruginosa present in 13 CF patients (13/68; 19.1 %) which displayed higher levels of antibiotic resistance than those displayed by P. aeruginosa isolates of distinct genotype.
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Affiliation(s)
- Catriona Logan
- Department of Microbiology, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Adele Habington
- Department of Microbiology, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Gráinne Lennon
- Department of Microbiology, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Juanita Grogan
- Department of Microbiology, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Margaret Byrne
- Department of Microbiology, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - John O'Leary
- Trinity College Dublin, Dublin, Ireland.,Department of Pathology, Coombe Women and Infants University Hospital, Dublin, Ireland
| | - Niamh O'Sullivan
- Department of Pathology, Coombe Women and Infants University Hospital, Dublin, Ireland.,Department of Microbiology, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
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Mowat E, Paterson S, Fothergill JL, Wright EA, Ledson MJ, Walshaw MJ, Brockhurst MA, Winstanley C. Pseudomonas aeruginosaPopulation Diversity and Turnover in Cystic Fibrosis Chronic Infections. Am J Respir Crit Care Med 2011; 183:1674-9. [DOI: 10.1164/rccm.201009-1430oc] [Citation(s) in RCA: 201] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Kidd TJ, Gibson JS, Moss S, Greer RM, Cobbold RN, Wright JD, Ramsay KA, Grimwood K, Bell SC. Clonal complex Pseudomonas aeruginosa in horses. Vet Microbiol 2011; 149:508-12. [DOI: 10.1016/j.vetmic.2010.11.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 11/18/2010] [Accepted: 11/23/2010] [Indexed: 10/18/2022]
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de Vrankrijker A, Brimicombe R, Wolfs T, Heijerman H, van Mansfeld R, van Berkhout F, Willems R, Bonten M, Ent CKVD. Clinical impact of a highly prevalent Pseudomonas aeruginosa clone in Dutch cystic fibrosis patients. Clin Microbiol Infect 2011; 17:382-5. [DOI: 10.1111/j.1469-0691.2010.03295.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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49
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Anuj SN, Whiley DM, Kidd TJ, Ramsay KA, Bell SC, Syrmis MW, Grimwood K, Wainwright CE, Nissen MD, Sloots TP. Rapid single-nucleotide polymorphism-based identification of clonal Pseudomonas aeruginosa isolates from patients with cystic fibrosis by the use of real-time PCR and high-resolution melting curve analysis. Clin Microbiol Infect 2011; 17:1403-8. [PMID: 21129101 DOI: 10.1111/j.1469-0691.2010.03439.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pseudomonas aeruginosa genotyping relies mainly upon DNA fingerprinting methods, which can be subjective, expensive and time-consuming. The detection of at least three different clonal P. aeruginosa strains in patients attending two cystic fibrosis (CF) centres in a single Australian city prompted the design of a non-gel-based PCR method to enable clinical microbiology laboratories to readily identify these clonal strains. We designed a detection method utilizing heat-denatured P. aeruginosa isolates and a ten-single-nucleotide polymorphism (SNP) profile. Strain differences were detected by SYBR Green-based real-time PCR and high-resolution melting curve analysis (HRM10SNP assay). Overall, 106 P. aeruginosa sputum isolates collected from 74 patients with CF, as well as five reference strains, were analysed with the HRM10SNP assay, and the results were compared with those obtained by pulsed-field gel electrophoresis (PFGE). The HRM10SNP assay accurately identified all 45 isolates as members of one of the three major clonal strains characterized by PFGE in two Brisbane CF centres (Australian epidemic strain-1, Australian epidemic strain-2 and P42) from 61 other P. aeruginosa strains from Australian CF patients and two representative overseas epidemic strain isolates. The HRM10SNP method is simple, is relatively inexpensive and can be completed in <3 h. In our setting, it could be made easily available for clinical microbiology laboratories to screen for local P. aeruginosa strains and to guide infection control policies. Further studies are needed to determine whether the HRM10SNP assay can also be modified to detect additional clonal strains that are prevalent in other CF centres.
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Affiliation(s)
- S N Anuj
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Qld, Australia.
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Hauser AR, Jain M, Bar-Meir M, McColley SA. Clinical significance of microbial infection and adaptation in cystic fibrosis. Clin Microbiol Rev 2011; 24:29-70. [PMID: 21233507 PMCID: PMC3021203 DOI: 10.1128/cmr.00036-10] [Citation(s) in RCA: 287] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A select group of microorganisms inhabit the airways of individuals with cystic fibrosis. Once established within the pulmonary environment in these patients, many of these microbes adapt by altering aspects of their structure and physiology. Some of these microbes and adaptations are associated with more rapid deterioration in lung function and overall clinical status, whereas others appear to have little effect. Here we review current evidence supporting or refuting a role for the different microbes and their adaptations in contributing to poor clinical outcomes in cystic fibrosis.
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Affiliation(s)
- Alan R Hauser
- Department of Microbiology/Immunology, Northwestern University, 303 E. Chicago Ave., Searle 6-495, Chicago, IL 60611, USA.
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