ABSTRACT INTRODUCTION: Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the CFTR gene. The gene mutation profile is extremely heterogeneous and mutations show a variable distribution among population groups. In SA the 3120+1G->A splice site mutation has been found predominantly in Black and Coloured patients. It occurs in Black CF patients at an estimated frequency of 46%. The CF carrier frequency is estimated at 1/34 in Black and 1/55 in Coloured populations, and based on these rates, it is clear that a significant number of Black and Coloured patients remain undiagnosed. Point mutations account for the majority of the mutations that have been found in the CFTR gene. Copy number mutations are, however, increasingly being detected in CF patients through the use of gene dosage-dependant assays. These mutations have been found to occur in the CFTR gene in various African American families and exon rearrangements are thought to account for 1.3% of all CF chromosomes across all populations. AIMS: To use haplotypes to analyse the origin(s) of the 3120+1G->A mutation and the likely frequencies of the remaining unknown mutations. To increase mutation detection in the SA Black and Coloured groups by searching for CFTR gene exons for copy number mutations. METHODS: In patients with at least one copy of the 3120+1G>A mutation haplotype studies will be used to elucidate the origin(s) of this mutation in SA Black and Coloured CF patients, by analyzing pyrosequencing SNP genotype data. In patients with at least one unknown mutation, haplotype studies will reveal the likely relative frequencies of the unknown mutations in these populations. In Black and Coloured CF patients with at least one unknown mutation, a multiplex ligation dependant probe amplification (MLPA) CF kit will be used for the detection of exon copy number mutations. RESULTS: The results of the haplotype data show that there is a G-G-C-G-T-A haplotype, for markers MetD-KM19-J44-T854T-Tub18-J32, associated with the 3120+1G->A mutation in both Black and Coloured patients. Unknown mutation-associated haplotypes indicate that there are two relatively common unknown mutations in each of these populations. MLPA results show that one patient is a carrier of an exon 2 deletion. CONCLUSION: A single origin for the 3120+1G>A mutation in Black and Coloured CF patients is supported by the data. Exon copy number changes in the CFTR gene are not a major mutational mechanism leading to CF in SA Black and Coloured patients.

A infecção crônica do trato respiratório é responsável pela grande morbidade e mortalidade em pacientes com fibrose cística (FC). P. aeruginosa, S. aureus e bactérias do complexo Burkholderia cepacia (CBc) estão entre os patógenos mais encontrados em pulmões de pacientes com FC, mas também são encontradas outros bacilos gram-negativos não fermentadores (BGN-NF) emergentes como Achromobacter sp., Stenotrophomonas maltophilia, Ralstonia sp., Pandoraea sp., entre outros. A correta caracterização desses patógenos impacta na sobrevida e qualidade de vida desses pacientes, e é um dos grandes desafios para laboratórios de microbiologia clínica devido à similaridade fenotípica entre eles. Este estudo tem como objetivo avaliar e propor estratégias e esquema de identificação acessível à maioria dos laboratórios para a identificação de BGN-NF emergentes e listar bactérias isoladas de pacientes com FC atendidos no Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto - USP (HCFMRP-USP), com ênfase nos BGN-NF emergentes. Foram utilizados meios de cultura seletivos, reação em cadeia da polimerase (PCR), análise de polimorfirmos (RFLP). Foram coletadas 264 amostras clínicas de 107 pacientes com FC no HCFMRP-USP entre julho/2011 a setembro/2012. Inicialmente, para selecionar os BGNNF dos pacientes com FC, deve ser realizada triagem fenotípica (coloração de Gram, teste da oxidação/fermentação de glicose e produção de oxidase). Devido à dificuldade de identificação dos BGN-NF emergentes por provas bioquímicas, deve ser realizada PCR com DNA destes microrganismos para identificação de gênero e/ou espécie, utilizando os primers específicos, nas condições estabelecidas pela padronização, a qual foi realizada para aumentar a especificidade de alguns primers que apresentaram amplificação de produtos inespecíficos. Provas bioquímicas convencionais devem ser realizadas para confirmar gêneros e identificar algumas espécies não detectadas por PCR, e para resultados fenotípicos diferente da PCR deve ser realizado API® - NE. Para identificação das bactérias do CBc, deve ser realizado análise de polimorfismo, o qual se mostrou mais efetivo do que PCR para identificação de espécies e genomovares. Dos 107 pacientes, 17 estavam colonizados por bactérias do CBc, 13 colonizados por Achromobacter sp., 10 colonizados por S. maltophilia, 2 colonizados por Ralstonia sp. e um paciente colonizado por Cupriavidus sp. e Pandoraea sp., com um isolamento de cada gênero. Os genomovares mais prevalentes foram B. cenocepacia IIIB, seguido de B. vietnamiensis, B. pyrrocinia, B. cepacia e B. multivorans. A maioria dos BGNNF esteve presente em crianças com idade até 17 anos. Os meios de cultura seletivos foram extremamente necessários por permitir o isolamento de vários BGN-NF, não isolados em outros meios de cultura utilizados. A metodologia de identificação empregada foi capaz de identificar todos BNG-NF isolados e pode ser muito útil e acessível à maioria dos laboratórios clínicos. / Chronic infection of the respiratory tract accounts for the high rate of morbidity and mortality of patients suffering from cystic fibrosis (CF). P. aeruginosa, S. aureus and bacteria of the Burkholderia cepacia (BCc) complex are among the pathogens most commonly found in the lungs of CF patients, but other emergent non-fermenting gram-negative bacilli (NFGNB), such as Achromobacter sp., Stenotrophomonas maltophilia, Ralstonia sp., Pandoraea sp., among others, are found as well. The correct identification of these pathogens affects the survival rate of patients and, due to their phenotypic similarity, presents itself as one of the great challenges that clinical microbiology laboratories face. The purpose of this study is to evaluate and propose strategies and methods that are accessible to the majority of laboratories for identifying emergent NFGNBs and listing isolated bacteria (with a focus on emergent NFGNB) in CF patients receiving routine care at the Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo - USP (HCFMRPUSP). The study employed selective culture media, polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP). From July 2011 to September 2012, 264 clinical samples were gathered from 107 CF patients at the HCFMRP-USP. A phenotypic screening (Gram staining, oxidase production and oxidation/fermentation of glucose) should be conducted as the first step to select the NFGNBs of CF patients. Due to the difficulty in identifying emergent NFGNBs via biochemical tests, a PCR using the DNA of these microorganisms should be carried out to identify their genus and/or species. The PCR should utilize the specific primers, at conditions established by this study, which was performed to increase the specificity of some primers that showed nonspecific amplification products. Conventional biochemical tests should be conducted to confirm genera and identify some species that the PCR failed to detect, and, in the case of phenotypic results that differ from those of the PCR, an API bacterial identification test should be conducted. RFLP analysis proven more effective than PCR in identifying species and genomovars, should be conducted to identify BCc bacteria. Of the 107 patients, 17 had positive cultures for BCc, 13 for Achromobacter sp., 10 for S. maltophilia, two for Ralstonia sp. and one patient had positive culture for Cupriavidus sp. and Pandoraea sp., with the genera isolated from each other. The most prevalent genomovar was the B. cenocepacia IIIB, followed by B. vietnamiensis, B. pyrrocinia, B. cepacia and B. multivorans. The majority of the NFGNBs were present in children up to age 17. Selective culture media were extremely necessary to allow the isolation of various NFGNBs that could not be isolated via alternative culture media. The identification methodology employed enabled the identification of all isolated NFGNBs and can be very useful and accessible to the majority of clinical laboratories.

Achromobacter sp. e Burkholderia sp. são considerados patógenos problemáticos em pacientes com fibrose cística (FC), principalmente por apresentarem linhagens que podem ser transmissíveis e multidroga resistentes. Este trabalho teve como objetivo analisar isolados de Achromobacter e do complexo Burkholderia cepacia (CBc) de pacientes com FC atendidos no Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto (HCFMRP-USP) e no Hospital das Clínicas da Faculdade de Ciências Médicas de Campinas (HCFCM-UNICAMP): identificar gênero/espécies; avaliar a sensibilidade a antimicrobianos; investigar relações genéticas entre os isolados por Pulsed-field Gel Electrophoresis (PFGE); elucidar a taxonomia e epidemiologia molecular dos isolados por Multilocus Sequence Typing (MLST) e correlacionar os resultados com dados clínicos. Entre julho/2011 a setembro/2014, nos dois hospitais, as espécies mais prevalentes de Achromobacter e CBc foram A. xylosoxidans e B. vietnamiensis, respectivamente. Os antibióticos mais efetivos contra isolados de Achromobacter sp. de pacientes do HCFMRP-USP foram imipenem e meropenem e do HCFCM-UNICAMP foram meropenem e ceftazidima. Os antibióticos mais efetivos contra CBc de pacientes do HCFMRP-USP foram sulfametoxazol-trimetoprim e meropenem e do HCFCM-UNICAMP foram ceftazidima e meropenem. Houve suspeita de contaminação cruzada entre alguns pacientes que apresentaram isolados com o mesmo perfil de PFGE. No HCFMRP-USP, isolados de B. vietnamiensis de pacientes diferentes tiveram o mesmo perfil de PFGE e apenas 2 pacientes tinham infecção crônica. No HCFCM-UNICAMP, isolados de B. cenocepacia IIIB de 4 pacientes apresentaram o mesmo pulsotipo, porém nenhum dos pacientes tinha infecção crônica. Isolados de B. vietnamiensis e B. multivorans de pacientes diferentes no HCFCM-UNICAMP também apresentaram o mesmo pulsotipo, e apenas um paciente colonizado por B. multivorans tinha infecção crônica. No HCFCM-UNICAMP, isolados de Achromobacter apresentaram perfis únicos de PFGE, enquanto que no HCFMRP-USP houve suspeita de contaminação cruzada somente entre pacientes colonizados por A. xylosoxidans, sendo que 3 destes pacientes estavam com infecção crônica. Nos dois hospitais, 17 STs foram identificados em isolados do CBc, 14 deles pela primeira vez e 3 STs (ST17, ST369 e ST911) apresentaram distribuição intercontinental. Em isolados de pacientes dos dois hospitais foram identificados alguns STs em comum (STs 1056, 1057, 369 e 911), o que pode sugerir ancestral comum. No total, 6 STs diferentes foram identificados em isolados de A. xylosoxidans de pacientes do HCFMRP-USP, dos quais 3 STs apareceram pela primeira vez e os outros 3 STs apresentaram distribuição intercontinental. Nenhuma das espécies apresentou linhagens epidêmicas descritas. Os pacientes colonizados cronicamente por A. xylosoxidans apresentaram valores de escore de Shwachman, índice de massa corporal (IMC) e função pulmonar menos preservados e