Uso de PCR e sequenciamento do rDNA 16S para identificação de bactérias do gênero Staphylococcus isoladas de mastite bovina

O objetivo deste trabalho foi identificar espécies de Staphylococcus (n=100) isoladas de mastite em rebanhos bovinos do Estado de Minas Gerais. Para esta finalidade foram utilizadas reações de PCR empregando oligonucleotídeos iniciadores descritos anteriormente para amplificar genes específicos de S. aureus (femA), S. intermedius (rDNA 16S) e S. hyicus (rDNA 16S-23S) e o sequenciamento do rDNA 16S. De acordo com as reações de PCR, 83 isolados foram identificados como S. aureus, 13 isolados como S. intermedius, dois como S. hyicus e dois isolados não foram identificados. Foram submetidos ao sequenciamento do rDNA 16S seis isolados identificados como S. aureus e os 17 restantes. Os seis isolados identificados como S. aureus confirmaram essa identificação. Dos outros 17 isolados, 13 foram identificados como S. chromogenes e quatro como S. hyicus, com similaridade igual ou superior a 99%. Baseando-se nos resultados da reação de PCR do gene femA e do sequenciamento do rDNA 16S, foram identificados 83 S. aureus, 13 S. chromogenes e quatro S. hyicus. Neste estudo os oligonucleotídeos iniciadores empregados na reação de PCR para S. intermedius não foram específicos, pois amplificaram também S. chromogenes; e os empregados na reação de PCR para S. hyicus não foram sensíveis, pois falharam na identificação de dois isolados de S. hyicus. A identificação definitiva das duas últimas espécies somente foi possível pelo sequenciamento do rDNA 16S.

Evaluation of PCR and multiplex PCR in relation to nested PCR for diagnosing Theileria equi

Conventional PCR (PCRTeq) for diagnosing Theileria equi and multiplex PCR (M/PCRTeq-Bc) for diagnosing T. equi and Babesia caballi were comparatively evaluated with nested PCR (N/PCR-Teq) for diagnosing equine piroplasmosis. In DNA sensitivity determinations, in multiple dilutions of equine blood that had tested positive for T. equi, PCR-Teq and N/PCR-Teq detected hemoparasite DNA in the larger dilutions (1:128), but did not differ significantly from the M/PCRTeq-Bc (1:64). In analyses on equine serum tested by ELISA, there was high agreement between this serological test and PCR-Teq (k = 0.780) and moderate agreement with N/PCR-Teq (k = 0.562) and M/PCRTeq-Bc (k = 0.488). PCR-Teq found a higher frequency of T. equi both in extensively and intensively reared horses, but this was not significant in relation to N/PCR-Teq (P>0.05), and both PCRs indicated that there was an endemic situation regarding T. equi in the population of horses of this sample. PCR-Teq was only significantly different from M/PCR-Teq-Bc (P<0.05). PCR-Teq presented high sensitivity and specificity, comparable to N/PCR-Teq, but with the advantage of higher speed in obtaining results and lower costs and risks of laboratory contamination. This accredits PCR-Teq for epidemiological studies and for determinations on affected horses.

Serological investigation and PCR in detection of pathogenic leptospires in snakes

Detection of Leptospira by PCR had not yet been described in snakes. This study investigated, by microscopic agglutination test (MAT) and PCR, the presence of antibodies to Leptospira spp. and Leptospira spp., respectively, in venomous and non-venomous wildlife and captivity snakes. All snakes were divided into three groups to be compared: Group 1 (wildlife snakes - WS); Group 2 (snakes in intensive captivity - IC), and Group 3 (collective semi-extensive captivity -CC). Of the 147 snakes studied, 52 (35.4%) were positive for leptospirosis by MAT, 8 (15.4%) belonging to Group 1 (WS), 34 (65.4%) to Group 2 (IC) and 10 (19.2%) to Group 3 (CC). Jararaca (Bothrops jararaca) presented the highest average titer (66.7%, N=22/33) among the three group studied, and Hardjo prajtino was the most prevalent serovar (88.5%, N=46/52), with titers varying from 100 to 3200. Leptospira interrogans was revealed by PCR in kidney and liver of caiçaca (Bothrops moojeni) and jararaca-pintada (Bothrops pauloensis), showing 100% and 93% identity respectively. Future studies should be carried out for better understanding of the role of snakes as a reservoir of Leptospira in nature.

