Salmonella Choleraesuis é o agente causador de um quadro septicêmico em suínos que pode apresentar altas taxas de mortalidade nos animais infectados. No presente estudo foram avaliadas 93 estirpes de S. Choleraesuis provenientes de suínos com sinais clínicos de infecção. Foram avaliadas estirpes originadas de sete granjas localizadas nos Estados de São Paulo, Paraná, Santa Catarina e Minas Gerais obtidas durantes os anos de 2015, 2016 e 2017. As estirpes de Salmonella foram submetidas a reação em cadeia pela polimerase para confirmação do sorovar pela amplificação do gene fliC, em seguida foram caracterizadas quanto ao perfil de resistência a antimicrobianos e a caracterização genotípica pelo polimorfismo do comprimento de fragmentos amplificados (AFLP). A determinação do perfil de resistência a antimicrobianos revelou que as 93 estirpes foram resistentes a penicilina, doxiciclina, sulfadimetoxina, clindamicina, tilosina, tilmicosina e tiamulina, sendo, portanto, todas multirresistentes. Os antimicrobianos com menores taxas de resistência foram cefitiofur (0%), marbofloxacina (1,1%), neomicina (10,8%) e enrofloxacina (18,3%). As estirpes foram discriminadas em 17 perfis de resistência diferentes, o perfil mais frequente reuniu 39 estirpes (42%) resistentes a penicilina, ampicilina, doxiciclina, oxitetraciclina, florfenicol, sulfadimetoxina, gentamicina, tulatromicina, tilosina, tilmicosina, tiamulina e clindamicina. A análise das estirpes pelo AFLP indicou todas as 93 estirpes foram agrupadas em um único perfil com mais de 94% de similaridade. A partir dos dados obtidos é possível verificar que as estirpes de S. Choleraesuis isoladas de suínos apresentaram baixa variabilidade genética e alta frequência de resistência aos antimicrobianos mais usados em suinocultura. / Salmonella Choleraesuis is the causative agent of septicemia in pigs and may present high mortality rates in infected animals. In the present study, 93 strains of S. choleraesuis from pigs with clinical signs of infection were evaluated. Strains from seven farms located in the states of São Paulo, Paraná, Santa Catarina and Minas Gerais obtained during the years 2015, 2016 and 2017 were evaluated. Salmonella strains were submitted to polymerase chain reaction for confirmation of serovar by amplification of the fliC gene were then characterized for antimicrobial resistance profile and genotype characterization by amplified fragment length polymorphism (AFLP). The determination of the antimicrobial resistance profile revealed that the 93 strains were resistant to penicillin, doxycycline, sulfadimethoxine, clindamycin, tylosin, tilmicosin and tiamulin, and were therefore multiresistant. The antimicrobials with the lowest resistance rates were cefitiofur (0%), marbofloxacin (1.1%), neomycin (10.8%) and enrofloxacin (18.3%). The strains were discriminated in 17 different resistance profiles, the most frequent profile consisted of 39 strains (42%) resistant to penicillin, ampicillin, doxycycline, oxytetracycline, florfenicol, sulfadimetoxin, gentamicin, tulathromycin, tylosin, tilmicosin, tiamulin and clindamycin. Analysis of the strains by AFLP indicated that all 93 strains were grouped into a single profile with more than 94% similarity. From the data obtained it is possible to verify that the strains of S. Choleraesuis isolated from pigs presented low genetic variability and high frequency of resistance to the antimicrobials most used in swine production systems.