exacerbações ligeiramente mais frequentes do que pacientes colonizados por bactérias do CBc. Este estudo possibilitou a correta identificação dos patógenos proporcionando a adoção de medidas de controle mais efetivas e tratamentos mais adequados, além de atualização do banco de dados epidemiológicos, o que facilita a análise colaborativa multicêntrica e auxilia no controle de infecção global destes patógenos. / Achromobacter sp. and Burkholderia sp. are troublesome pathogens in cystic fibrosis (CF) patients, mainly because they may have transmissible and multidrug resistant strains. The aim of this study was to analyze the Achromobacter and Burkholderia cepacia complex (Bcc) isolates from CF patients treated at the Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto (HCFMRP-USP) and Hospital das Clínicas da Faculdade de Ciências Médicas de Campinas (HCFCM-UNICAMP); to identify genus/species; to evaluate antimicrobial susceptibility; to investigate clonal relatedness among isolates by Pulsed-field Gel Electrophoresis (PFGE); to elucidate taxonomy and molecular epidemiology of the isolates by Multilocus Sequence Typing (MLST), and to relate the results to clinical data. Between July/2011 and September/2014, in both hospitals, the most prevalent species of Achromobacter and Bcc were A. xylosoxidans and B. vietnamiensis, respectively. The most effective antibiotics against Achromobacter sp. isolates of patients from HCFMRP-USP were imipenem and meropenem, and from HCFCM-UNICAMP were meropenem and ceftazidime. The most effective antibiotics against Bcc isolates of patients from HCFMRP-USP were sulfamethoxazole-trimethoprim and meropenem, and from HCFCM-UNICAMP were ceftazidime and meropenem. Cross-contamination was suspected among some patients who presented isolates with the same PFGE profile. In HCFMRP-USP, isolates of B. vietnamiensis from different patients showed the same PFGE profile, and only 2 patients had chronic infection. In HCFCM-UNICAMP, isolates of B. cenocepacia IIIB of 4 patients showed the same pulsetype, but none of the patients had chronic infection. Isolates of B. vietnamiensis and B. multivorans from different patients from HCFCM-UNICAMP also showed the same pulsetype, and only one patient colonized by B. multivorans had chronic infection. In HCFCM-UNICAMP, Achromobacter isolates showed unique profiles of PFGE, whereas in HCFMRP-USP cross-contamination was only suspected among patients colonized by A. xylosoxidans, and 3 of these patients had chronic infection. In both hospitals, 17 STs were identified in Bcc isolates, 14 of them for the first time and 3 STs (ST17, ST369 and ST911) presented intercontinental distribution. In both hospitals, some common STs (STs 1056, 1057, 369 and 911) were identified, which may suggest a common ancestor. In total, 6 different STs were identified in A. xylosoxidans isolates of patients from HCFMRP-USP, of which 3 STs were identified for the first time, and the other 3 STs presented intercontinental distribution. None of the species presented described epidemic strains. Patients chronically colonized by A. xylosoxidans showed less preserved Shwachman score, body mass index (BMI) and lung function, and slightly more frequent exacerbations than patients colonized by Bcc bacteria. This study provided the correct identification of the pathogens, allowing the adoption of more effective control measures and adequate treatments, besides updating the epidemiological database, which facilitates the multicentric collaborative analysis and assists in the control of global infection of these pathogens

INTRODUÇÃO: O tratamento da fibrose cística (FC) envolve o uso de medicamentos fornecidos através de nebulizadores e seu funcionamento adequado é essencial. OBJETIVOS: Avaliar o desempenho de nebulizadores a jato utilizados por pacientes com FC e comparar dois manômetros para avaliação dos compressores. MÉTODOS: Estudo descritivo, transversal, de avaliação dos nebulizadores usados pelos pacientes com FC da Associação Mineira de Assistência a Mucoviscidose. Os pacientes trouxeram compressores (Proneb Ultra®) e nebulizadores (Pari LC plus®) para avaliação. O desempenho do compressor foi avaliado por medidas de pressão operacional através dos manômetros PARI PG101® (PARI GmbH, Starnberg, Alemanha) e FSA analógico (Famabras, Itaquaquecetuba, Brasil).As variáveis de eficiência do nebulizador foram: O débito de volume nebulizado (DVN), taxa de oferta da medicação (TOR) e volume residual (VR) foram calculados por diferenças de peso de cada nebulizador após 10 minutos de nebulização de solução salina (2,5ml). O diâmetro médio de massa da partícula (DMM) foi calculado através da equação proposta por Standaert et al. A análise estatística incluiu o pacote R (v.2.15) e MINITAB, com alfa=0,05. O coeficiente Kappa foi calculado para avaliar concordância de valores entre os equipamentos, e curva ROC construída para calcular o valor aferido no manômetro FSA com melhor sensibilidade/especificidade, utilizando o manômetro PARI PG101® como referência. A associação entre valores de pressão, DVN, TOR e VR foi calculada pela correlação de Spearman. RESULTADOS: Avaliados 146 sistemas com tempo mediano de uso de 32(12-60) meses±36 meses. Cinquenta e sete (39%) não funcionaram adequadamente, com valores pressóricos inferiores à metade da referência. Os sistemas com funcionamento inadequado comprometeram as variáveis de eficiência dos nebulizadores A concordância entre os diferentes métodos de avaliação de acordo com a classificação; com funcionamento adequado e inadequado através do coeficiente Kappa foi 0,81(IC95%- 0,65-0,97), p<0,001. Na avaliação da sensibilidade e especificidade foi observado