PCR Multiplex fluorescente para detecção de bactérias em sêmen bovino

Este estudo teve como objetivo avaliar o limiar de detecção da técnica de PCR multiplex fluorescente aliada a eletroforese capilar na detecção de agentes infecciosos em amostras de sêmen experimentalmente contaminadas com concentrações decrescentes das bactérias Brucella abortus, Leptospira interrogans sorovar pomona, Campylobacter fetus e Haemophilus somnus. Amostras de sêmen bovino foram experimentalmente contaminadas com concentrações decrescentes de bactérias obtidas através de diluições seriadas na base 10 de modo a obter-se amostras contendo desde 1 vez até 10-7 bactérias/mL a partir da concentração inicial de Leptospira pomona, Brucella abortus, Campylobacter fetus e Haemophilus somnus. As diluições foram efetuadas individualmente para cada bactéria, bem como nas diferentes concentrações necessárias para a padronização do teste de multiplex PCR. As extrações de DNA de todas as soluções contendo espermatozóides e bactérias analisadas no presente estudo foram realizadas segundo protocolo descrito por Heinemann et al. (2000). Os produtos de PCR multiplex foram avaliados por eletroforese em gel de poliacrilamida 8% e separação eletroforética por sistema capilar em equipamento automático de análise de fragmentos de DNA MegaBace. Observou-se a amplificação de fragmentos de 193pb, 330pb, 400pb e 415pb a partir do DNA de B. abortus, L. pomona, H. somnus, C. fetus, respectivamente. Na análise por eletroforese capilar de produtos da PCR multiplex do DNA para detecção simultânea dos quatro patógenos observou-se a sinal de positividade até a diluição de 10-3 bactérias/mL vezes da concentração inicial da solução estoque de cada bactéria. A técnica de PCR multiplex aliada à eletroforese capilar foi usada pela primeira vez para o diagnóstico direto de quatro bactérias patogênicas no sêmen, demonstrando ser um método rápido na detecção de bactérias causadoras de doenças reprodutivas.

Caracterização das lesões por Cysticercus bovis, na inspeção post mortem de bovinos, pelos exames macroscópico, histopatológico e pela reação em cadeia da polimerase (PCR)

Considerando a necessidade do conhecimento da cisticercose bovina e do aperfeiçoamento dos métodos de diagnóstico desta doença, objetivou-se verificar a ocorrência do Cysticercus bovis nos diversos locais anatômicos, tais como: cabeça, coração, esôfago, diafragma, língua, fígado e carcaça, examinados pelo Serviço de Inspeção Federal. O diagnóstico foi feito por macroscopia, microscopia e PCR com extração de DNA por fervura para a identificação do metacestóide. Dos 22043 bovinos abatidos, 713 (3,23%) estavam infectados. O coração foi o sítio anatômico mais afetado, com 1,90% (420/22043), seguido da cabeça, 1,11% (245/22043), do esôfago, 0,08% (18/22043), da carcaça, 0,07% (15/22043), do diafragma, 0,03% (7/22043), do fígado, 0,02% (5/22043) e da língua, 0,01% (3/22043). Dos cistos obtidos, 58,35% (416/713) estavam mortos e 41,65% (297/713), vivos. As diferenças entre os sítios anatômicos e a condição morfológica dos cistos foram significativas (p < 0,05). Dos 416 cistos mortos, 253 foram examinados por apresentarem características de: lesões nodulares firmes, brancacentas, com material amarelado, por vezes com aspecto calcário, no interior. O exame microscópico revelou granulomas comumente representados por centro necrótico e/ou mineralizado, envolto por histiócitos dispostos em paliçada, células gigantes multinucleadas, infiltrado misto, predominantemente de mononucleares, e fibrose. Por vezes, a periferia das lesões tinha características de tecido de granulação e mineralização em forma de lâminas lineares. Os restos parasitários foram identificados como um material hialino acelular, contendo elementos ovais e circulares, basofílicos, acidófilos e incolores, denominados corpúsculos calcários. Em algumas lesões foram observados raros corpúsculos, dispersos na reação inflamatória. Nódulos fibrosos, ricos em infiltrado linfóide ou crônico ativos, foram frequentemente visualizados. Dos cistos vivos examinados, 65% (13/20) foram positivos para C. bovis , confirmando o diagnóstico ambulatorial e a eficácia do método de PCR utilizado. Em virtude da positividade observada para C. bovis nos exames histopatológico e PCR, particularmente em fígado e esôfago, sugere-se que seja reformulado o artigo 176 do Regulamento de Inspeção Industrial e Sanitária de Produtos de Origem Animal, incluindo estes locais na rotina de inspeção nos matadouros.

