Thesis (M.Sc.)--University of Alberta, 1997. / Submitted to the Faculty of Graduate Studies and Research in partial fulfilment of the requirements for the degree of Master of Science, Department of Agricultural, Food and Nutritional Science. Also available online.

Theses (Ph. D.)--Marshall University, 2006. / Title from document title page. Includes abstract. Document formatted into pages: contains xv, 153 p. Bibliography: p. 141-151.

Thesis (Ph.D.) - University of Queensland, 2005. / Includes bibliography.

Thesis (Ph.D.)--University of Florida, 2004. / Typescript. Title from title page of source document. Document formatted into pages; contains 94 pages. Includes Vita. Includes bibliographical references.

Cystic Fibrosis (CF) is a life threatening autosomal recessive disorder caused by a mutation in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene, leading to irregular secretions and inflammation in tubular organs. Disease manifestations of CF are heterogeneous in severity and can be present in the sinopulmonary, hepatic, gastrointestinal, and genitourinary tract. Since the 1960’s, physicians and scientists have described a less severe form of CF known as atypical CF, usually seen in adults. Patients with atypical CF tend to have one severe CF mutation on one chromosome, and one less common, mild CF mutation on their other chromosome; or have one severe mutation on one chromosome and an abnormal number of trinucleotide repeats in the CFTR gene on their other chromosome. Today, of the approximately 1000 patients diagnosed with CF per year in the United States, roughly 10% are diagnosed with the atypical presentation of the disease as adults. Patients suffering from atypical CF typically have only one organ system that is dysfunctional, and their clinical symptoms may be less severe than those of a classical case where there are two severe CF mutations. Common symptoms include idiopathic bronchiectasis, chronic sinusitis, congenital bilateral absence of the vas deferens (CBAVD), and idiopathic pancreatitis. Unlike patients suffering from the classical presentation of the disease, most are pancreatic sufficient – however the possibility of pancreatic insufficiency still exists. Patients with atypical CF represent a diagnostic challenge for physicians due to the mild, slowly progressing array of clinical symptoms, the general lack of knowledge about atypical CF, and the general association of CF as a childhood disease. Increasing physician awareness of the adult population with CF is a paramount in improving the diagnosis, care and treatment of patients with atypical CF. Missed diagnoses can result in hospital admissions and morbidity that may have been avoidable. The goal of this thesis is to describe the causes of CF, the common symptoms seen in both CF and atypical CF, the proper diagnosis of atypical CF, and to identify the therapies, both current and in development, used to treat atypical CF.

Orientador: José Dirceu Ribeiro / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-16T17:48:38Z (GMT). No. of bitstreams: 1 Dentini_Priscila_M.pdf: 10675938 bytes, checksum: afc138751a1f11e6991384ca9bbee25c (MD5) Previous issue date: 2010 / Resumo: Objetivos: Determinar a prevalência da colonização/infecção pelo Complexo Burkholderia cepacia (CBc) e os respectivos genomovares em pacientes com fibrose cística (FC) e comparar os indicadores clínicos, nutricionais, tomográficos e funcionais de gravidade da lesão pulmonar em dois grupos de pacientes: GI: pacientes colonizados/infectados pelo CBc e GII: pacientes sem colonização/infecção pelo CBc, com a finalidade de avaliar o impacto deste microrganismo na deterioração pulmonar. Métodos: Foi realizado um estudo clínico-laboratorial, prospectivo, com 222 pacientes com FC, acompanhados nos ambulatórios pediatria e adultos da UNICAMP. Os pacientes foram divididos em 2 grupos: GI (n=50) e GII (n=134). Os microrganismos foram identificados por meio de testes bioquímicos convencionais, pelo Vitek2®Compact, PCR do gene recA, e nested-PCR com primers espécie-específicos. O seqüenciamento do gene recA foi realizado para cepas com PCR inconclusivas. Os