o ponto de corte de 23,5 PSI no manômetro FSA mostrou sensibilidade=99% e especificidade=79% (p<0,001). Houve associação significativa entre DVN, VR e pressões aferidas. CONCLUSÕES: Uma proporção significativa dos sistemas de nebulização não funcionou adequadamente. As variáveis de eficiência da nebulização estavam comprometidas indicando que a pressão gerada no compressor é um aspecto crítico na eficiência do tratamento. O método alternativo da avaliação dos compressores se apresentou adequado para ser utilizado nos compressores utilizados no tratamento da FC. / INTRODUCTION: Cystic fibrosis (CF) treatment of involves the use of medications supplied through nebulizers and their proper functioning is essential. OBJECTIVES: To evaluate the performance of jet nebulizers used by CF patients and to compare two pressure gauges Compressors evaluation. METHODS: This was a descriptive, cross - sectional study of the nebulizers used by patients with CF of the Mucoviscidosis Care Association of Minas Gerais. The patients brought compressors (Proneb Ultra®) and nebulizers (Pari LC plus®) for evaluation. The performance of the compressor was evaluated by operating pressure measurements using PARI PG101® manometers (PARI GmbH, Starnberg, Germany) and analog FSA (Famabras, Itaquaquecetuba, Brazil). The variables of efficiency of nebulization under study were: nebulizer delivery volume (NDV), drug output rate (DOR), and residual volume (RV), which were calculated by weighing each nebulizer before nebulization and 10 minutes after nebulization using a saline solution (2.5 mL). The mass median diameter (MMD) was calculated using the equation proposed by Standaert et al. Statistical analysis included the package R (v.2.15) and MINITAB, with alpha = 0.05. The Kappa coefficient was calculated to evaluate agreement of values between the equipment\'s, and ROC curve constructed to calculate the value measured in the FSA manometer with better sensitivity / specificity, using the PARI PG101® manometer as reference. The association between pressure values, NDV, DOR and RV was calculated by the Spearman correlation. RESULTS: We evaluated 146 systems with a median time of use of 32 (12-60) months ± 36 months. Fifty-seven (39%) did not function properly, with pressure values lower than half the reference. The systems with inadequate functioning compromised the efficiency variables of the nebulizers. The agreement between the different evaluation methods according to the classification; with adequate and inadequate functioning through the Kappa coefficient was 0.81 (95% CI -0.65-0.97), p <0.001. In the evaluation of sensitivity and specificity, the cut-off point of 23.5 PSI on the FSA manometer showed sensitivity = 99% and specificity = 79% (p <0.001). There was a significant association between NDV, DOR, RV and measured pressures. CONCLUSIONS: A significant number of the nebulizer systems were ineffective. The variables of nebulization efficiency were compromised, which indicated that the pressure generated by the compressor was a critical aspect for treatment efficiency. The alternative method of compressors evaluation was suitable for use in CF treatment routine.

INTRODUÇÃO: O tratamento da fibrose cística (FC) envolve o uso de medicamentos fornecidos através de nebulizadores e seu funcionamento adequado é essencial. OBJETIVOS: Avaliar o desempenho de nebulizadores a jato utilizados por pacientes com FC e comparar dois manômetros para avaliação dos compressores. MÉTODOS: Estudo descritivo, transversal, de avaliação dos nebulizadores usados pelos pacientes com FC da Associação Mineira de Assistência a Mucoviscidose. Os pacientes trouxeram compressores (Proneb Ultra®) e nebulizadores (Pari LC plus®) para avaliação. O desempenho do compressor foi avaliado por medidas de pressão operacional através dos manômetros PARI PG101® (PARI GmbH, Starnberg, Alemanha) e FSA analógico (Famabras, Itaquaquecetuba, Brasil).As variáveis de eficiência do nebulizador foram: O débito de volume nebulizado (DVN), taxa de oferta da medicação (TOR) e volume residual (VR) foram calculados por diferenças de peso de cada nebulizador após 10 minutos de nebulização de solução salina (2,5ml). O diâmetro médio de massa da partícula (DMM) foi calculado através da equação proposta por Standaert et al. A análise estatística incluiu o pacote R (v.2.15) e MINITAB, com alfa=0,05. O coeficiente Kappa foi calculado para avaliar concordância de valores entre os equipamentos, e curva ROC construída para calcular o valor aferido no manômetro FSA com melhor sensibilidade/especificidade, utilizando o manômetro PARI PG101® como referência. A associação entre valores de pressão, DVN, TOR e VR foi calculada pela correlação de Spearman. RESULTADOS: Avaliados 146 sistemas com tempo mediano de uso de 32(12-60) meses±36 meses. Cinquenta e sete (39%) não funcionaram adequadamente, com valores pressóricos inferiores à metade da referência. Os sistemas com funcionamento inadequado comprometeram as variáveis de eficiência dos nebulizadores A concordância entre os diferentes métodos de avaliação de acordo com a classificação; com funcionamento adequado e inadequado através do coeficiente Kappa foi 0,81(IC95%- 0,65-0,97), p<0,001. Na avaliação da sensibilidade e especificidade foi observado o ponto de corte de 23,5 PSI no manômetro FSA mostrou sensibilidade=99% e especificidade=79% (p<0,001). Houve associação significativa entre DVN, VR e pressões aferidas. CONCLUSÕES: Uma proporção significativa dos sistemas de nebulização não funcionou adequadamente. As variáveis de eficiência da nebulização estavam comprometidas indicando que a pressão gerada no compressor é um aspecto crítico na eficiência