Molecular typing of Candida albicans strains isolated from nosocomial candidemia

Yeasts of the genus Candida have been recognized as important microorganisms responsible for nosocomial fungemia. Six blood-stream and two intravenous central catheter C. albicans strains were isolated from eight patients and studied by electrophoretic karyotyping of chromosomal DNA by pulsed-field gel electrophoresis. Seven chromosomal DNA profiles were identified. Two patients showed isolates with the same profile, suggesting nosocomial transmission. Karyotyping of C. albicans revealed an excellent discriminatory power among the isolates and may therefore be useful in the study of nosocomial candidemia.

Avaliação do efeito da microfauna do tanque de arejamento no efluente final

O presente trabalho, efetuado na Estação de Tratamento de Águas Residuais do Freixo (ETAR do Freixo), decorreu durante um período de nove meses, (entre Dezembro de 2012 e Agosto de 2013), e teve como principais objetivos: - a observação microscópica e respetiva identificação dos organismos presentes nas lamas ativadas dos reatores biológicos da ETAR (incidindo nos protozoários, metazoários e bactérias filamentosas); - estabelecer a relação entre os organismos identificados/quantidade respetiva e a sedimentabilidade das lamas ativadas e sua influência no processo de depuração; - avaliar a variação das espécies identificadas com as alterações processuais. Para o efeito, a metodologia utilizada foi: - a colheita diária de amostras em vários pontos da ETAR; - a determinação dos parâmetros operacionais e caracterização das amostras recolhidas, tendo sido efetuadas 6039 análises físico-químicas, incluindo ao afluente à ETAR, ao afluente e ao conteúdo dos dois reatores biológicos, à corrente de recirculação de lamas e ao efluente; - a visualização diária microscópica ótica sem contraste de fase dos microrganismos presentes nos reatores biológicos; - a visualização microscópica ótica com contraste de fase da microfauna presente nos reatores biológicos, sendo efetuadas 16 identificações e quantificações dos protozoários presentes nas lamas ativadas dos dois reatores e 10 identificações e quantificações das bactérias filamentosas presentes nos dois reatores biológicos. O início do estudo ocorreu num período em que se começou a verificar um aumento excessivo de espumas nos decantadores secundários, resultando numa fraca sedimentabilidade das lamas e numa menor qualidade do efluente final. Na tentativa de reduzir a excessiva ascensão do manto de lamas que se verificou, foram efectuadas alterações operacionais, consistindo: - na alteração da razão de recirculação da decantação secundária para os reatores biológicos; - na introdução de um composto altamente concentrado em matéria orgânica na corrente de recirculação de lamas; - na alteração da extração de lamas biológicas. Verificou-se que as alterações processuais efetuadas foram muito eficazes na diminuição do manto de lamas da decantação secundária, bem como muito eficazes na qualidade do efluente final. Durante os meses de Fevereiro a Agosto fez-se o acompanhamento diário de todas as condições de operação de modo a manter e validar o procedimento de operação, o qual se considerou muito eficaz em termos de obtenção de uma água tratada de excelente qualidade. Durante o estudo efetuado, verificou-se que a população microbiológica existente nos dois reatores biológicos se manteve praticamente inalterada durante todo o período, sendo os móveis de fundo e os sésseis os grupos dominantes. Esta dominância traduziu-se na elevada qualidade do efluente final que se observou a partir do mês de Fevereiro, tendo dificultado o estudo de novas condições de operação, mas facilitando a validação do procedimento adotado. No que se refere às bactérias filamentosas, verificou-se que são diversas as espécies presentes nos reatores biológicos e que existem em grande abundância, sendo que o Tipo 0092 é claramente dominante. O excessivo crescimento deste tipo de bactérias mostrou ser o maior problema a nível microbiológico no processo de tratamento da instalação, tornando-se crítico no período de inverno em que a temperatura e os picos de pluviosidade se mostraram condições favoráveis ao seu desenvolvimento. Para além da temperatura outros fatores mostraram-se responsáveis pelo seu crescimento tais como a razão Alimento/Microrganismo (A/M), a idade das lamas, a carga mássica afluente e o teor de oxigénio dissolvido nos reatores biológicos. Pode-se concluir que apesar de não se trabalhar com os valores teóricos dos parâmetros microbiológicos e operacionais considerados ideais, a ETAR do Freixo, possui um tratamento bastante eficaz na remoção da carga orgânica, na remoção de nutrientes e na remoção de sólidos suspensos totais, apesar da não existência de uma etapa de afinação final como a filtração.