pacientes foram classificados pelo escore clínico de Schwachman e as medidas de peso/idade, estatura/idade e IMC/idade foram utilizadas para avaliar o estado nutricional. As alterações tomográficas foram classificadas pelo escore de Bhalla e a função pulmonar foi avaliada por espirometria. Os dados foram comparados entre os grupos com a finalidade de avaliar o impacto do CBc na lesão pulmonar. Resultados: A prevalência do CBc foi de 22,5% e dos genomovares: Bukholderia multivorans (30,0%), seguido de Burkholderia cepacia (24,0%), Burkholderia cenocepacia IIIA (10,0%), Burkholderia cenocepacia IIIB (2%) e Burkholderia vietnamiensis (2,0%). No grupo I, 26,0% dos pacientes estavam infectados, 18,0% apresentaram colonização transitória e 56,0% colonização intermitente pelo CBc. Não houve diferença estatística na média de pontos do escore de Schwachman (p=0,07), nem na classificação da gravidade (p=0,611), porém houve diferença nas variáveis: estado nutricional (p=0,020) e atividade geral (p=0,026). Houve diferença estatística na média de pontos do escore de Bhalla (p=0,04) e entre os parâmetros: gravidade da bronquiectasia (p=0,007), espessamento peribrônquico (p=0,013), extensão das bronquiectasias (p=0,010), generalidades da árvore bronquial (p=0,020). O teste de função pulmonar mostrou: CVF(%) (p=0,076), VEF1(%) (p=0,066), FEF25-75% no (p=0,312) e VEF1/CVF (p=0,312). Classificação dos distúrbios ventilatórios: DVO no GI=4,8% e GII=23,8%, DVR no GI e GII=9,5%, DVM no GI=19,0% e GII=1,6% e DVM com CVF reduzida no GI=47,6% e GII=30,2%. Na avaliação nutricional houve diferença significante entre as médias de peso(kg) e estatura(cm) (p=0,02). Conclusões: A prevalência do CBc em nosso centro é significativamente superior aos dados apresentados pela literatura nacional e internacional. A maior prevalência da Burkholderia multivorans difere da maioria dos estudos. Há a suspeita de que possa ter ocorrido infecção cruzada entre os pacientes ou que seja uma característica regional. Os escore de Shwachman, escore de Bhalla, espirometria e dados nutricionais mostraram que o CBc tem sério impacto na deterioração pulmonar e na piora clínica. Os métodos fenotípicos são úteis para a identificação presuntiva do CBc. O Vitek® apresentou boa acurácia na identificação do CBc, porém com alguns erros decorrentes de limitações do método/equipamento. O PCR, nested-PCR e seqüenciamento do gene recA apresentaram boa especificidade na identificação do CBc e dos genomovares, entretanto, ainda ocorrem algumas limitações, decorrentes da variedade genotípica, sendo necessária a utilização de métodos mais abrangentes, como o MSLT / Abstract: Objectives: Determine the Burkholderia cepacia complex (BCC) colonization/infection and genomovar prevalence in cystic fibrosis patients and compare the clinical, tomographic and functional severity indicators of lung injury in two groups of patients: GI - patients colonized or infected with BCC and GII - patients without BCC colonization or infection, with the aim of assessing the impact of this microorganism in pulmonary deterioration. Methods: A clinical-laboratory and prospective study was conducted with 222 CF patients seen in the CF outpatient (pediatrics and adults) in UNICAMP. Patients were divided into two groups: GI (n = 50) and GII (n = 134). Microorganisms were identified by conventional biochemical tests, Vitek2®Compact, recA-PCR and recA-nested-PCR with species-specific primers. The recA gene sequencing was performed for strains with inconclusive PCR reactions. Patients were classified by Schwachman's clinical score and measures of weight/age, height/age and BMI/age were used to assess nutritional status. The tomography changes were classified by Bhalla's score and lung function was assessed by spirometry. Data were compared between groups with the aim of assessing the CBC impact in lung injury. Results: The BCC prevalence was 22.5% and the most prevalent genomovars was: Bukholderia multivorans (30.0%), followed by Burkholderia cepacia (24.0%), Burkholderia cenocepacia IIIA (10.0%), Burkholderia cenocepacia IIIB (2%) and Burkholderia vietnamiensis (2.0%). In group I, 