Dentre as espécies conhecidas do gênero Arcobacter, as espécies A. butzleri, A. cryaerophilus e A. skirrowii são consideradas potecialmente zoonóticas, podendo ser transmitidas por alimentos de origem animal. O presente estudo teve como objetivos isolar e caracterizar fenotipica e genotipicamente cepas de Arcobacter spp. provenientes de carcaças de suínos e amostras de ambiente de abatedouro localizado no Estado de São Paulo. As cepas isoladas foram submetidas a reação em cadeia pela polimerase para a identificação e detecção de um grupo de genes de virulência. A concentração inibitória mínima frente a nove antimicrobianos usados para o controle da infecção pelo agente foi determinada e as cepas foram analisadas através do PFGE e pelo AFLP. Dentre as 30 carcaças avaliadas, 25 foram positivas para o agente e 70 cepas foram selecionadas e identificadas como Arcobacter spp. As espécies isoladas foram A. butzleri (n=61), A. cryaerophilus (n=7) e A. skirrowii (n=2). A frequência dos possíveis genes de virulência encontrada variou de 71,4% a 100% para os genes tlyA, pldA, cj1349, ciaB, cadF e mviN. Não foram detectados os genes hecA, hecB e irgA. O perfil de virulência ciaB/ cj1349/ mviN/ cadF/ pldA/ tlyA foi o mais frequente e detectado em 66% das cepas. Todas as cepas foram sensíveis à gentamicina e tetraciclina e 77,1% foram multirresistentes, dentre estas o perfil mais frequente foi de resistência a azitromicina/ florfenicol/ ácido nalidíxico/ telitromicina/ clindamicina Houve grande diversidade genotípica entre as cepas através do PFGE e do AFLP, e ambas a técnicas apresentaram o mesmo poder discriminatório na análise das cepas isoladas. / Among the known species of the genus Arcobacter, the species A. butzleri, A. cryaerophilus and A. skirrowii are considered potentially zoonotic and can be transmitted by food of animal origin. This study aimed to isolate and characterize phenotypically and genotypically strains of Arcobacter spp from swine carcasses and slaughterhouse environment samples located in the State of São Paulo. The isolated strains were subjected to polymerase chain reaction for identification and detection of a group of putative virulence genes. The minimum inhibitory concentration was determined against nine antimicrobials indicated for the control of infection by the agent and the strains were analyzed by PFGE and by AFLP. Among the 30 carcasses evaluated, 25 were positive for the agent and 70 strains were selected and identified as Arcobacter spp. The isolated species were A. butzleri (n = 61), A. cryaerophilus (n = 7) and A. skirrowii (n = 2). The frequency of virulence genes found ranged from 71.4 % to 100 % for genes tlyA , pldA , cj1349 , ciaB , cadF and mviN . The genes hecA, hecB and irgA were not detected. The virulence profile ciaB/ cj1349/ mviN/ cadF/ pldA/ tlyA was the most frequent and detected in 66 % of the strains. All strains were susceptible to gentamicin and tetracycline and 77.1% were multirresistant, among these the most common profile of resistance was azithromycin/ florfenicol/ nalidixic acid/ telithromycin/ clindamycin There were large genotypic diversity among strains by PFGE and AFLP and both techniques showed the same discriminatory power in the analysis of the isolated strains.

Cette étude est motivée par les besoins réels de calcul dans la physique des réacteurs. Notre objectif est de concevoir les algorithmes parallèles, y compris en proposant efficaces noyaux algébriques linéaires et méthodes numériques parallèles.Dans un environnement many-cœurs en mémoire partagée tel que le système Intel Many Integrated Core (MIC), la parallélisation efficace d'algorithmes est obtenue en termes de parallélisme des tâches à grain fin et parallélisme de données. Pour la programmation des tâches, deux principales stratégies, le partage du travail et vol de travail ont été étudiées. A des fins de généralité et de réutilisation, nous utilisons des interfaces de programmation parallèle standard, comme OpenMP, Cilk/Cilk+ et TBB. Pour vectoriser les tâches, les outils disponibles incluent Cilk+ array notation, pragmas SIMD, et les fonctions intrinsèques. Nous avons évalué ces techniques et proposé un noyau efficace de multiplication matrice-vecteur dense. Pour faire face à une situation plus complexe, nous proposons d'utiliser le modèle hybride MPI/OpenMP pour la mise en œuvre de noyau multiplication matrice-vecteur creux. Nous avons également conçu un modèle de performance pour modéliser les performances sur MICs et ainsi guider l'optimisation. En ce qui concerne la résolution de systèmes linéaires, nous avons proposé un solveur parallèle évolutif issue de méthodes Monte Carlo. Cette méthode présente un degré de parallélisme abondant, qui s’adapte bien à l'architecture multi-coeurs. Pour répondre à certains des goulots d'étranglement fondamentaux de ce solveur, nous proposons un modèle d'exécution basée sur les tâches qui résout complètement ces problèmes. / This study is driven by the real computational needs coming from different fields of reactor physics, such as neutronics or thermal hydraulics, where the eigenvalue problem and resolution of linear system are the key challenges that consume substantial computing resources. In this context, our objective is to design and improve the parallel computing techniques, including proposing efficient linear algebraic kernels and parallel numerical methods. In a shared-memory environment such as the Intel Many Integrated Core (MIC) system, the parallelization of an algorithm is achieved in terms of fine-grained task parallelism and data parallelism. For scheduling the tasks, two main policies, the work-sharing and work-stealing was studied. For the purpose of generality and reusability, we use common parallel programming interfaces, such as OpenMP, Cilk/Cilk+, and TBB. For vectorizing the task, the available tools include Cilk+ array notation, SIMD pragmas, and intrinsic functions. We evaluated these techniques and propose an efficient dense matrix-vector multiplication kernel. In order to tackle a more complicated situation, we propose to use hybrid MPI/OpenMP model for implementing sparse matrix-vector multiplication. We also designed a performance model for characterizing performance issues on MIC and guiding the optimization. As for solving the linear system, we derived a scalable parallel solver from the Monte Carlo method. Such method exhibits inherently abundant parallelism, which is a good fit for many-core architecture. To address some of the fundamental bottlenecks of this solver, we propose a task-based execution model that completely fixes the problems.