do tratamento. O método alternativo da avaliação dos compressores se apresentou adequado para ser utilizado nos compressores utilizados no tratamento da FC. / INTRODUCTION: Cystic fibrosis (CF) treatment of involves the use of medications supplied through nebulizers and their proper functioning is essential. OBJECTIVES: To evaluate the performance of jet nebulizers used by CF patients and to compare two pressure gauges Compressors evaluation. METHODS: This was a descriptive, cross - sectional study of the nebulizers used by patients with CF of the Mucoviscidosis Care Association of Minas Gerais. The patients brought compressors (Proneb Ultra®) and nebulizers (Pari LC plus®) for evaluation. The performance of the compressor was evaluated by operating pressure measurements using PARI PG101® manometers (PARI GmbH, Starnberg, Germany) and analog FSA (Famabras, Itaquaquecetuba, Brazil). The variables of efficiency of nebulization under study were: nebulizer delivery volume (NDV), drug output rate (DOR), and residual volume (RV), which were calculated by weighing each nebulizer before nebulization and 10 minutes after nebulization using a saline solution (2.5 mL). The mass median diameter (MMD) was calculated using the equation proposed by Standaert et al. Statistical analysis included the package R (v.2.15) and MINITAB, with alpha = 0.05. The Kappa coefficient was calculated to evaluate agreement of values between the equipment\'s, and ROC curve constructed to calculate the value measured in the FSA manometer with better sensitivity / specificity, using the PARI PG101® manometer as reference. The association between pressure values, NDV, DOR and RV was calculated by the Spearman correlation. RESULTS: We evaluated 146 systems with a median time of use of 32 (12-60) months ± 36 months. Fifty-seven (39%) did not function properly, with pressure values lower than half the reference. The systems with inadequate functioning compromised the efficiency variables of the nebulizers. The agreement between the different evaluation methods according to the classification; with adequate and inadequate functioning through the Kappa coefficient was 0.81 (95% CI -0.65-0.97), p <0.001. In the evaluation of sensitivity and specificity, the cut-off point of 23.5 PSI on the FSA manometer showed sensitivity = 99% and specificity = 79% (p <0.001). There was a significant association between NDV, DOR, RV and measured pressures. CONCLUSIONS: A significant number of the nebulizer systems were ineffective. The variables of nebulization efficiency were compromised, which indicated that the pressure generated by the compressor was a critical aspect for treatment efficiency. The alternative method of compressors evaluation was suitable for use in CF treatment routine.

The bronchiectatic lung is a diseased state in which the airways are chronically damaged and dilated. This state is found in the clinical entities of cystic fibrosis and non-cystic fibrosis bronchiectasis. These are two highly relevant chronic suppurative lung diseases in which an understanding of the microbiology of these patients is considered key to appropriate management. This has traditionally been via the use of traditional culture techniques. However, with the development of molecular methodologies, the previously perceived wisdom is being challenged. In both cystic fibrosis and non-cystic fibrosis bronchiectasis, Pseudomonas aeruginosa is considered the most significant pathogen. In CF there has been considerable concern surrounding the risk of transmission of Pseudomonas aeruginosa between patients on the basis of a significant quantity of research into this matter. In contrast, there has been very little research performed into the equivalent risk in non-cystic fibrosis bronchiectasis. In this thesis we describe an extensive single-centre epidemiological review of Pseudomonas aeruginosa spanning both these diseases. Via this we have shown evidence of cross-infection within a non-cystic fibrosis bronchiectasis cohort. This epidemiological review has included multiple genotyping methods including multilocus sequence typing and whole genome sequencing, As an extension of the epidemiological review, we have performed an in silico prediction of hypermutator status from the whole genome sequencing data to provide greater understanding of the likelihood of cross-infection, and have also demonstrated a culture-independent adaption of multilocus sequence typing for potential screening for cross-infection. In addition to Pseudomonas aeruginosa, we have also looked at the wider bacterial community in the lungs of patients with these two conditions via culture-independent techniques. We have shown that whilst Pseudomonas aeruginosa is often an important component, these are clearly complex communities. We have primarily investigated the cohort with non-cystic fibrosis bronchiectasis, but we have demonstrated associations between clinically-relevant markers and complexity of the bacterial communities within the lungs of both these cohorts of patients. Whilst we have used the gold-standard technique of 16S rRNA sequencing, we have also shown the validity of a simple and potentially more feasible profiling technique for standard clinical care. In summary, through the application of culture-dependent and independent molecular techniques, this research has shed light on the epidemiology of Pseudomonas aeruginosa within our respiratory cohorts, and the complexity and clinical relevance of the wider microbial communities within these patients. Such studies are essential if we are to advance our understanding of the bronchiectatic lung and optimise strategies for patient management.