26.0% of patients were infected, 18.0% had transient colonization and 56.0% intermittent colonization by BCC. There was no statistical difference in the average point of Schwachman's score (p = 0.07) or in the severity classification (p = 0.611) but had differences in variables: nutritional status (p = 0.020) and general activity (p = 0.026). In the average point Bhalla's score was statistical difference (p = 0.04) and between the parameters: severity of bronchiectasis (p = 0.007), peribronchial thickening (p = 0.013), extent of bronchiectasis (p = 0.010), general the bronchial tree (p = 0.020). The pulmonary function test showed: FVC (%) (p = 0.076), FEV1 (%) (p = 0.066), FEF25-75% (p = 0.312) and FEV1/FVC (p = 0.312). Respiratory disorders classification: DVO in GI and GII = 4.8% = 23.8%, DVR in GI and GII = 9.5%, DVM in GI and GII = 19.0% = 1.6% and with DVM FVC decreased in GI and GII = 47.6% = 30.2%. Nutritional assessment was significant difference between the mean weight (kg) and height (cm) (p = 0.02.) CCoonncclluussiioonnss:: The BCC prevalence in our center is significantly higher than the dates provided by national and international literature. The increased Burkholderia multivorans prevalence differs from the most studies. It is suspected that may have been cross-infection between patients or is a regional characteristic. The Shwachman's and Bhalla score, spirometry and nutritional data showed that the BCC has serious impact on the deterioration and worsening pulmonary clinic. The phenotypic methods are useful for the presumptive BCC identification. The Vitek2®Compact showed good accuracy in BCC identification of, but with some errors due to limitations of the method/equipment. PCR, nested-PCR and recA sequencing showed good specificity in BCC genomovars identifying, however, there are still some limitations, stemming from different genotype, being necessary to use more comprehensive methods, such as the MSLT / Mestrado / Saude da Criança e do Adolescente / Mestre em Saude da Criança e do Adolescente

Disrupted sleep and nocturnal hypoxia are common in cystic fibrosis (CF). However, the predictors of nocturnal hypoxia in CF are still controversial. In order to identify the risk factors for nocturnal desaturation and sleep disturbances, we carried out a clinical and polysomnographic investigation of CF patients. We studied 30 clinically stable CF cases with clinical lung disease (mean age=12.8; mean forced expiratory volume in 1 second FEV1=65.2), 10 CF cases without significant lung disease (mean age=13.3; mean FEV1=99.8), and 20 controls (mean age=15.5). Patients were evaluated by spirometry, 6-min walk test (6MWT), the ShwachmanâKulczycki (SâK) score, and full overnight polysomnography. Cases with clinical lung disease had lower body mass index, forced vital capacity, and SâK scores. During sleep, five CF cases with clinical lung disease (15%) had SaO2 <90% during more than 30% of total sleep timeand 11 cases (36.6%) had a nadir SaO2 below 85%. FEV1 values for CF cases with clinical lung disease were related to nadir SaO2 (P<0.03) and to mean oxygen saturation SaO2 (P=0.02). A receiver operating characteristic (ROC) analysis determined FEV1 at 64% to be predictive of nocturnal desaturation as defined by minimum SaO2 <85% (sensitivity=92.3%; specificity=77.3%) or SaO2<90% for 30% of sleep time (sensitivity=81.8%; specificity=85.2%). Frequency of impaired sleep was not different in CF cases with (N=5) and without significant lung disease (N=2, P=0.53). Sleep architecture was not significantly different between the two groups. Sleep apnea was present in three CF cases with clinical lung disease and in one case without significant lung disease. In summary, desaturation during sleep can be predicted by FEV1<64%with good sensitivity and specificity. There are no significant differences in sleep architecture between clinically stable CF cases with and without significant lung disease. The recognition of biological markers that can predict clinical deterioration in cystic fibrosis (CF) is a key issue in everyday care of these patients. The (S-K) scores and (FEV1) have been considered