Development of new methodologies in sample treatment for proteomics workflow based on enzymatic probe sonication technology and mass spectrometry

Thesis submitted to the Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia, for the degree of Doctor of Philosophy in Biochemistry

Analysis of the clonal relationship among clinical isolates of Salmonella enterica serovar Infantis by different typing methods

Salmonella Infantis has been the second most common serovar in Argentina in the last two years, being isolated mostly from paediatric hospitalised patients. In order to determine the clonal relationship among Salmonella Infantis strains, we examined 15 isolates from paediatric patient faeces in Argentina (12 geographically related and 3 geographically non-related) by using antimicrobial susceptibility, plasmid profiling, repetitive extragenic palindromic (REP) PCR, enterobacterial repetitive intergenic consensus (ERIC) PCR, and low-frequency restriction analysis of chromosomal DNA by pulsed field gel electrophoresis (PFGE). Four Spanish strains were included as controls of clonal diversity in molecular techniques. Antibiotype and plasmid profile was not useful as epidemiological tools. PFGE and REP-PCR were able to discriminate between Argentinean and Spanish isolates of Salmonella Infantis allowing to detect genetically related strains in three different cities. This finding indicates that a possible spread of a clone of this serovar in the North-eastern Region of Argentina has taken place in 1998.

The removal of xenobiotic compounds from wastewater through the use of biological processes and advanced oxidation technologies

Dissertação apresentada para obtenção do Grau de Doutor em Engenharia Química e Bioquímica pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Genetic diversity and antimicrobial resistance of enterococcal isolates from Southern region of Brazil

In the present study, a total of 455 enterococcal isolates, recovered from patients living in the city of Porto Alegre, State of Rio Grande do Sul, Brazil, during the period from July 1996 to June 1997, were identified to the species level by conventional biochemical and microbiological tests, and assayed for their susceptibilities to antimicrobial agents. The genetic diversity of antimicrobial resistant strains was evaluated by pulsed-field gel electrophoresis (PFGE) analysis of SmaI restricted chromosomal DNA. The most frequent species was Enterococcus faecalis (92.8%). Other species identified were: E. faecium (2.9%), E. gallinarum (1.5%), E. avium (1.1%), E. hirae (0.7%), E. casseliflavus (0.4%), E. durans (0.4%) and E. raffinosus (0.2%). The overall prevalence of isolates with high-level resistance (HLR) to aminoglycosides was 37.8%. HLR to gentamicin was found in 24.8%. No strains with acquired resistance to vancomycin were found. PFGE analysis showed the predominance of clonal group A, comprising strains isolated from different clinical specimens obtained from patients in three hospitals. These results suggest intra and inter-hospital dissemination of one predominant clonal group of E. faecalis isolates with HLR to gentamicin in the hospitals included in this study.

Clinical and epidemiological aspects of HTLV-II infection in São Paulo, Brazil: presence of Tropical Spastic Paraparesis/HTLV-Associated Myelopathy (TSP/HAM) simile diagnosis in HIV-1-co-infected subjects

In this study, the epidemiological and clinical features observed in solely HTLV-II-infected individuals were compared to those in patients co-infected with HIV-1. A total of 380 subjects attended at the HTLV Out-Patient Clinic in the Institute of Infectious Diseases "Emilio Ribas" (IIER), São Paulo, Brazil, were evaluated every 3-6 months for the last seven years by infectious disease specialists and neurologists. Using a testing algorithm that employs the enzyme immuno assay, Western Blot and polymerase chain reaction, it was found that 201 (53%) were HTLV-I positive and 50 (13%) were infected with HTLV-II. Thirty-seven (74%) of the HTLV-II reactors were co-infected with HIV-1. Of the 13 (26%) solely HTLV-II-infected subjects, urinary tract infection was diagnosed in three (23%), one case of skin vasculitis (8%) and two cases of lumbar pain and erectile dysfunction (15%), but none myelopathy case was observed. Among 37 co-infected with HIV-1, four cases (10%) presented with tropical spastic paraparesis/HTLV-associated myelopathy (TSP/HAM) simile. Two patients showed paraparesis as the initial symptom, two cases first presented with vesical and erectile disturbances, peripheral neuropathies were observed in other five patients (13%), and seven (19%) patients showed some neurological signal or symptoms, most of them with lumbar pain (five cases). The results obtained suggest that neurological manifestations may be more frequent in HTLV-II/HIV-1-infected subjects than those infected with HTLV-II only.

