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.

Orientadores: José Dirceu Ribeiro, Camila Isabel Santos Schivinski / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-25T16:15:32Z (GMT). No. of bitstreams: 1 Parazzi_PalomaLopesFrancisco_M.pdf: 3954861 bytes, checksum: 8928c4e51b5e3873d43ddcec22c35069 (MD5) Previous issue date: 2014 / Resumo: Introdução: Na fibrose cística (FC) os testes que avaliam a aptidão física tem sido estudado como marcador de prognóstico ou como ferramenta de avaliação da condição cardiorrespiratória. Objetivo: avaliar e comparar variáveis da ventilação pulmonar utilizando a capnografia volumétrica (capV): VE, VCO2, VE/VCO2, VD/VT, PetCO2; variáveis de espirometria: VEF1%, CVF% e VEF1/CVF; e parâmetros cardiorrespiratórios: FCar, FR, SpO2 no repouso e durante teste de esforço em crianças, adolescentes e adultos jovens entre 6 a 25 anos de idade, com (GFC) e sem fibrose cística (GC). Método: estudo clínico, prospectivo, controlado, com 128 indivíduos, 64 com FC, de ambos os gêneros, de Hospital Universitário. Todos realizaram exercício em esteira e os exames propostos após aprovação do Comitê de Ética da Instituição e assinatura do termo de Consentimento Livre e Esclarecido. Resultados: os pacientes com FC apresentaram valores estatisticamente diferentes para as variáveis de CapV e espirometria ao longo do teste de exercício. Antes do exercício as variáveis também foram diferentes, porém com significância estatística para: espirometria, SpO2, FR, VCO2, VE/VCO2, PetCO2 e escala de Borg. A comparação entre os grupos de pacientes com FC e GC foi realizada pelos testes Kruskal-Wallis e Mann-Whitney. Conclusão: a CapV é um instrumento que pode ser utilizado para análise de parâmetros ventilatórios durante o exercício físico. Todas as variáveis cardiorrespiratórias, da espirometria e da capnografia foram diferentes nos pacientes com FC quando comparados aos indivíduos saudáveis antes, durante e após exercício físico / Abstract: Introduction: In cystic fibrosis (CF) tests that assess physical fitness has been studied as a prognostic marker or as a tool for assessing the cardiorespiratory fitness Objective: To evaluate and compare variables of pulmonary ventilation using volumetric capnography (CAPV): VE, VCO2, VE/VCO2, VD/VT, PetCO2; spirometric variables: % FEV1 , FVC and FEV1/FVC % ; and cardiorespiratory parameters: FCar , RR, SpO2 at rest and during exercise testing in children, adolescents and young adults aged 6-25 years of age with (GFC) and without cystic fibrosis (GC). Method: Clinical, prospective, controlled study with 128 subjects, 64 with CF, of both genders, of University Hospital. All patients underwent treadmill exercise tests and proposed after approval by the Institutional Review Board and signing the consent form. Results: CF patients had statistically different values for the variables CAPV and spirometry throughout the exercise test. Before exercise variables were also different, but with statistical significance for spirometry, SpO2, RR, VCO2, VE/VCO2, PetCO2 Borg scale. The comparison between groups of patients with CF and control groups was performed by Kruskal - Wallis and Mann - Whitney tests. Conclusion: CAPV is a tool that can be used for analysis of ventilatory parameters during exercise. All cardiorespiratory variables, spirometry and capnography were different in CF patients compared to healthy subjects before and after exercise / Mestrado / Saude da Criança e do Adolescente / Mestra em Ciências

