Browsing by Author "Surette, Michael"
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- ItemOpen AccessThe Cystic Fibrosis Microbiome and its Association with Incident Infections with Mycobacteroides (Mycobacterium) abscessus(2021-05-13) Bharadwaj, Lalit; Parkins, Michael; Storey, Douglas; Arrieta, Marie-Claire; Surette, MichaelInfection with M. abscessus complex (MABC) is increasingly detected within CF populations. MABC infection has been associated with exaggerated lung function decline and poses significant treatment complexities. We performed a retrospective case-control study of twenty-one patients with MABC infection matching each to two randomly identified age (+/-2 yrs) and gender-matched uninfected controls. Total genomic DNA from sputum was extracted, amplified and Illumina MiSeq paired-end sequencing of the hypervariable V3 region of the 16S rRNA gene was performed. Demographics and dynamic variables of disease were recorded and compared between groups. 174 sputum samples (median 8, IQR (6-12)) from MABC cases and 42 control samples were assessed. The sputum microbiota from patients who would develop MABC infection in the subsequent two years differed from controls (p=0.038, R2 = 2.5%, PERMANOVA). In particular, sputum from MABC cases – prior to its identification – had higher alpha-diversity; Shannon diversity (p=0.023), Observed species (p=0.042) and lower P. aeruginosa relative and absolute abundance (p=0.035). We observed significant changes in community structure over time during potent antibacterial therapies, returning to baseline upon their discontinuation. These data suggest that sputum microbiome analysis and P. aeruginosa bioburden should be evaluated in multi-center studies as potential biomarkers to predict MABC infection and treatment response.
- ItemOpen AccessGenetic interactions in the development of spatial patterns in bacteria(2007) Davidson, Carla Jean; Surette, Michael; Prusinkiewicz, Przemyslaw
- ItemOpen AccessPhenotypic and Genotypic Characterization of the Streptococci Isolated from Sputum of Adult Cystic Fibrosis Patients(2013-08-27) Thornton, Christina; Surette, Michael; Storey, DouglasThe cystic fibrosis (CF) lung microbiome is a complex polymicrobial community with numerous organisms involved in disease progression. The non-pyogenic streptococci, such as the Streptococcus milleri group, have been implicated in CF disease progression and pathogenesis, but other members are less understood as there has been limited study. The objectives of this study were to characterize a collection of diverse non-pyogenic streptococci and investigate their pathogenic potential and interactions with principal CF pathogens. Genotypic analysis fully characterized 100 unique isolates from CF sputum that did not identify with known species of streptococci by partial 16S rRNA sequencing. To examine these unique isolates, I did extensive genotypic characterization with cpn60, sodA, rpoB and ddl in addition to full 16S rRNA sequencing. 48 isolates identified as novel streptococci isolates, of which 20 of the novel presented with divergent multiple 16S rRNA gene sequences. Phenotypic characterization was expanded to a larger collection of 297 non-pyogenic streptococci isolates with profiling done by several assays. I observed poor correlation between genotypic methods and there was high phenotypic heterogeneity, particularly with regards to increased β-hemolysis under anaerobic condition on human blood as compared to standard conditions. Due to chronic antibiotic use by CF patients, the assessment of the streptococci antibiotic resistome from 459 isolates was done against nine antibiotics relevant in CF treatment. High antibiotic resistance was observed against the macrolides azithromycin (56.4%) and erythromycin (51.6%). Investigation of the molecular mechanisms of macrolide resistance yielded an unexpected result in that nearly half the isolates were found to have point mutations at position 2058 or 2059 of the 23S ribosomal subunit, an uncommon molecular mechanism of resistance within the streptococci. The synergistic interactions of the oropharyngeal flora (OF) with P. aeruginosa were investigated with the construction of transposon mutant libraries in two of the synergen isolates. Mutants were obtained that displayed attenuation or up-regulation of these synergistic interactions and will be used for further study and identification. The work presented here provides the framework to elucidate the role of the diverse streptococci in CF disease progression.
- ItemOpen AccessSIMULATION AND VISUALIZATION OF GENETIC REGULATORY NETWORKS(2001-12-18) Baker, Charles; Carpendale, Sheelagh; Surette, MichaelGene regulation networks are a significant biological research area. Simulations and visualizations of genetic processes are being created as biologists grapple with the vast amounts of new genetic information. We present a genetic network simulation environment that visualizes protein-gene interactions and concentrations as they occur during the simulation. In addition, the layout of this genetic simulation can be changed into a visualization of a conceptual model of the simulated genetic network. The visual simulation and network visualization are integrated by animating the change between the simulation view and the visualization view. The flagella system of Escherichia coli has been used to verify the results of this tool and to provide a working model. This particle-based real-time visual simulations of genetic networks allows for virtual experimentation using similar methodologies of live experiments.