Introdução: As bronquiectasias não-fibrocísticas são uma doença supurativa crônica caracterizada pela dilatação anormal e irreversível de um ou mais brônquios e são a via final de uma grande variedade de doenças, embora possam não ter uma causa identificável. Elas levam ao comprometimento da função pulmonar, colonização bacteriana crônica das vias aéreas, infecções respiratórias de repetição, redução da tolerância ao exercício e piora na qualidade de vida, entre outras coisas. Existem poucos estudos na literatura que abordam os fatores relacionados ao prognóstico desses pacientes. Objetivos: O objetivo deste estudo é avaliar a taxa de mortalidade e os fatores relacionados à morbidade e à mortalidade de uma coorte de pacientes com bronquiectasias não-fibrocísticas durante um seguimento de 6 a 8 anos e testar a habilidade dos escores Bronchiectasis Severity Index (BSI) e FACED de predizer a mortalidade dos pacientes na nossa coorte. Materiais e métodos: Trata-se de um estudo prospectivo de uma coorte de 70 pacientes com bronquiectasias não-fibrocísticas que foram originalmente recrutados de Maio de 2008 a Agosto de 2010. O estudo original forneceu os dados necessários para a classificação de gravidade da doença segundo os escores BSI e FACED e todos os dados usados para esse propósito foram coletados na avaliação inicial. Após o cálculo dos escores, os pacientes foram separados em diferentes grupos de acordo com a gravidade da doença. Nós também avaliamos os prontuários de todos os pacientes para determinar o número de hospitalizações por exacerbações após a avaliação inicial, o desfecho a longo prazo para cada paciente e a causa do desfecho quando apropriado. Os desfechos foram definidos como favoráveis e desfavoráveis (sobreviventes submetidos a transplante pulmonar e óbito por todas as causas) e foram determinados até 1° de março de 2016. Resultados: Dos 70 pacientes, 27 (38,57%) haviam morrido e 1 (1,43%) sido submetido ao transplante pulmonar. Análise de sobrevivência demonstrou que o tempo médio para a ocorrência dos desfechos desfavoráveis foi de 74,67 ± 4,00 meses (IC 66,82 – 82,52). A principal causa de óbito foi a exacerbação infecciosa aguda das bronquiectasias (60,7% dos óbitos). Na nossa coorte, o modelo de risco proporcional de Cox identificou a idade (p=0,035; HR 1,04; IC 1,01 – 1,08), o VEF1 % do previsto (p=0,045; HR 0,97; IC 0,93 – 0,99) e a Pemax (p=0,016; HR 0,97; IC 0,94 – 0,99) como preditores independentes de desfechos desfavoráveis. A maior parte dos pacientes (44,3%) foi classificada como tendo doença grave pelo escore BSI e 97,2% como tendo doença leve ou moderada (48,6% cada) pelo escore FACED. De maneira geral, o escore FACED foi um melhor preditor de desfechos desfavoráveis na nossa população de pacientes (log-rank test, FACED p = 0,001 e BSI p = 0,286). A análise da curva ROC demonstrou que ambos os escores foram similares na predição de desfechos desfavoráveis (área sob a curva BSI 0,65; FACED 0,66), mas nenhum deles foi um bom preditor para essa população específica de pacientes. Conclusão: Os pacientes da nossa coorte apresentaram maior comprometimento da função pulmonar e uma taxa de mortalidade mais alta do que o previamente reportado na literatura. A principal causa de óbito foi a exacerbação infecciosa aguda da doença. A idade mais avançada, o VEF1 % do previsto e uma Pemax mais baixa foram os fatores independentemente associados aos desfechos desfavoráveis. Os escores FACED e BSI não foram bons preditores de mortalidade para este grupo de pacientes, contrastando com os dados disponíveis na literatura até o momento, portanto outros estudos incluindo um maior número de pacientes são necessários para validar o uso deles na nossa população. / Background: Non-cystic fibrosis bronchiectasis is a chronic suppurative disease characterized by an abnormal and irreversible dilation of one or more bronchi. It is the final pathway of a large number of diseases, although it can be present without an identifiable cause. It leads to impaired lung function, chronic bacterial colonization, recurrent respiratory tract infections, reduced exercise tolerance and poor quality of life, among other things. There are few studies about prognostic factors in these patients. Objectives: The goal of this study is to assess the mortality rates and the factors related to the morbidity and mortality on a cohort of patients with non cystic fibrosis bronchiectasis during a 6 to 8-year follow-up and to test the ability of the Bronchiectasis Severity Index (BSI) and FACED scores in predicting mortality in our cohort. Materials and methods: This was a prospective cohort analysis of 70 patients with non-cystic fibrosis bronchiectasis who were originally recruited from May 2008 to August 2010. The original study records provided the necessary data for the determination of the disease severity scores (BSI and FACED) and all the data used for that purpose were collected at baseline. After the calculation of the scores, patients were separated into different groups according to disease severity. We also reviewed the records of all patients to determine the number of hospitalizations for exacerbations after baseline, the long-term outcome for each patient and the cause of the outcome when appropriate. Outcomes were defined as favorable and unfavorable (survivors who underwent lung transplantation and death from all causes) and were determined as of