QUANTITATIVE VS. CONVENTIONAL PCR FOR DETECTION OF HUMAN ADENOVIRUSES IN WATER AND SEDIMENT SAMPLES

SUMMARY Human Adenoviruses (HAdV) are notably resistant in the environment. These agents may serve as effective indicators of fecal contamination, and may act as causative agents of a number of different diseases in human beings. Conventional polymerase chain reaction (PCR) and, more recently, quantitative PCR (qPCR) are widely used for detection of viral agents in environmental matrices. In the present study PCR and SYBR(r)Green qPCR assays were compared for detection of HAdV in water (55) and sediments (20) samples of spring and artesian wells, ponds and streams, collected from dairy farms. By the quantitative methodology HAdV were detected in 87.3% of the water samples and 80% of the sediments, while by the conventional PCR 47.3% and 35% were detected in water samples and sediments, respectively.

MOLECULAR CHARACTERIZATION OF AMERICAN CUTANEOUS LEISHMANIASIS IN THE TRI‑BORDER AREA OF ASSIS BRASIL, ACRE STATE, BRAZIL

SUMMARY In this study, Leishmaniaspecies were identified by Polymerase Chain Reaction (PCR). The epidemiology of patients suspected of having American Cutaneous Leishmaniasis in the municipality of Assis Brasil, Acre State, located in the Brazil/Peru/Bolivia triborder was also investigated. By PCR, the DNA of Leishmaniawas detected in 100% of the cases (37 samples) and a PCR-Restriction Fragment Length Polymorphism (RFLP) of the hsp 70gene identified the species in 32 samples: Leishmania (Viannia) braziliensis (65.6%) , L. (V.) shawi (28.1%) , L. (V.) guyanensis (3.1%) and mixed infection L. (V.) guyanensis and L. (Leishmania) amazonensis (3.1%)This is the first report of L. (V.) shawiand L. (L.) amazonensis in Acre. The two predominant species were found in patients living in urban and rural areas. Most cases were found in males living in rural areas for at least three years and involved in rural work. This suggests, in most cases, a possible transmission of the disease from a rural/forest source, although some patients had not engaged in activities associated with permanence in forestall areas, which indicate a possible sandflies adaptation to the periurban setting.

Genetic characterization of Portuguese Fasciola hepatica isolates

Dissertation presented to obtain the Master Degree in Molecular, Genetics and Biomedicine

Nested-PCR using MPB64 fragment improves the diagnosis of pleural and meningeal tuberculosis

Fluids in which Mycobacterium tuberculosis are seldom found, such as pleural and cerebrospinal liquids, are good candidates to be studied using PCR techniques. We detail our experience with a PCR assay applied to pleural and cerebrospinal fluids using the primer MPB64. Seventy three specimens were analyzed: 30 pleural fluids (PF), 26 pleural biopsies (PB) and 17 cerebrospinal fluids (CSF). The gold standard for the diagnosis of tuberculous meningitis was the positive culture for M. tuberculosis in CSF. Tuberculous pleural effusion was diagnosed when cultures of PF and/or PB were positive for M. tuberculosis, or the PB histology showed granulomas. Our results, compared to the gold standards employed, showed a sensitivity of 70%, specificity of 88%, positive predictive value of 82% and negative predictive value of 80%. The high specificity of the MPB64 fragment while still retaining a good sensitivity makes it very well suited for pleural and cerebrospinal tuberculosis diagnosis.

Monitoramento de pacientes com AIDS para o desenvolvimento de doença por citomegalovirus (CMV) usando-se PCR multiplex

O citomegalovirus é um patógeno importante em indivíduos infectados pelo vírus da imunodeficiência humana (HIV). A carga viral do CMV parece ser preditora da sintomatologia das infecções citomegálicas em pacientes com a síndrome da imunodeficiência adquirida (AIDS). Um protocolo de PCR multiplex que fornece informações de quantificação de DNA amplificando somente um ou dois genes alvo do CMV foi utilizado neste trabalho. Amostras mensais de sangue foram coletadas de 270 pacientes com AIDS. Vinte pacientes tiveram positividade para dois alvos por 3 ou mais consecutivas e apresentaram doença por CMV no decorrer do estudo. Os pacientes que não apresentaram positividade ou alternância de amostras positivas somente para um gene viral não desenvolveram doença ligada ao CMV. Os resultados sugerem que a PCR multiplex é um protocolo útil para a identificação dos pacientes com alta carga viral e maior risco de desenvolvimento de doença por CMV.

Prenatal toxoplasmosis diagnosis from amniotic fluid by PCR

Toxoplasmosis is one of the most common infections all over the world. Most cases are asymptomatic, except in immunosuppressed individuals and fetuses, which can be seriously damaged. Prenatal diagnosis should be made as soon as possible since treatment of the mother can minimize fetal sequelae. Our aim in this study was to test the polymerase chain reaction technique (PCR) in 86 samples of amniotic fluid from women who seroconverted during pregnancy. DNA was amplified using external primers and, in a second step, internal primers, in a nested PCR system. Samples were also inoculated into mice and the newborn were evaluated by T. gondii serology, skull x-ray, transfontanel ultrasound, fundoscopic examination, lumbar puncture and clinical examination. PCR was positive in seven cases and negative in 79. Among PCR-positive cases, two were negative by inoculation into mice and by clinical evaluation; among PCR-negative ones, three had clinical evidence of toxoplasmosis and one was positive after inoculation into mice. PCR showed values of sensitivity = 62.5% and specificity = 97.4%; the values of inoculation into mice where 42.9% and 100%, respectively. Although PCR should not be used alone for prenatal diagnosis of congenital toxoplasmosis, it is a promising method and deserves more studies to improve its efficacy.