the best independent predictors of impairment/disability. The aim of this study was to evaluate the role of high-resolution computed tomography of the chest (HRCT) and the use of the Bhalla score in the detection of functional disability in CF. Cases of both genders, aged older than six years, with CF clinically stable were studied with spirometry, basal oxygen saturation SpO2, the 6MWT, HRCT and the S-K score. Twenty-five patients (15 male, mean age 14.2Â5.6) with FEV1 (range 28.6-98.0; mean 62.5Â21.8) were studied. Nine patients had severe/moderate respiratory insufficiency (40<FEV1&#8804;59), nine had mild (59<FEV1&#8804;79) and six had normal function (FEV1>79). Bronchiectasis was the most frequent finding. Peribronchial thickening, mucus plugging and emphysema, despite being less severe, were also commonly observed. None of the cases presented bullae. Total scores of CT abnormalities varied from 7 to 25 (13.8Â4.4). The ROC curve showed the high sensitivity/specificity for Bhalla and S-K scores in the prediction of clinical disability as measured by the FEV1. By comparison, the Bhalla scores showed higher sensitivity than the S-K scores. SpO2 and the 6MWT were not good predictors of disability as measured by functional pulmonary tests. Melatonin, a natural hormone secreted by the pineal gland, has an important function in the synchronization of circadian rhythms, including the sleepâwake cycle, and has been shown to possess significant anti-oxidant properties. To evaluate the effects of exogenous melatonin on sleep and inflammation and oxidative stress markers in CF we conducted a randomized double-blind placebo controlled study initially involving 20 patients with CF. One case failed to conclude the study. All subjects were clinically stable when studied and without recent infectious exacerbation or hospitalization in the last 30 days. Groups were randomized for placebo (N= 10; mean age 12.10Â6.0) or melatonin 3.0 mg (N=9; mean age 16.62Â8.26) during 21 days. Actigraphy was performed during 6 days before start of medication and in the third week (days 14 to 20) of treatment. Isoprostane and nitrite levels were determined in exhaled breath condensate (EBC) at baseline (day 0) and after treatment (Day 21). Melatonin improved sleep efficiency (p=0.01) and tended to improve sleep latency (p= 0.08). Melatonin reduced EBC nitrite (p=0.01) but not isoprostane. In summary, melatonin administration reduces nitrite levels in EBC and improves sleep measures in clinically stable CF patients. / A Fibrose CÃstica (FC) à uma doenÃa crÃnica e progressiva acompanhada por episÃdios repetidos de infecÃÃes respiratÃrias. Neste trabalho, realizaram-se investigaÃÃes relacionadas aos aspectos polissonogrÃficos, de tomografia computadorizada de alta resoluÃÃo do tÃrax (TCAR) e um estudo sobre os efeitos da melatonina em pacientes com FC, que serÃo descritos a seguir. Na FC, as alteraÃÃes do sono e a dessaturaÃÃo noturna da oxi-hemoglobina sÃo comuns, no entanto, os preditores dessa dessaturaÃÃo ainda sÃo controversos e a indicaÃÃo para a realizaÃÃo de polissonografia ainda nÃo foi definida. Com o objetivo de identificar os fatores de risco associados com hipÃxia noturna e com as alteraÃÃes do sono, realizou-se uma investigaÃÃo clÃnica e polissonogrÃfica de pacientes com FC com e sem envolvimento pulmonar. Trata-se de um estudo transversal de pacientes clinicamente estÃveis com (N=30; mÃdia de idade = 12,8 anos; mÃdia de volume expiratÃrio forÃado no primeiro segundo (VEF1= 65,2%) e sem (N=10; mÃdia de idade =13,3; mÃdia de VEF1 = 99,8%) doenÃa pulmonar e controles (N=20; mÃdia de idade =15,5). Os pacientes foram avaliados por meio das provas de funÃÃo pulmonar (PFP), teste da caminhada de seis minutos (TC6min), pelo escore Swhachman-Kulczycki (S-K) e polissonografia de noite inteira. Os pacientes com doenÃa pulmonar apresentavam Ãndices mais baixos de massa corpÃrea, VEF1, capacidade vital forÃada e escore S-K. Durante o sono, entre os pacientes com FC e doenÃa pulmonar, cinco (15%) tinham SpO2 <90% durante mais de 30% do tempo total de sono e 11 (36,6%) tinham SpO2 mÃnima. Observou-se uma correlaÃÃo entre