March 1st, 2016. Results: Out of 70 patients, 27 (38.57%) had died and 1 (1.43%) had undergone lung transplantation by the end of the study. Survival analysis demonstrated that the mean time for the occurrence of an unfavorable outcome was 74.67 ± 4.00 months (CI 66.82 – 82.52). The main cause of death among non-survivors was an acute infectious exacerbation of bronchiectasis (60.7% of the deceased). In our cohort, the multivariate Cox proportional hazard model analysis identified age (p=0.035; HR 1.04; CI 1.01 – 1.08), FEV1 % of predicted (p=0.045; HR 0.97; CI 0.93 – 0.99) and MEP (p=0.016; HR 0.97; CI 0.94 – 0.99) as independent predictors of unfavorable outcomes. Most patients (44.3%) were classified as having severe disease when BSI was used and 97.2% as having a mild or moderate disease (48.6% each) when FACED was used. Overall the FACED score was better at predicting unfavorable outcomes in our population of patients (log-rank test, FACED p = 0.001 and BSI p = 0.286). AUC from the ROC analysis shows us that both scores are similar in predicting poor outcomes in our cohort (BSI 0.65; FACED 0.66), but they weren't good predictors for this specific population. Conclusion: Patients in our cohort had worst lung function and a higher mortality rate than previously reported and the main cause of death among them was an acute infectious exacerbation of bronchiectasis. Older age, lower FEV1 % of predicted and lower MEP were independently linked to the occurrence of poor outcomes. FACED and BSI scores were not accurate in predicting mortality in our cohort, contradicting the available data at the moment, so other studies including a greater number of subjects are needed to validate their use in our population.

Orientador: José Vicente Tagliarini / Resumo: CAMPOS, C. S. M. 2018. Avaliação da incidência e evolução das manifestações das doenças nasais em pacientes portadores de fibrose cística. 2018. Dissertação (Mestrado) – Faculdade de Medicina de Botucatu, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, 2018. Introdução: A fibrose cística é uma doença originada da mutação do gene responsável pela codificação da proteína CFTR. A ausência ou defeito dessa proteína leva a um transporte irregular de sal e água em células mucosas respiratórias e de glândulas exócrinas podendo resultar em diversas manifestações clínicas. As alterações otorrinolaringológicas frequentes são rinossinusite crônica e polipose nasal. Objetivo: Avaliar a incidência e a evolução de doenças nasais em pacientes portadores de fibrose cística com exame videonasolaringoscópico documentado em prontuário do período de agosto de 2015 a agosto de 2017. Casuística e Métodos: Realizou-se a coleta de dados de 65 pacientes acompanhados no ambulatório de fibrose cística do Hospital das Clínicas de Botucatu. Foram incluídos os pacientes que possuíam exames videonasolaringoscópicos realizados durante o período de acompanhamento e que concordaram em participar do estudo. Realizou-se um estudo de coorte com avaliação dos dados epidemiológicos, presença de comorbidades, achados nos exames videonasolaringoscópicos, positivação de cultura de orofaringe e resposta ao tratamento clínico. Resultados: Foram analisados 51 pacientes. A mutação delta F508 esteve pr... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: CAMPOS, C.S.M. 2018. Evaluation of the incidence and evolution of the manifestations of nasal diseases in patients with cystic fibrosis. 2018. Thesis (Master) – Botucatu Medical School, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, 2018. Introduction: Cystic fibrosis is a disease originated from the mutation of the gene responsible for the coding of the CFTR protein. The absence or defect of this protein leads to an irregular transport of salt and water in respiratory mucous cells and exocrine glands, resulting in several clinical manifestations. Frequent otorhinolaryngological changes are chronic rhinosinusitis and nasal polyps. Objective: To evaluate the incidence and evolution of nasal diseases in patients with cystic fibrosis with a videonasolaryngoscopic exam documented in medical records from August 2015 to August 2017. Casuistry and Methods: Data were collected from 65 patients followed in the cystic fibrosis outpatient clinic Botucatu Medical School. Patients who had videonasolaryngoscopic examinations performed during the follow-up period and who agreed to participate in the study were included. A cohort study was conducted with epidemiological data, presence of comorbidities, findings in videonasolaryngoscopic examinations, oropharyngeal culture positivity and response to clinical treatment. Results: Fifty-one patients were analyzed. The delta F508 mutation was present in 20 patients. The comorbidities evaluated were: bronchiectasis (n = 39), p... (Complete abstract click electronic access below) / Mestre