Nested-PCR for the detection of Mycoplasma hyopneumoniae in bronchial alveolar swabs, frozen tissues and formalin-fixed paraffin-embedded swine lung samples: comparative evaluation with immunohistochemical findings and histological features

The diagnosis of Mycoplasma hyopneumoniae infection is often performed through histopathology, immunohistochemistry (IHC) and polymerase chain reaction (PCR) or a combination of these techniques. PCR can be performed on samples using several conservation methods, including swabs, frozen tissue or formalin-fixed and paraffin-embedded (FFPE) tissue. However, the formalin fixation process often inhibits DNA amplification. To evaluate whether M. hyopneumoniae DNA could be recovered from FFPE tissues, 15 lungs with cranioventral consolidation lesions were collected in a slaughterhouse from swine bred in herds with respiratory disease. Bronchial swabs and fresh lung tissue were collected, and a fragment of the corresponding lung section was placed in neutral buffered formalin for 48 hours. A PCR assay was performed to compare FFPE tissue samples with samples that were only refrigerated (bronchial swabs) or frozen (tissue pieces). M. hyopneumoniae was detected by PCR in all 15 samples of the swab and frozen tissue, while it was detected in only 11 of the 15 FFPE samples. Histological features of M. hyopneumoniae infection were presented in 11 cases and 7 of these samples stained positive in IHC. Concordance between the histological features and detection results was observed in 13 of the FFPE tissue samples. PCR was the most sensitive technique. Comparison of different sample conservation methods indicated that it is possible to detect M. hyopneumoniae from FFPE tissue. It is important to conduct further research using archived material because the efficiency of PCR could be compromised under these conditions.

Detection of virulence-associated genes of Pasteurella multocida isolated from cases of fowl cholera by multiplex-PCR

The current systems of breeding poultry, based on high population density, increase the risk of spreading pathogens, especially those causing respiratory diseases and those that have more than one host. Fowl Cholera (FC) is one such pathogen, and even though it represents one of several avian diseases that should be considered in the differential diagnosis of notifiable diseases that present with sudden death, the pathogenesis and virulence factors involved in FC are still poorly understood. The objective of this study was to investigate twelve genes related to virulence in 25 samples of Pasteurella multocida isolated from FC cases in the southern region of Brazil through the development of multiplex PCR protocols. The protocols developed were capable of detecting all of the proposed genes. The ompH, oma87, sodC, hgbA, hgbB, exBD-tonB and nanB genes were present in 100% of the samples (25/25), the sodA and nanH genes were present in 96% (24/25), ptfA was present in 92% (23/25), and pfhA was present in 60% (15/25). Gene toxA was not identified in any of the samples studied (0/25). Five different genetic profiles were obtained, of which P1 (negative to toxA) was the most common. We concluded that the multiplex-PCR protocols could be useful tools for rapid and simultaneous detection of virulence genes. Despite the high frequency of the analyzed genes and the fact that all samples belonged to the same subspecies of P. multocida, five genetic profiles were observed, which should be confirmed in a study with a larger number of samples.

Identification of new flagellin-encoding fliC genes in Escherichia coli isolated from domestic animals using RFLP-PCR and sequencing methods

Identification of Escherichia coli requires knowledge regarding the prevalent serotypes and virulence factors profiles allows the classification in pathogenic/non-pathogenic. However, some of these bacteria do not express flagellar antigen invitro. In this case the PCR-restriction fragment length polymorphism (RFLP-PCR) and sequencing of the fliC may be suitable for the identification of antigens by replacing the traditional serology. We studied 17 samples of E. coli isolated from animals and presenting antigen H nontypeable (HNT). The H antigens were characterized by PCR-RFLP and sequencing of fliC gene. Three new flagellin genes were identified, for which specific antisera were obtained. The PCR-RFLP was shown to be faster than the serotyping H antigen in E. coli, provided information on some characteristics of these antigens and indicated the presence of new genes fliC.