- ItemOpen AccessStudying Infection Transmission Dynamics Amongst Individuals with Cystic Fibrosis(2023-11-27) Izydorczyk, Conrad; Parkins, Michael; Church, Deirdre; Pillai, Dylan; Wasmuth, James; Surette, MichaelCystic fibrosis (CF) impairs the natural immune defenses of the lungs and leaves affected individuals susceptible to incident and chronic lung infections by a variety of microbial pathogens. The potential for patient-to-patient transmission of lung infections between persons with CF (pwCF) was first realized in the 1980's with incident infections caused by members of the Burkholderia cepacia complex, followed in the 1990’s by the recognition of epidemic strains of the archetypal CF pathogen, Pseudomonas aeruginosa. To mitigate this risk, progressively stringent infection prevention and control (IPC) guidelines have been implemented to prevent further spread amongst pwCF. However, few longitudinal studies assessing the potential for transmission of CF pathogens have been performed. Accordingly, the primary objective of this thesis was to investigate the natural history and potential for transmission of four key CF pathogens amongst pwCF attending the Southern Alberta Adult CF Clinic (SAACFC) in Calgary, Canada between 2002-2020: Escherichia coli, Haemophilus influenzae, Stenotrophomonas maltophilia, and P. aeruginosa. Whole-genome sequencing +/- pulse field gel electrophoresis were utilized for investigating infection transmission to achieve maximal resolution. A wide variety of genomic approaches were investigated for the inference of patient-to-patient transmission from genomic data, including several measures of genetic relatedness, phylogenetics, and pangenome analyses. These were combined with investigations of epidemiological linkages between pwCF to identify potential transmission opportunities. While a high degree of strain sharing was observed for all examined species, healthcare associated patient-to-patient transmission was rare through two decades. No instances of potential transmission were observed between 2002-2020 for E. coli, H. influenzae, or S. maltophilia, while infrequent transmission was postulated for P. aeruginosa. However, evidence of widespread historical transmission of epidemic P. aeruginosa strains was observed prior to patients entering the SAACFC. These findings corroborate the paradigm that most lung infections in pwCF in the current era of rigorous IPC mandates are acquired by independent acquisition events from independent environmental sources. Overall, the findings of this thesis contribute not only to CF and infection control literature, but also to the application of whole-genome sequencing to the study of infection transmission.
- ItemOpen AccessThe Design and Application of a Molecular Profiling Strategy to Identify Polymicrobial Acute Sepsis Infections(2015-08-14) Faria Crowder, Monica; Conly, John; Surette, MichaelSepsis is a term used to describe an array of clinical presentations ranging from mild body dysfunction to multiple organ failure. These clinical signs result from a systemic inflammatory response to microbes or microbial products present in sterile sites such as blood. Current clinical diagnostics rely on culture techniques to identify systemic infections. However, culture lacks sensitivity and a positive result is only obtained in 40% of cases thereby limiting our knowledge of sepsis microbiology. This doctoral study described the development of methods for direct detection of bacteria or bacterial products in blood. A method of lysing host cells and a bacterial DNA extraction protocol was developed and evaluated on mock bacterial communities spiked into whole blood. The results indicated that viable bacteria could be recovered down to 10 CFU/ml using this method. Paired-end Illumina sequencing of the 16S rRNA gene also indicated that the bacterial DNA extraction method enabled recovery of bacterial DNA from spiked blood. This method demonstrated improved detection of systemic bacterial infections involving bacteria as well as their products in three cohorts of clinically septic patients. Application of the paired-end Illumina 16S rRNA sequencing to saponin treated blood from intensive care unit (ICU) and emergency department (ED) patients indicated there were bacterial DNA profiles present in whole blood. These patterns were examined alongside the patient’s clinical data and indicated common molecular profiling patterns were associated with the primary source of infection. Polymicrobial DNA was present in the blood samples with the taxonomic profiles suggesting commensal microbiota were implicated in addition to a principal pathogen. Bacterial DNA from Streptococcus and Staphylococcus were abundant in patients that died in the ICU. Overall this study identified common bacterial DNA patterns in the blood of septic patients which were associated with the patients’ primary source of infection, implicated the commensal microbiota in systemic infection and suggested that sepsis infection may not always involve persistent bacterial bloodstream infections. Rather, this study concluded that bacterial products or viable organisms are likely cyclically present and cleared from the bloodstream resulting in a robust inflammatory response.