os nÃveis de VEF1 e os nÃveis mÃdios de SpO2 (p=0,02) e valores mÃnimos da SpO2 (p<0,03). A Receiver Operating Curve (ROC) mostrou que o VEF1 < 64% à um preditor da dessaturaÃÃo noturna ao se considerar o nadir, SpO2 menor que 85% (sensibilidade = 92,3% e especificidade = 77,3%) ou SpO2 < 90% durante mais de 30% (sensibilidade = 81,8% e especificidade = 85,2%). A frequÃncia das alteraÃÃes do sono, quando se considerou a qualidade subjetiva do sono (IQSP), nÃo foi diferente entre os casos de FC com (N=5) e sem comprometimento pulmonar (N=2, P=0.53). A arquitetura do sono nÃo foi significativamente diferente entre os casos de FC com e sem doenÃa pulmonar. Apneia obstrutiva do sono estava presente em trÃs casos com doenÃa pulmonar e em um caso sem doenÃa pulmonar. Em conclusÃo, a dessaturaÃÃo durante o sono pode ser prevista por um VEF1 < 64% com boa sensibilidade e especificidade. NÃo hà diferenÃas significantes entre os casos de FC clinicamente estÃveis com e sem envolvimento pulmonar. Sugere-se que a polissonografia pode ser Ãtil em casos selecionados de FC com e sem doenÃa pulmonar quando hà suspeita de apneia obstrutiva do sono. Em relaÃÃo ao estudo com TCAR do tÃrax, deve ser enfatizado que o reconhecimento de marcadores de gravidade, capazes de predizer a deterioraÃÃo clÃnica na fibrose cÃstica à de fundamental importÃncia para o manuseio terapÃutico dos pacientes. O escore de S-K e o VEF1 sÃo considerados os melhores preditores independentes do prognÃstico em FC. O objetivo desse estudo foi avaliar o papel da TCAR e o escore de Bhalla na avaliaÃÃo da gravidade de pacientes com FC. Casos de ambos os sexos, com idade superior a seis anos, clinicamente estÃveis, foram avaliados mediante espirometria, nÃveis basais de saturaÃÃo de oxigÃnio (SpO2), TC6min, TCAR e escores S-K e Bhalla. Vinte e cinco pacientes (15 homens, idade mÃdia 14,2  5,6) com VEF1 (variaÃÃo 28,6-98,0; mÃdia 62,5  21,8) foram estudados. Nove pacientes apresentavam insuficiÃncia respiratÃria moderada/grave (40 < VEF1 &#8804; 59), nove tinham insuficiÃncia respiratÃria leve (59 < VEF1 &#8804; 79) e seis tinham funÃÃo normal (VEF1 > 79). As bronquiectasias foram o achado tomogrÃfico mais frequente. Espessamento peribrÃnquico, rolha de muco e enfisema, apesar de menor gravidade, foram tambÃm comumente observados. Nenhum dos casos apresentava bolhas. Os escores totais das anormalidades tomogrÃficas variaram de 7 a 25 (13,8  4,4). A curva (ROC) mostrou alta sensibilidade/especificidade para o escore Bhalla na prediÃÃo da gravidade da doenÃa medida pelo VEF1. De forma comparativa, os escores Bhalla apresentaram maior sensibilidade do que os escores S-K. Os nÃveis basais de SpO2 e o TC6min nÃo foram bons preditores de gravidade avaliada pelos testes de funÃÃo pulmonar. Realizou-se um estudo sobre os efeitos da melatonina na FC. A melatonina à um hormÃnio natural secretado pela glÃndula pineal, tem uma funÃÃo importante na sincronizaÃÃo do ritmo circadiano, incluindo o ciclo vigÃlia-sono e tem propriedades antioxidantes. Com o objetivo de avaliar os efeitos da melatonina no sono, na inflamaÃÃo e no estresse oxidativo pulmonar realizou-se um estudo randomizado, duplo-cego e controlado por placebo. Vinte pacientes com FC foram inicialmente avaliados. Um paciente nÃo concluiu o estudo. Todos os indivÃduos estavam clinicamente estÃveis por ocasiÃo do estudo, ou seja, nÃo tinham apresentado exacerbaÃÃes infecciosas ou hospitalizaÃÃes nos Ãltimos 30 dias. Os grupos foram randomizados para o uso de placebo (N= 10; mÃdia da idade 12,10  6,0) ou melatonina 3,0 mg (N=9; mÃdia da idade 16,62  8,26) durante 21 dias. Um registro actigrÃfico foi realizado durante seis dias, antes do inÃcio da medicaÃÃo e na terceira semana (dias 14 a 20) do tratamento. Os nÃveis de isoprostano e nitrito foram determinados no condensado de ar exalado (CAE) no inÃcio do estudo (dia 0) e depois do tratamento (dia 21). A melatonina melhorou a eficiÃncia do sono (p=0,01) e nitrito do CAE, porÃm nÃo reduziu o isoprostano. Em conclusÃo, em pacientes com FC clinicamente estÃveis, a administraÃÃo de melatonina reduz os nÃveis de nitrito e melhora os parÃmetros de sono.