Origem Anómala da Artéria Coronária Esquerda a Partir da Artéria Pulmonar

OBJECTIVE: To assess the frequency and severity of the anomalous origin of the left coronary artery (ALCA) from the pulmonary artery (PA). DESIGN OF THE STUDY: Prospective study of case series between March 1991 and December 1994. SETTING: Referral-based Paediatric Cardiology Department of a Tertiary Care Center. PATIENTS AND METHODS: Five consecutive patients (pts) with anomalous origin of the LCA from the PA; there were three infants aged 4 months and two children one 8 year and one 9 year old. There were three girls and two boys. All pts had clinical and 2D-echo and Doppler investigation prior to cardiac catheterization (CC). Indication for CC was based in the association of symptoms and signs of myocarditis or dilated cardiomyopathy of acute or subacute onset and electrocardiographic (ECG) signs of ischemia in infants. In older patients (pts) diagnosis was suspected mainly from ECG. During CC in all pts, aortograms and when necessary selective coronary angiograms were performed. Surgical correction was performed in all children. In two pts stress exercise ECG and stress Thallium studies before and after surgery were performed. RESULTS: two pts had "adult" an three had "infantile" type of ALCA from the PA. CC was performed and diagnosis was confirmed at surgery in all cases. In one child, correct diagnosis was made by ECO prior to CC and in one case LCA to PA fistula was suspected on Colour-Doppler study. No complications were attributed to CC. Several types of surgery were performed: reimplantation of the ALCA from the PA to the aorta (three pts); tunnel connection of the aorta to the ALCA via the PA (one pt) and left internal mammary to LCA anastomosis (one pt). Two infants died intraoperatively due to extensive myocardial infarction and poor left ventricular function. All the three survivors are asymptomatic after a mean follow up of 34 months. Two oldest pts are currently in New York Heart Association functional class I with normal ECG and improved myocardial perfusion on Thallium scan despite almost total occlusion of LCA at the site of implantation in the aorta as diagnosed on coronary angiogram. CONCLUSIONS: ALCA from PA is associated with major morbidity and mortality. Diagnosis should be suspected in pts with unexplained myocardial ischemia on ECG and even more if it is associated to clinical signs of dilated cardiomyopathy or myocarditis. Careful assessment on ECO and pulsed Doppler and colour flow mapping should make the diagnosis in most cases. Although surgery can be performed based only on ECO diagnosis, we strongly advise for angiography in all cases as in our experience there are false negative diagnosis by ECO. Preoperative Thallium studies can be useful for the selection of the type of surgery as pts with very little viable myocardium will not survive the establishment of a direct systemic to coronary blood flow and may be candidates for heart transplantation.

Distribuição de Contaminantes Orgânicos em Solos Calcários – Influência dos minerais de Argila

O solo é um recurso multifuncional e vital para a humanidade, apresentando funções ecológicas, técnico-industriais, socioeconómicas e culturais, estabelecendo um vasto capital natural insubstituível. Face à sua taxa de degradação potencialmente rápida que, devido ao crescente desenvolvimento económico e incremento da população mundial, tem vindo a aumentar nas últimas décadas, o solo é, atualmente, um recurso finito e limitado. Devido a esta problemática, o presente documento visa abordar a progressiva preocupação sobre as questões geoambientais e toda a investigação que as envolvem, avaliando o modo como os contaminantes se dispersam pelo solo nas diferentes fases do mesmo (fases sólida, líquida e gasosa). A parte experimental centrou-se na análise da adsorção do benzeno, a partir da determinação das isotérmicas de adsorção. Para tal, foram previamente preparados reatores com calcário, sendo alguns deles previamente contaminados com um biocombustível, biodiesel, a uma concentração constante. Este processo foi monitorizado com base na evolução temporal da concentração na fase gasosa, através da cromatografia gasosa. De entre os objetivos, procurou-se analisar a distribuição dos contaminantes pelas fases constituintes do solo, ajustar os dados experimentais obtidos os modelos matemáticos de Langmuir, Freundlich e Polinomial, e verificar e discutir as soluções mais adequadas.