Orientador: Carlos Emilio Levy / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-25T23:09:16Z (GMT). No. of bitstreams: 1 Mauch_RenanMarrichi_M.pdf: 2012702 bytes, checksum: 947bbc196f2331b0a48b9596a06effdc (MD5) Previous issue date: 2014 / Resumo: A Fibrose Cística (FC) é uma doença genética decorrente da disfunção da proteína reguladora da condutância transmembrana (CFTR), essencial para o transporte de íons e água pela membrana celular, sendo a doença pulmonar a mais preponderante das manifestações, havendo colonização bacteriana seguida de infecções, principalmente por Pseudomonas aeruginosa, bactéria de maior relevância para pacientes com FC. Neste estudo, buscamos padronizar e avaliar o valor diagnóstico e prognóstico de um teste de ELISA (Enzyme-linked immunosorbent assay) para pesquisa de anticorpos séricos IgG anti-P. aeruginosa, comparando os resultados com a cultura microbiológica de material respiratório (padrão-ouro atual). Os níveis de anticorpos foram avaliados primeiramente em um estudo transversal, com 117 pacientes com FC atentidos no HC-Unicamp, buscando determinar a acurácia do teste, e paralelamente em um estudo longitudinal, com 78 pacientes inicialmente sem infecção crônica por P. aeruginosa, buscando monitorar a variação dos níveis de anticorpos em diferentes períodos de coleta de amostras. Observamos que a taxa de soropositividade e a mediana dos níveis de IgG anti-Pseudomonas foram significativamente maiores em pacientes cronicamente infectados pela bactéria, tendo o teste sensibilidade de 96,8%, especificidade de 98,1%, valor preditivo positivo de 96,8% e valor preditivo negativo de 98,1% para a detecção da infecção crônica. Houve aumento progressivo dos níveis de anticorpos dos pacientes ao longo do tempo, com maior significância em dois períodos de coleta, entre pacientes que apresentaram evolução no perfil de colonização/infecção por P. aeruginosa. Foi possível, pela pesquisa de anticorpos, a detecção da bactéria até 15 meses antes do primeiro isolamento positivo em cultura e pacientes com níveis de anticorpos elevados no início do estudo apresentaram maior risco de posterior evolução no perfil de colonização/infecção por P. aeruginosa. Concluímos que a sorologia pode ser um recurso diagnóstico de grande utilidade para a detecção precoce da infecção pulmonar P. aeruginosa em pacientes com FC, complementando resultados da cultura microbiológica. Introduzindo-a na rotina de acompanhamento dos pacientes, será possível a terapia antimicrobiana precoce, o que poderá ajudar a melhorar a função pulmonar dos pacientes e sua qualidade de vida / Abstract: Cystic Fibrosis (CF) is a genetic disease, resulting from disfunction of the CFTR protein, which is essential for the transportation of ions and water across the cell membrane, being the pulmonary disease the most prominent manifestation, where there is bacterial colonization followed by infections, mainly caused by Pseudomonas aeruginosa, the most relevant bacterium for CF patients. The aim of this study was to standardize and to evaluate the diagnostic and prognostic values of an ELISA (Enzyme-linked immunosorbent assay) test for detection of serum anti-P. aeruginosa IgG antibodies, comparing the results with the microbiological respiratory culture (current gold standard). The antibody levels were first evaluated in a cross sectional study, with 117 CF patients attended at the HC-Unicamp, seeking to evaluate the accuracy of the test, and in a parallel longitudinal study, with 78 patients initially without P. aeruginosa chronic infection, seeking to monitor the variation in the antibody levels in different periods of sample collection. We observed that the seropositivity rate and the median of the anti-Pseudomonas IgG antibody levels were significantly higher in chronically infected patients, with the serological test presenting a sensitivity of 96.8%, specificity of 98.1%, positive predictive value of 96.8% and negative predictive value of 98.1% for detection of chronic infection. There was a progressive increase of the antibody levels in the patients over time, with greater significance, in two collection periods, among patients who presented evolution in the P. aeruginosa colonization/infection status. Through antibody measurement, we could detect the bacterium until 15 months before the first positive isolation in microbiological culture and the patients with elevated antibody levels in the baseline showed higher risk for later evolution in the P. aeruginosa colonization/infection status. We conclude that serology can be a very useful diagnostic resource for early detection of P. aeruginosa pulmonary infection, complementing microbiological results. By introducing it on the follow-up routine, the early antimicrobial therapy will be possible, which will help to improve the patients¿ lung function and quality of life / Mestrado / Saude da Criança e do Adolescente / Mestre em Ciências