Orientador: Antonio Fernando Ribeiro / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-20T12:30:23Z (GMT). No. of bitstreams: 1 Enes_GiovanadaSilvaTavares_M.pdf: 802222 bytes, checksum: 877dccb29eaf785982eed2f02beb39c6 (MD5) Previous issue date: 2012 / Resumo: A Fibrose Cística é uma doença autossômica recessiva, sistêmica, hereditária, crônica e progressiva e pode levar à morte. São características da doença as secreções mucosas espessas e viscosas que obstrui os ductos das glândulas exócrinas e contribuem para o aparecimento de doença pulmonar obstrutiva crônica, insuficiência pancreática com má digestão e má absorção e conseqüente desnutrição secundária, além de níveis elevados de eletrólitos no suor. Por ser uma doença crônica, ela exige cuidados sistemáticos pela vida toda, e na maioria dos casos quem exerce a função de cuidadora é a mãe. Além de viver uma nova experiência de ser mãe, ela terá que conviver com a frustração dele ser doente.Com este estudo foi possível compreender a relação que mãe e filho doente crônico constroem desde o momento do diagnóstico e conhecimento do tratamento, permeados por sentimentos como culpa e solidão. Assim, essas mães renunciam suas próprias vidas em função do cuidado do filho. Cuidados esse compartilhado com uma equipe de saúde multiprofissional ainda deficitária. Apesar de ter sido avaliado por elas como positivo, as sugestões por melhorias também surgiram: como uma melhor articulação entre os serviços de saúde nos diversos níveis, uma maior divulgação da doença e o aumento do número de dias de atendimento. Outro aspecto importante encontrado foi sobre importância do papel do psicólogo não só na atuação com o paciente e a família durante todo o tratamento; mas também na necessidade de oferecer um espaço para que os profissionais de saúde despreparados pudessem compartilhar suas angústias e frustrações o que reflete diretamente na assistência prestada / Abstract: The Cystic Fibrosis is a disease systemic, hereditary, chronic and progressive and it can lead to the death. There are characteristic of the disease the thick and viscous mucous secretions what it obstructs the ducts of the exocrine glands and contribute to the appearance of chronic obstructive pulmonary disease, pancreatic insufficiency with bad digestion and bad absorption and consequent secondary malnutrition, besides elevated levels of electrolytes in the sweat. Because of being a chronic disease, she demands systematic cares for the life completely, and in most of the cases who plays the function of care is the mother. Besides surviving a new experience of being a mother, she will have to coexist in spite of the fact that his frustration to be doente.Com this study there were possible understood the relation what mother and chronic sick son build from the moment of the diagnosis and knowledge of the treatment, permeated by feelings as fault and solitude. So, these mothers renounce his lives themselves in function of the care of the son. Taken care this shared one with a team of still deficient multiprofessional health. In spite of having been valued by them like positive, the suggestions for improvements also appeared: like a better articulation between the health services in several levels, a bigger spread of the disease and the increase of the number of service days. Another considered important aspect was on importance of the paper of the psychologist not alone in the acting with the patient and the family during the whole treatment; but also in the necessity of offering a space so that the unprepared health professionals could share his anguishes and frustrations what thinks straightly about the given presence / Mestrado / Saude da Criança e do Adolescente / Mestre em Ciências

Cystic Fibrosis is one of the most common genetic recessive diseases among Caucasians and is caused by mutations in the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene on chromosome 7. There are different classes of CFTR mutation, leading to differences in disease severity among patients. In addition to the CFTR genotype, secondary genetic factors, modifier genes, also influence CF phenotypes. Due to the dysfunction of CFTR protein and production of thickened mucus, bacterial infection in the lungs is favored and can lead to further clinical complications in CF patients. Pseudomonas aeruginosa is one of the most common bacteria detected among patients. The aim of this project was to investigate four candidate modifier genes, Factor B, Complement Factor 3, Toll-like Receptor 4 and Heme oxygenase-1, which might affect the status of Pseudomonas aeruginosa infection. A total of 22 single nucleotide polymorphisms (SNPs) were selected in these four genes and they were tested against five phenotypic traits, including age of diagnosis, FEV1% predicted andstandard deviation value, age of first Pseudomonas aeruginosa infection and Pseudomonas aeruginosa infection status. Among the selected SNPs, both case-control studies and family-based