Produção de milheto em consórcio com gramíneas forrageiras no semiárido cearense.

Resumo: Objetivou-se avaliar gramíneas com reconhecida tolerância a períodos de estresse hídrico em consórcio com a cultura do milheto e doses de nitrogênio. O ensaio foi realizado em Sobral-CE, em delineamento em blocos casualizados com os tratamentos sendo o consórcio da cultura do milheto com o capim-buffel ou capim-massai, com 3 doses de adubação em cobertura para o milheto, sendo: 0, 50 e 100 kg ha-1 de nitrogênio, e o tratamento testemunha sendo o plantio do milheto solteiro sem adubação de cobertura; com 3 blocos. Avaliaram-se os dados biométricos e produtividade de massa seca. O consórcio de culturas anuais com gramíneas forrageiras é alternativa interessante para produção de volumoso em região semiárida. O consórcio de milheto e capim-massai mostrou-se superior para dados biométricos e produtividade. O emprego de 100 kg ha-1 de N em cobertura na cultura do milheto propiciou maior produtividade de massa seca. [Millet production with forage consortium in semiarid region of State of Ceará]. Abstract: This study aimed to evaluate grasses with recognized tolerance to periods of water stress in partnership with millet cultivation and doses of nitrogen. The test was conducted in Sobral-CE, at a randomized block with treatments and millet culture consortium with buffel grass or massai grass with 3 fertilizer levels at coverage for millet, as follows: 50 and 100 kg ha-1 of nitrogen, and the control treatment being the planting millet single without cover fertilization; with 3 blocks. Evaluated were the biometric data and dry matter productivity. The consortium of annual crops with grasses is interesting alternative to massive production for semi-arid region. The consortium millet and massai grass was superior to biometric data and productivity. The use of 100 kg ha-1 of N topdressing in the millet culture provided greater dry mass productivity.

Identificação de genoespécies do complexo Borrelia burgdorferi sensu lato (s.l.) circulantes na fauna ixodideológica em portugal

Dissertação para obtenção do grau de Mestre em Microbiologia Médica

Recommendations for the detection of Leptospira in urine by PCR

In the present study PCR was applied to detect leptospires in human urine. Several approaches for sample processing were evaluated to optimize the detection of leptospires in urine mixed with this bacterium. Furthermore, some changes in the composition of the reaction mix were studied. No amplification was observed in acidic urine, therefore neutralization of the sample immediately after collection is strongly recommended. PBS gave better results than Tris or NaOH as neutralizing reagents. Freezing and thawing of samples before processing yielded negative results. Elimination of epithelial cells, leukocytes and crystals by centrifugation at 3,000 rpm at room temperature increased sensitivity. In addition, both the washing step after collecting leptospires by centrifugation and the inclusion of 0.1% bovine serum albumin in the reaction mix minimized the interference of other inhibitory compounds. These modifications were useful to improve the detection of Leptospira in urine by PCR.

Differentiation of Candida species obtained from nosocomial candidemia using RAPD-PCR technique

Thirteen strains of the genus Candida were isolated from catheter, urine and surgical wounds from individual patients of the Santa Casa de Misericórdia, Belo Horizonte, MG, Brazil. Ten strains were characterized as Candida albicans, two as Candida glabrata, and one as Candida parapsilosis. Isolates were evaluated for molecular relatedness by random amplified polymorphic DNA technique using 15 primers. The analysis of the genomic DNA obtained revealed a low intraspecific polymorphism and did not allow for the differentiation between strains of the same species obtained from distinct clinical sources (catheter, urine and surgical wounds). The RAPD profiles generated were able to differentiate among the species of Candida albicans, Candida parapsilosis and Candida glabrata strains isolated in this study.

Assessment of chemiluminescence and PCR effectiveness in relation to conventional serological tests for the diagnosis of Chagas' disease

While testing 414 sera for the diagnosis of Chagas' disease, the conventional reactions of indirect hemagglutination, indirect immunofluorescence and the immunosorbent assay showed a sensitivity of 95.7%, 100% and 98.2% and a specificity of 98%, 98% and 96.4%, respectively, and an excellent association using Fisher's exact test. Chemiluminescence presented 100% sensitivity and 89.6% specificity, while PCR showed 100% specificity and 1.2% sensitivity. It is believed that the three conventional serological reactions are still adequate for diagnosing Chagas' disease.

Carga proviral do HTLV-1 e HTLV-2: um método simples através da PCR quantitativa em tempo real

Os vírus linfotrópicos de células T humanas, quando integrados ao genoma da célula hospedeira, provírus, têm como marcador de replicação seu DNA proviral. A carga proviral parece ser um importante fator no desenvolvimento de patologias associadas a estes retrovírus. Neste estudo foi desenvolvida uma metodologia para quantificação absoluta da carga proviral dos HTLV-1 e HTLV-2 através da PCR em tempo real. Cinqüenta e três amostras de doadores de sangue com teste de ELISA reagente foram submetidas à metodologia, que utilizou o sistema TaqMan® para três seqüências alvo: HTLV-1, HTLV-2 e albumina. A quantificação proviral absoluta foi determinada através da proporção relativa entre o genoma do HTLV e o genoma da célula hospedeira, levando em consideração o número de leucócitos. O método apresentado é sensível (215 cópias/mL), prático e simples para quantificação proviral, além de eficiente e adequado para confirmação e discriminação da infecção pelos tipos virais.