Orientador: Carmen Sílvia Bertuzzo / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-22T19:39:30Z (GMT). No. of bitstreams: 1 Marcelino_AlineRobertaBariani_M.pdf: 1077026 bytes, checksum: b7315e705aba4125ea2a4e2574a78b6b (MD5) Previous issue date: 2013 / Resumo: A Fibrose Cística (FC) é uma doença autossômica recessiva causada por mutações no gene CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) que acarretam em defeito ou na ausência da proteína por ele sintetizada. A CFTR, produto deste gene é uma proteína canal, localizada na membrana apical das células, responsável pela condução de íons cloreto. As mutações levam à ausência da proteína CFTR ou a alteração qualitativa/quantitativa da proteína, que acarreta no desequilíbrio osmótico entre os meios intra e extracelular. Como consequência há a ocorrência de muco viscoso e de difícil excreção nos pulmões e obstrução dos ductos pancreáticos, afetando desta forma o sistema respiratório e digestório. São conhecidas mais de 1.900 mutações no gene CFTR, sendo que mesmo em pacientes com mutações iguais como a F508del - com alta prevalência na população brasileira - há divergência entre os fenótipos observados. Dessa forma, o genótipo CFTR parece não ser determinante na modulação da gravidade clínica, uma vez que, indivíduos com mesmo genótipo CFTR apresentam manifestações clínicas diferentes. Outros genes, diferentes do CFTR foram associados à gravidade clínica dos pacientes, revelando que os produtos por eles expressos exercem algum tipo de ação modificadora do fenótipo da FC. Tais genes foram denominados modificadores e atuam em fatores secundários relacionados à evolução do quadro clínico, como a articulação do sistema imune. Os genes COX2 e IFRD1, com ação importante no sistema imune e no recrutamento de células de defesa foram identificados como modificadores da FC em estudos prévios realizados em uma população diferente da brasileira. No presente estudo, os polimorfismos -765G>C e 8473T>C no gene COX2 e 57460C>T no gene IFRD1, candidatos a modificadores, foram identificados nos pacientes e um estudo de associação genótipo-fenótipo foi conduzido a fim de verificar a ação moduladora de tais polimorfismos nos pacientes estudados. Nenhuma associação foi encontrada, exceto para o íleo meconial (p=0,028 - em pacientes com duas mutações identificadas no gene CFTR pertencentes à classe I, II e III) e para a polipose nasal (p=0,022 - em pacientes sem considerar o genótipo CFTR) para o polimorfismo 8473T>C no gene COX2 / Abstract: Cystic fibrosis (CF) is an autosomal recessive disease caused by CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene mutations that lead to defective polypeptide or lack of the protein CFTR. The CFTR is a channel protein located in the apical cells membrane, responsible for chloride ions conductance. The mutations lead to an osmotic disequilibrium between intra and extracellular mediums, which causes viscous mucus production that is hard to be eliminated from lungs and pancreatic ducts, affecting, this way, respiratory and digestive systems. More than 1,900 CFTR different mutations are known, and even patients that carries identical mutations as F508del - the most common one in Brazilian population - shows a great discrepancy between the phenotypes that are observed. Thus, CFTR genotype seems not to be crucial in disease clinical course modulation, once different subjects carrying the same CFTR mutations reveal distinctive clinical manifestations. Genes besides CFTR were associated to CF patients clinical manifestation, revealing that the molecules they express have some kind of modifier activity in CF phenotype. Such genes were labeled as modifier genes and they act in secondary factors related to clinical course evolution as immune system response. The genes COX2 and IFRD1 have an important role in immune system and defense cell recruitment and they were identified as CF modifiers in previous studies that analyzed different population from the Brazilian one. In this current study, the polymorphisms -765G>C, 8473T>C and 57460C>T located in these genes were identified in our patients and association genotype-phenotype were carried out in order to verify the modulator activity of such variants in the studied casuistic. There was not found association, except for meconium ileus (p=0,028 - in patients with two CFTR mutations from class I, II and III) and for nasal polyposis (p=0,022 - in patients whose CFTR genotype was not considered) to 8473T>C polymorphism in COX2 gene / Mestrado / Ciencias Biomedicas / Mestre em Ciências Médicas