Molecular diagnosis of Anaplasma marginale in cattle: quantitative evaluation of a real-time PCR (Polymerase Chain Reaction) based on msp5 gene

The rickettsia Anaplasma marginale is considered the main agent of bovine anaplasmosis. Due the nonspecific clinical signs of the anaplasmosis, the diagnosis of infection depends of laboratory confirmation. In recent years, molecular diagnostic methods have been used to detect A. marginale in cattle. However, the existence of a large number of assays of different sensitivity and cost makes the choice of an appropriate test difficult. In the present study, a real-time Polymerase Chain Reaction (PCR) based on the msp5 target gene was quantitatively assessed and compared to an end point PCR. Both reactions were subjected to sensitivity and specificity evaluation using plasmid DNA and samples from cattle experimentally infected with A. marginale. A comparative field trial of the tests was carried out using samples of cattle from a stable enzootic area for A. marginale. The real-time PCR showed a higher sensitivity than the end point PCR. This reaction (i.e. real-time PCR) was able to detect one copy of the msp5 gene in 100 ηg of plasmidial DNA, and more than 80% of its results were positive among experimentally infected animals seven days after infection. In addition, based on in silico analysis, the real-time PCR evaluated in the present study appears to be useful for the detection of A. ovis.

Detecção de Brucella abortus em tecidos bovinos utilizando ensaios de PCR e qPCR¹

Objetivou-se no presente estudo avaliar as técnicas reação em cadeia da polimerase (PCR) e PCR em Tempo Real (qPCR) para detectar Brucella abortus, a partir de tecidos bovinos com lesões sugestivas de brucelose. Para isto, 21 fragmentos de tecidos bovinos coletados em abatedouros de Mato Grosso do Sul foram processados e submetidos ao cultivo microbiológico e extração do DNA genômico para realização das reações de PCR e qPCR. No cultivo microbiológico, oito amostras apresentaram crescimento bacteriano e cinco foram confirmadas como B. abortus por PCR. Diretamente das amostras de tecido, DNA do gênero Brucella (oligonucleotídeos IS711) foi detectado em 13 (61,9%) amostras de tecido e 17 (81%) amostras de homogeneizado. Já com os oligonucleotídeos espécie-específicos BruAb2_0168F e BruAb2_0168R, 14 (66%) amostras de tecido e 18 (85,7%) amostras de homogeneizado foram amplificadas. Seis amostras positivas na PCR espécie-específica foram sequenciadas e o best hit na análise BLASTn foi B. abortus. Na qPCR, 21 (100%) amostras de tecidos e 19 (90,5%) amostras de homogeneizado foram positivas para B. abortus. Dez amostras de DNA de sangue bovino de rebanho certificado livre foram utilizadas como controle negativo nas análises de PCR e qPCR utilizando-se os oligonucleotídeos BruAb2_0168F e BruAb2_0168R. Na PCR nenhuma amostra amplificou, enquanto que na qPCR 2 (20%) amplificaram. Conclui-se que as duas técnicas detectam a presença de B. abortus diretamente de tecidos e homogeneizados, porém a qPCR apresentou maior sensibilidade. Os resultados obtidos indicam que a qPCR pode representar uma alternativa rápida e precisa para a detecção de B. abortus diretamente de tecidos, e ser utilizada em programas de vigilância sanitária, por apresentar sensibilidade e especificidade satisfatórias.

Evaluation of a PCR multiplex for detection and differentiation of Mycoplasma synoviae, M. gallisepticum, and M. gallisepticum strain F-vaccine

Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS) are the mycoplasma infections of most concern for commercial poultry industry. MG infection is commonly designated as chronic respiratory disease (CRD) of chickens and infections sinusitis of turkeys. MS causes sub clinical upper respiratory infection and tenosynovitis or bursitis in chickens and turkeys. The multiplex PCR was standardized to detect simultaneously the MS, MG field strains and MG F-vaccine strain specific. The generic PCR for detection of any species of Mollicutes Class was performed and compared to the multiplex PCR and to PCR using species-specific primers. A total of 129 avian tracheal swabs were collected from broiler-breeders, layer hens and broilers in seven different farms and were examined by multiplex PCR methods. The system (multiplex PCR) demonstrated to be very rapid, sensitive, and specific. Therefore, the results showed a high prevalence of MS in the flocks examined (27.9%), and indicate that the MS is a recurrent pathogen in Brazilian commercial poultry flocks.

