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• W76119950 abstract "Background and Aims: Pseudomonas aeruginosa is an adaptable environmental organism capable of causing opportunistic infections in humans and animals. It is the most important cause of endobronchial infection amongst persons with cystic fibrosis (CF) and a major determinant of morbidity and mortality. Accurate diagnosis and epidemiological surveillance are important strategies for the clinical management of CF patients worldwide. Improving the understanding of acquisition pathways and population biology also represent important elements for defining the ecological behaviour and epidemiology of infectious diseases. In keeping with these approaches the research described in this thesis was based on three broad aims: (i) to improve the identification and genotypic characterisation of P. aeruginosa within clinical microbiology laboratories; (ii) to improve the understanding of epidemiology and transmission of P. aeruginosa infection; (iii) to determine the population structure, biodiversity and evolutionary dynamics of P. aeruginosa. Methods:i) Rates of P. aeruginosa misidentification: P. aeruginosa-specific PCR was used to determine if 2267 P. aeruginosa isolates from 561 CF patients were correctly identified by 17 clinical laboratories. Misidentified isolates underwent phenotypic tests, amplified rDNA restriction analysis and partial 16S rRNA gene sequence analysis. Participating laboratories were also surveyed on how they identified P. aeruginosa from CF sputum. ii) Comparison of P. aeruginosa strain typing methods: The discriminatory power and concordance of enterobacterial repetitive intergenic consensus (ERIC)-PCR, pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) among 104 CF sputum and control isolates was determined. PFGE and MLST were also performed on 30 paired isolates collected up to 354 days apart to assess within host evolution. iii) Molecular epidemiology of P. aeruginosa within Australian cystic fibrosis centres: A cross-sectional prevalence study involving 983 CF patients and 18 Australian CF centres was undertaken. P. aeruginosa isolates (n=2887) were genotyped using ERIC-PCR. MLST was used to confirm the typing results. Demographic and clinical details for each patient were also recorded. iv) Molecular epidemiology of P. aeruginosa in horses: This study sought to determine the genotypic relatedness between genital equine P. aeruginosa isolates collected from a limited geographical region. ERIC-PCR typing was performed on 93 isolates collected between 2005 and 2009 from 2058 thoroughbred horses at 66 studs. MLST was used to confirm the most frequently encountered strains. v) Biodiversity, population structure and evolution of P. aeruginosa: MLST was used to determine the population structure and genotype of 501 isolates derived from a broad range of temporally and spatially related habitats. Evolutionary patterns of descent were determined by eBURST, the population recombination rate was estimated using a composite likelihood method, and molecular events giving rise to single- and double-locus variants within clonal complexes were used to determine the contribution of recombination to recent clonal divergence. Results:Ninety-eight percent of isolates from 95% of patients were correctly identified as P. aeruginosa. Achromobacter xylosoxidans, Stenotrophomonas maltophilia, and Inquilinus limosus were most commonly misidentified as P. aeruginosa. Interestingly, 12 (40%) patients had previously grown the misidentified species in their sputum (Chapter 2). ERIC-PCR, PFGE and MLST all displayed high levels of concordance, however lower discrimination was seen with ERIC-PCR. Fifty ERIC-PCR types yielded 54 PFGE types and 59 sequence types. MLST also proved useful for detecting novel and known strains, and for inferring relatedness amongst unique PFGE types. Forty-seven percent of the paired isolates produced PFGE patterns that differed by one to five bands, whereas with MLST all paired isolates remained identical (Chapter 3). Thirty-eight percent of Australian CF patients harboured unique P. aeruginosa strains, while 62% were infected with one or more shared strain. The most common shared strains, AUST-01 and AUST-02, were detected in most CF centres and 40% of Australian patients. Analysis of clinical data suggested infection with AUST-01, AUST-02 and AUST-06 was associated with greater treatment burden (Chapter 4). While P. aeruginosa was not detected in thoroughbred stallions, 53/93 (57%) mares harboured shared strains, which included a single dominant genotype detected in 42 (45%) mares from 13 horse studs (Chapter 5). Biodiversity analyses revealed limited association between genotype and ecological setting. Fifty-three (19%) strains were detected in multiple habitats, and 31% of CF strains were present in other clinical groups, animals, or the environment. However, highly prevalent CF strains were restricted only to patients with CF. Population analysis indicated a non-clonal epidemic population structure and marked evidence of recombination was observed across all sequences over time and within recently diverged alleles (Chapter 6). Conclusions: This thesis describes low rates of P. aeruginosa misidentification amongst a broad cross-section of CF patients. MLST also represented a categorical tool with a resolving power similar to PFGE for typing. MLST is particularly suited for long-term clinical monitoring and detecting novel strains. Shared strains of P. aeruginosa were common throughout Australia. Although most shared CF strains appeared in small clusters and few CF centres, highly prevalent genotypes were broadly disseminated suggesting widespread cross-infection. Isolates collected from thoroughbred horses also showed a high proportion shared genotypes. However, the present study failed to demonstrate any evidence of venereal transmission thus indicating other acquisition mechanisms. Finally, population analyses confirmed a non-clonal epidemic population and limited association between genotype and ecological setting. Consequently, environmental exposure is a likely source of acquisition for many CF patients. However, highly prevalent CF shared strains were restricted only to patients with CF suggesting person-to-person transmission and/or host specificity." @default.
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• W76119950 date "2012-01-01" @default.
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• W76119950 title "Diagnosis, epidemiology and population structure of Pseudomonas aeruginosa in cystic fibrosis" @default.
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