Class of 2012 Abstract / Specific Aims: We sought to determine the influence of genetic variation of ADRB2 on the airway response to albuterol in patients with CF when compared to matched healthy controls at baseline and at 60 minutes following the administration of albuterol (2.5mg diluted in 3ml normal saline). Methods: Baseline pulmonary function (forced vital capacity, FVC, forced expiratory flow in 1-second, FEV1, mid-maximal expiratory flow, MMF, and forced expiratory flow at 50% of the FVC) was assessed in 17 patients with CF and 31 healthy subjects. Main Results: As expected, the healthy group had higher baseline pulmonary function when compared to the CF group (FVC=97±3 vs. 83±5; FEV1=95±3 vs. 72±6; MMF=90±4 vs. 54±8, % predicted for healthy and CF, respectively, mean±SE, p<0.05 for all. We compared Arg16Arg to Arg16Gly/Gly16Gly subjects. There was no effect of genotype on the response to albuterol in healthy subjects. However, in the CF group, we found that the Arg16Arg group (n=6) had an attenuated response to β-agonist when compared to the Gly-containing group (n=11) (FVC=0±0.9 vs. 6±3: FEV1=3±1 vs. 7±4: MMF=12±3 vs. 12±5 % change, for Arg16Arg and Gly-containing groups, respectively, p<0.05 for FVC, p=0.06 for FEV1). Conclusions: These results demonstrate a differential response to β-agonists according to genetic variation of the ADRB2 at amino acid 16. Due to the differences in FVC and FEV1 but not in MMF, these data suggest that the genetic difference in airway function is primarily in bronchodilation of the larger airways.

Viral respiratory infections (VRI) are common in children with cystic fibrosis (CF) and are associated with significant clinical deterioration. Little previous research has been conducted on VRI in adults with CF. This thesis describes a prospective study to determine the epidemiology and clinical impact of VRI among 100 adults with CF.The incidence of identifiable VRI was 1.66 cases/patient-year. Rhinovirus accounted for 72.5% of viruses. Identifiable VRI was associated with increased risk of pulmonary exacerbation, increased respiratory symptoms and higher C-reactive protein levels. Changes in the climate and seasons affected the incidence of identifiable VRI. Rhinovirus was most common in autumn and other viruses predominated during winter. Warmer ambient temperatures were associated with increased risk of rhinovirus infection while other viruses were more common in colder temperatures. Genetic sequencing of a subset of 42 rhinoviruses identified during the study showed that rhinovirus A accounted for 69% of cases and was associated with more severe respiratory symptoms and higher C-reactive protein levels than rhinovirus B.The impact of identifiable VRI on changes to bacterial communities within the lungs of patients with CF was investigated. Ribosomal intergenic spacer analysis (RISA) was developed as a tool to profile the bacterial diversity of CF sputum and was compared with standard culture and 16S rRNA gene pyrosequencing. No consistent effect of identifiable VRI on the microbial diversity of CF sputum was detected with any of these methods in longitudinal analysis of a subset of 18 patients.

No description available.