Development of a Real-time PCR test for porcine group A rotavirus diagnosis

Group A Rotavirus (RVA) is one of the most common causes of diarrhea in humans and several animal species. A SYBR-Green Real-Time polymerase chain reaction (PCR) was developed to diagnose RVA from porcine fecal samples, targeting amplification of a 137-bp fragment of nonstructural protein 5 (NSP5) gene using mRNA of bovine NADH-desidrogenase-5 as exogenous internal control. Sixty-five samples were tested (25 tested positive for conventional PCR and genetic sequencing). The overall agreement (kappa) was 0.843, indicating 'very good' concordance between tests, presenting 100% of relative sensitivity (25+ Real Time PCR/25+ Conventional PCR) and 87.5% of relative sensitivity (35- Real Time PCR/40- Conventional PCR). The results also demonstrated high intra- and inter-assay reproducibility (coefficient of variation ≤1.42%); thus, this method proved to be a fast and sensitive approach for the diagnosis of RVA in pigs.

Use of RAPD-PCR to identify true hybrid plants from crosses between closely related progenitors

RAPD-PCR molecular markers were used to identify common bean and soybean hybrid plants derived from crosses between closely related progenitors, with no apparent phenotypic differences. Primers OP-F12 and OP-0O3 were used to identify true hybrids derived from crosses between common bean cultivars Rudá (A 285) and AN 910408, and soybean cultivars Cristalina and Bossier, respectively. Each primer generated one polymorphic DNA band which was present in the male progenitor and absent in the female progenitor. As RAPD bands are normally inherited as dominant characters, the presence of these bands in the F1 plants confirmed their status.

Application of the differential display RT-PCR strategy for the identification of inflammation-related mouse genes

The inflammatory response elicited by various stimuli such as microbial products or cytokines is determined by differences in the pattern of cellular gene expression. We have used the differential display RT-PCR (DDRT-PCR) strategy to identify mRNAs that are differentially expressed in various murine cell types stimulated with pro-inflammatory cytokines, microbial products or anti-inflammatory drugs. Mouse embryonic fibroblasts (MEFs) were treated with IFNs, TNF, or sodium salicylate. Also, peritoneal macrophages from C3H/Hej mice were stimulated with T. cruzi-derived GPI-mucin and/or IFN-g. After DDRT-PCR, various cDNA fragments that were differentially represented on the sequencing gel were recovered, cloned and sequenced. Here, we describe a summary of several experiments and show that, when 16 of a total of 28 recovered fragments were tested for differential expression, 5 (31%) were found to represent mRNAs whose steady-state levels are indeed modulated by the original stimuli. Some of the identified cDNAs encode for known proteins that were not previously associated with the inflammatory process triggered by the original stimuli. Other cDNA fragments (8 of 21 sequences, or 38%) showed no significant homology with known sequences and represent new mouse genes whose characterization might contribute to our understanding of inflammation. In conclusion, DDRT-PCR has proven to be a potent technology that will allow us to identify genes that are differentially expressed when cells are subjected to changes in culture conditions or isolated from different organs.

Detection of cytomegalovirus infections by PCR in renal transplant patients

Cytomegalovirus (CMV) is the single most important infectious agent affecting recipients of organ transplants. To evaluate the incidence and the clinical importance of CMV infection in renal transplants in Brazil, 37 patients submitted to renal allograft transplants were tested periodically for the presence of cytomegalovirus DNA in urine using the polymerase chain reaction (PCR), and for the presence of IgM and IgG antibodies against CMV by enzyme-linked immunosorbent assay (ELISA) and indirect immunofluorescence (IIF). The PCR-amplified products were detected by gel electrophoresis and confirmed by dot-blot hybridization with oligonucleotide probes. Thirty-two of the 37 patients (86.4%) were positive by at least one of the three methods. In six patients, PCR was the only test which detected the probable CMV infection. Ten patients had a positive result by PCR before transplantation. In general, the diagnosis was achieved earlier by PCR than by serologic tests. Active infection occurred more frequently during the first four months after transplantation. Sixteen of the 32 patients (50%) with active CMV infection presented clinical symptoms consistent with CMV infection. Five patients without evidence of active CMV infection by the three tests had only minor clinical manifestations during follow-up. Our results indicate that PCR is a highly sensitive procedure for the early detection of CMV infection and that CMV infection in renal transplant patients is a frequent problem in Brazil.