Introdução: O tratamento dos pacientes com fibrose cística envolve o uso de medicamentos ototóxicos, sendo que os mais frequentemente utilizados são os antibióticos aminoglicosídeos. Devido ao uso frequente deste tipo de medicamento, os pacientes com fibrose cística apresentam risco de desenvolver perda auditiva. Objetivo: o objetivo deste estudo foi avaliar a audição dos pacientes com fibrose cística pela audiometria de altas frequências (AAF) e emissões otoacústicas por produto de distorção (EOAPD). Pacientes e métodos: estudo transversal retrospectivo e prospectivo, incluindo 75 indivíduos, sendo 39 do grupo de estudo e 36 do grupo controle. Foram realizados os exames de AAF (de 250 a 16.000 Hz) e EOAPD. Resultados: o grupo de estudo apresentou limiares na AAF significativamente mais elevados em 250, 1.000, 8.000, 9.000, 10.000, 12.500 e 16.000 Hz. (p=0,004) e maior prevalência de alterações nas EOAPD em 1.000 e 6.000 Hz (p=0,001), com amplitudes significativamente mais baixas em 1.000, 1.400 e 6.000 Hz. Houve associação significativa entre as alterações dos limiares auditivos na AAF com o número de cursos de aminoglicosídeos realizados (p=0,005). Oitenta e três por cento dos pacientes que realizaram mais de 10 cursos de aminoglicosídeos apresentaram perda auditiva na AAF. Conclusão: Um número expressivo de pacientes com fibrose cística que receberam repetidos cursos de aminoglicosídeos apresentou alterações na AAF e EOAPD. realização de 10 ou mais cursos de aminoglicosídeos esteve associada às alterações na AAF. / Introduction: the treatment of patients with cystic fibrosis involves the use of ototoxic drugs, and the most frequently used are the aminoglycoside antibiotics. Due to the frequent use of this drug, cystic fibrosis patients are at risk to develop hearing loss. Objective: the aim of this study was to evaluate the hearing of patients with cystic fibrosis by high frequency audiometry (HFA) and distortion product otoacoustic emissions (DPOAE). Patients and methods: retrospective and prospective crosssectional study including 75 individuals, 39 of the study group and 36 in the control group. HFA (250 – 16,000 Hz) and DPOAE tests were conducted. Results: the study group had thresholds significantly higher in the HFA in 250, 1,000, 8,000, 9,000, 10,000, 12,500 and 16,000 Hz (p=0.004) and higher prevalence of abnormal DPOAE at 1,000 and 6,000 Hz (p=0.001), with significantly lower amplitudes of 1,000, 1,400 and 6,000 Hz. There was a significant association between changes in hearing thresholds in HFA with the number of courses of aminoglycosides performed (p=0.005). Eighty-three percent of patients who completed more than 10 courses of aminoglycosides had hearing loss in HFA. Conclusion: a significant number of patients with cystic fibrosis who received repeated courses of aminoglycosides showed alterations in HFA and DPOAE.

Despite affecting many organ systems, the leading cause of morbidity and mortality in the cystic fibrosis (CF) population is lung disease. For the current studies we investigated elements of CF lung disease in a porcine model of CF and in people with CF. Our primary analysis tool was chest computed tomography (CT). To investigate early CF lung disease we examined three week old CF and non-CF pigs. We found three week old CF pigs to have large, irregular tracheal smooth muscle bundles, airways of reduced size, airways of irregular shape, and airways of abnormal distensibility. Three week old CF pig lung parenchyma was more heterogenous in density than three week non-CF pigs, especially in the right cephalad lung. The degree of lung tissue heterogeneity in CF pigs correlated with the degree of lung infection. Three week old CF pigs also had significantly more air trapping upon exhalation, evidence of airflow obstruction, than non-CF pigs. The degree of air trapping correlated with the degree of mucus accumulation in the airways. These data show that CF pigs spontaneously develop hallmark features of CF lung disease within weeks of birth, and that abnormal airway growth and development in CF may contribute to lung disease. This study helped set the foundation for future comparative studies involving CF therapeutics, for example, antibiotics and mucolytics. In adults with CF we performed a before drug, after drug study. The drug was ivacaftor, and it restores the basic underlying defect in a subset of people with CF: impaired function of a particular anion channel. We hypothesized that abnormal airway smooth muscle behavior in people with CF, known as “CF asthma,” is, in part, a primary pathogenic mechanism of CF lung disease. We tested our hypothesis by assaying smooth muscle tone before and after administration of ivacaftor. We limited the time duration to two days. We reasoned two days was long enough for ivacaftor to become effective, but not long enough to reverse long standing lung infection and inflammation which could affect smooth muscle function independently. The implication being, that observed changes would be directly due to restoration of the CF defect. We found evidence suggesting relaxation of airway and vascular smooth muscle tone. And, the change in airway smooth muscle tone correlated with the change in vascular smooth muscle tone. These data suggest that impaired smooth muscle function is a primary element of CF lung disease. Many of the people in our two day ivacaftor study returned for follow up after one year of ivacaftor therapy. We hypothesized that radiographic features of lung disease would improve following one year of ivacaftor therapy. We observed no change in lung volume upon inspiration, but a reduction in expiratory lung volume, approximately half of which occurred within two days. Our airway measurements were confounded by errors in scan reconstruction, however, other published studies report airway wall thinning over long term ivacaftor administration. Taken together, these studies of pigs with CF and people with CF, help us understand this disease.