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

Cystic fibrosis (CF) is a common lethal hereditary disease resulting from mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CFTR dysfunction affects multiple organ systems and most morbidity and mortality in CF results from lung disease. The CF lung appears healthy at birth, but spontaneously develops airway disease characterized by infection, inflammation, mucus plugging and airway remodeling. A CF pig model was recently generated to determine the events that initiate lung disease. CF pigs recapitulate many findings seen in humans with CF, including the spontaneous development of lung disease. I used newborn CF pigs to investigate two leading hypotheses regarding CF disease initiation: abnormal airway surface liquid (ASL) composition and defective mucociliary transport (MCT). I developed an assay to study ASL composition and found that CF ASL contained similar sodium concentrations, elevated potassium concentrations, and a decreased fraction of volatile material. I developed an assay to measure MCT in vivo. By tracking individual particles in 3-dimensions I found that newborn pigs exhibit a ventrally directed cilia orientation in the trachea. I also found that MCT is highly heterogeneous and particles traveled at different speeds within airways and between airways, challenging the classic view that airway mucus exists as continuous blanket. Comparing particle transport revealed that non-CF and CF newborn pigs exhibit similar basal particle clearance and speeds. Cholinergic stimulation induces mucus and fluid secretion. Particles became stuck in newborn CF pigs after cholinergic stimulation and stasis persisted with tissue submersion. This challenged the leading hypothesis that attributes CF airway disease pathogenesis to ASL depletion. I hypothesized that adherent mucus impairs mucociliary transport in CF airways and I developed an assay to visualize mucus stasis in submerged tracheal segments ex vivo. CF trachea stimulated in vivo exhibited highly adhesive mucus entities that emerged exclusively from submucosal gland ducts. These adherent entities impaired MCT even with extremely high ASL depths. Non-CF trachea with combinatorial disruption of HCO3- and Cl- transport reproduced the defect in CF signifying that anion transport disruption was responsible for adherent mucus. These data suggest that CFTR disruption directly produces multiple host defense defects, including defective bacterial killing and abnormally adherent mucus. Therapeutic targeting of the described defects may provide new opportunities to intervene early and improve the lives of those with CF.

Cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel that when mutated causes the disease cystic fibrosis (CF). Many obstacles hinder the understanding of CF disease pathogenesis, impeding advancements in understanding how mutations cause disease, and slowing the progress towards new treatments. To this end, we have profiled the transcriptome (mRNA and microRNA) of human and newborn pig CF and non-CF airway epithelia. We show that the use of cross-species transcriptomics allows the identification of genes differentially expressed owing to the loss of CFTR, and not due to confounding environmental or secondary disease progression influences. The identification of reduced OAS1 expression in CF samples is a case in point. We also demonstrate the utility of transcriptome profiling and longitudinal studies in pigs, providing greater understanding of the molecular mechanisms underlying CF disease progression. MicroRNAs (miRNAs) comprise a large family of ~21-nt long non-coding RNAs that function as key post-transcriptional regulators of gene expression. Very little is known of how CFTR is regulated in the cell, both transcriptionally and post-transcriptionally. We discovered three miRNAs: miR-509-3p, miR-494 and miR-138 with possible CFTR regulatory functions. miR-509-3p or -494 directly target the CFTR mRNA, and decrease CFTR levels when over expressed; while inhibiting them had the opposite effect. Upon stimulating human airway epithelial cells with TNFα or IL-1β, we observed an increase in expression of both miRNAs mediated in part by the NF-κB transcription factor complex, with a concurrent decrease in CFTR expression. Gene ontology classification of predicted targets of miR-509-3p and/or miR-494 expressed in the airway epithelium revealed enrichment for genes in ion transport pathways. To our knowledge, this is the first suggestion of a possible role for miRNAs regulating a broad range of important epithelial electrolyte and fluid transport proteins. The study of miR-138 mediated regulation of CFTR expression has led to novel discoveries in the field of CFTR transcriptional control. We discovered SIN3A to be a novel transcriptional repressor of CFTR, interacting with CTCF on the CFTR promoter at the -20.9 kb DHS. By validating SIN3A as a conserved target of miR-138, we also discovered miR-138 to be a novel transcriptional regulator/activator of CFTR. The most common CFTR mutation, ΔF508, causes protein misfolding, degradation, and CF. Manipulating the miR-138/SIN3A regulatory network improved the biosynthesis of CFTR-ΔF508, restoring Cl- transport to human CF airway epithelia. To our knowledge, this is the first example of an individual miRNA having such broad regulatory functions. This discovery also provided novel targets for restoring CFTR function in cells affected by the most common CF mutation. To this end, we are utilizing the molecular signatures of miR-138 over-expression and SIN3A knockdown to identify candidate genes for RNA interference screens, and to identify candidate small molecule drugs that might mimic the effects of these two interventions. The goal of this approach is to develop a new therapeutic agent that restores anion transport to airway epithelia and other cell types and tissues affected by CF.