Phenotypical and genotypical characterization of Bordetella pertussis strains isolated in São Paulo, Brazil, 1988-2002

Whooping cough or pertussis was a major cause of childhood morbidity and mortality in the world until the introduction of a whole-cell vaccine in the 1940's. However, since the early 1980's whooping cough cases have increased in many countries, becoming an important problem of public health. This increase may be due to accuracy of laboratory diagnosis and reporting of the disease, a decline in immunity over time, demographic changes, and adaptation of the bacterial population to vaccine-induced immunity. The purpose of this study was to analyze phenotypically and genotypically a collection of 67 Bordetella pertussis isolates recovered during the period 1988-2002 in São Paulo State, Brazil to determine their characteristics and relatedness. All isolates were submitted to susceptibility testing to erythromycin, serotyping, and 56 isolates were analyzed by Pulsed Field Gel Electrophoresis (PFGE). All isolates were susceptible to erythromycin and the majority of them belonged to serotype 1,3. The 56 isolates were classified into 11 PFGE profiles according to the differences in banding patterns. Although more than 60% of the isolates were recovered from patients aged less than three months, almost 15% of them were isolated from adolescents/adults evidencing the increase in the incidence of pertussis among this group of age.

Epidemiological characterization, antimicrobial resistance and virulence mechanisms of human and animal streptococci

Dissertação para obtenção do Grau de Doutor em Biologia

Molecular characterization of vancomycin-resistant Enterococci strains eight years apart from its first isolation in São Paulo, Brazil

E. faecium was the first reported VRE species, carrying the vanA gene in Brazil. In spite of this, vancomycin-resistant E. faecalis has become the predominant species in Brazilian hospitals. The aim of this study was to evaluate the genetic relatedness of VREs isolated in a Brazilian teaching hospital eight years apart from its first isolation. We analyzed 38 VRE strains obtained from 81 surveillance cultures of patients admitted to the four largest intensive care units in Hospital São Paulo in February, 2006. Presence of the vanA gene was assayed by PCR and PFGE analysis was used for molecular characterization. All VRE strains carried the vanA gene. Two distinct clonal groups were observed among vancomycin-resistant E. faecalis. Vancomycin-resistant E. faecium belonged to five distinct clones were demonstrated by molecular typing. All of these clones were different from the first vancomycin-resistant enterococci clone isolated eight years ago in our hospital.

Extended-spectrum beta-lactamases among Enterobacteriaceae isolated in a public hospital in Brazil

Extended-spectrum β-lactamases (ESBL) in enterobacteria are recognized worldwide as a great hospital problem. In this study, 127 ESBL-producing Enterobacteriaceae isolated in one year from inpatients and outpatients at a public teaching hospital at São Paulo, Brazil, were submitted to analysis by PCR with specific primers for blaSHV, blaTEM and blaCTX-M genes. From the 127 isolates, 96 (75.6%) Klebsiella pneumoniae, 12 (9.3%) Escherichia coli, 8 (6.2%) Morganella morganii, 3 (2.3%) Proteus mirabilis, 2 (1.6%) Klebsiella oxytoca, 2 (1.6%) Providencia rettgeri, 2 (1.6%) Providencia stuartti, 1 (0.8%) Enterobacter aerogenes and 1 (0.8%) Enterobacter cloacae were identified as ESBL producers. BlaSHV, blaTEM and blaCTX-M were detected in 63%, 17.3% and 33.9% strains, respectively. Pulsed field gel eletrophoresis genotyping of K. pneumoniae revealed four main molecular patterns and 29 unrelated profiles. PCR results showed a high variety of ESBL groups among strains, in nine different species. The results suggest the spread of resistance genes among genetically different strains of ESBL-producing K. pneumoniae in some hospital wards, and also that some strongly related strains were identified in different hospital wards, suggesting clonal spread in the institutional environment.

Three transducers for one photodetector: essays for optical communications

Dissertation presented to obtain the PhD degree in Electrical and Computer Engineering - Electronics

Smqnr VARIANTS IN CLINICAL ISOLATES OF Stenotrophomonas maltophilia IN BRAZIL

SUMMARYStenotrophomonas maltophilia contains a novel chromosomally-encoded qnr gene named Smqnr that contributes to low intrinsic resistance to quinolone. We described Smqnr in 13 clinical isolates of S. maltophilia from two Brazilian hospitals, over a 2-year period. The strains were identified by API 20 NE (bioMérieux, France). Susceptibility by microdilution method to trimetroprim/sulfamethoxazole, ciprofloxacin, levofloxacin, minocycline, ceftazidime, chloramphenicol and ticarcillin/clavulanate was performed according to CLSI. PCR detection of Smqnr gene was carried out. The sequence of Smqnr was compared with those deposited in GenBank. Pulsed-field gel electrophoresis (PFGE) of all strains was performed. Thirteen Smqnr positives isolates were sequenced and three novel variants of Smqnr were identified. All 13 Smqnr isolates had distinguishable patterns by PFGE. This is the first report of Smqnr in S. maltophilia isolated in Brazil.