analysis were performed in order to establish any correlation between the genotypes and the phenotypes. In addition, haplotype analysis was performed to determine whether there was interaction between SNPs or whether there were unidentified SNPs in the vicinity of the selected ones that might contribute to the observed phenotypic traits. Among the 22 chosen SNPs, 13 of them were found to be significantly linked to one or more of the tested phenotypes. The three most significant associations were BF_2557 with lung function, HMOX1_9531 with lung function and BF_7202 with age of diagnosis. Several haplotypes were significantly associated with one of the five phenotypes. There was no evidence for the presence of unidentified SNPs or interaction between SNPs. Most of haplotype associations were likely due to the presence of a single SNP which was found to be significantly linked to the phenotype. Conclusively, both SNPs and haplotype analyses suggest that the four candidate genes are modifiers of disease severity in CF. / Medicine, Faculty of / Medicine, Department of / Experimental Medicine, Division of / Graduate

Introduction: Emerging pathogens (EP) in cystic fibrosis (CF) include organisms that have infected individuals with CF for many years e.g. Burkholderia multivorans and Mycobacterium abscessus and more recently identified potential pathogens in CF e.g. Pneumocystis jirovecii and Pandoraea spp. The clinical implications of infection with these organisms are emerging but much remains unknown. Current evidence suggests that infection with some EP is associated with a worse prognosis. This thesis aimed to investigate the epidemiology, prevalence and clinical impact of EP in adults with CF.Methods: (1) The prevalence of P. jirovecii was determined in adults attending Manchester Adult Cystic Fibrosis Centre (MACFC) who were clinically stable versus those experiencing an acute pulmonary exacerbation (PEx). (2) The prevalence of M. abscessus at MACFC was determined, isolates of M. abscessus were strain typed, and cross infection risk was assessed. The clinical impact of Gram-negative EP was assessed by: (3) assessing their prevalence and determining if any patients attending MACFC harboured identical strains and had opportunities for cross infection to occur, and by (4) following these patients longitudinally and comparing outcome with age, gender and FEV1 matched Pseudomonas aeruginosa infected controls. Results: (1) P. jirovecii was detected via sputum PCR in 10 (4.4%) of 226 samples tested from 111 patients. P. jirovecii was more likely to be detected in samples taken from an acute pulmonary exacerbation compared with samples taken from stable patient visits (7 (9.2%) of 76 exacerbations samples versus 3 (2%) of 150 stable visit samples, p = 0.033). (2) Prevalence of M. abscessus was stable at ≤3.6% from 2010 to 2015. 21 patients (91.3%) with a positive culture for M. abscessus since 2010 were infected with M. abscessus subsp abscessus. 2 clusters of 7 and 6 patients harboured strains with identical variable number tandem repeat profiles and some of these patients had opportunities for cross infection to occur. 28.6% of patients developed M. abscessus pulmonary disease, 38.1% were persistently culture positive with no related pulmonary disease, and 33.3% spontaneously cleared M. abscessus from their sputum. (3) Prevalence of Gram-negative EP ranged from 1.9% (Ralstonia spp.) to 6.2% (B. multivorans). Small numbers of patients shared strains of B. multivorans; Stenotrophomonas S. maltophilia and Achromobacter; Ralstonia and Pandoraea species. Epidemiological connections consistent with possible cross infection were found in patients infected with Pandoraea and Ralstonia species. (4) Patients with B. multivorans; S. maltophilia; Ralstonia spp. and Pandoraea spp. had higher antibiotic requirements than P. aeruginosa infected matched controls. B. multivorans; Achromobacter spp.; Ralstonia spp. and Pandoraea spp patients had median FEV1 (% predicted) values ≥10% (absolute) lower than the overall median FEV1.Conclusion: Prevalence of all EP investigated at MACFC was low. P. jirovecii was approximately 5 times more likely to be detected in patients with acute PEx compared with stable patients suggesting it may be a cause of PEx. Results suggest that some patients attending MACFC may have acquired infection with M. abscessus subsp abscessus, Pandoraea spp. or Ralstonia spp. through cross infection. Patient numbers are too small to establish this with certainty and a common environmental source is possible. Gram-negative EP other than Achromobacter spp. were associated with higher acute antibiotic requirements than P. aeruginosa matched controls suggesting these EP are associated with an increased risk of PEx. The fact that many Gram-negative EP were associated with lower median lung function may indicate that these EP cause accelerated lung function decline or that patients with more advanced disease are at most risk of acquiring EP.