Prostate cancer remains a significant health concern for men throughout the world. Accumulating epidemiologic and molecular evidence suggests that inflammation is an important component in the aetiology of prostate cancer. Supporting this hypothesis, population studies have found an increased risk of prostate cancer in men with a prior history of certain sexually transmitted infections or prostatitis. More general evidence of a relationship between inflammation and prostate cancer has been provided by reports indicating that daily use of non steroidal anti-inflammatory drugs (NSAIDs) may be associated with a lower incidence of prostate cancer. The exact mechanism whereby inflammation might act in tumour development and progression remains to be elucidated, but is likely to be complex. The genetic contribution to inflammatory responses involved in the development of prostate cancer has not yet been extensively or systematically studied. However, this thesis evaluates the role of various inflammation-related genes in the pathogenesis of prostate cancer. The macrophage scavenger receptor 1 (MSR1) is a transmembrane protein that is mainly expressed by macrophages. This receptor mediates the binding, internalization and processing of a wide range of macromolecules, and is suggested to play a major role in the recognition and clearance of pathogenic and damaged cells. Recent reports have suggested MSR1 to be a candidate gene for hereditary prostate cancer. Therefore, we screened the MSR1 gene among men with hereditary prostate cancer and identified 18 sequence variants. One previously reported truncation mutation was found more frequently in men with prostate cancer than in unaffected men, in accordance with previously published results. However, the difference in frequencies we found between these groups was not statistically significant. In addition, we genotyped five common polymorphisms in MSR1 in 215 men with unselected prostate cancer and 425 controls. No association between any of the five common variants and prostate cancer were found. We then performed a comprehensive genetic study using extensive populationbased case-control material to evaluate possible associations between sequence variants in inflammation-related genes and prostate cancer. The first gene to be examined was interleukin-1 receptor antagonist (IL-1-RN), encoding a cytokine that plays an important role in regulation of the inflammatory response by binding to the IL-1 receptor and thus inhibiting the binding of the pro-inflammatory cytokines IL-1α and IL-1β. Collectively, these three cytokines exert a central role in the protection against diverse lesions, ranging from microbial colonisation to infection and malignant transformation. The genetic analysis of IL-1RN revealed that the most common haplotype was significantly associated with prostate cancer risk for patients with prostate cancer, and further this association appears to be stronger in cases with advanced disease. The macrophage inhibitory cytokine-1 (MIC-1), a member of the transforming growth-factor-β superfamily has been shown to exert diverse biological functions, including regulation of macrophage activity in the inflammatory response and both growth inhibition and induction of apoptosis in epithelial and other tumour cell lines. The genetic analysis of MIC-1 revealed that a seuqence variant (H6D) appears to be associated with a decreased prostate cancer risk. We also performed measurements of MIC-1 serum levels among patients with prostate cancer and healthy controls. These data indicate that serum MIC-1 levels are associated with an increased risk for prostate cancer. Further, the clear relation between clinical stage and MIC-1 level also suggest that MIC-1 may be useful as a prognostic factor, where high serum concentration is associated with a poor prognosis. In summary, our results provide further support for the assumption that polymorphisms in inflammatory genes play critical roles in prostate cancer susceptibility. Additional studies are needed to elucidate the mechanisms whereby the demonstrated variations contribute to prostate cancer development.

Some yeast strains secrete extracellular polypeptide toxins known to have potential growth inhibitory activity on sensitive yeast cells. These yeast strains are known as killer yeasts and their toxins are named as killer toxins or killer proteins. Yeast killer proteins are found inhibitory to Gram-positive bacteria in several studies which were based on microbial interactions of the producer strains tested with sensitive strains. K5 type yeast killer protein produced by Pichia anomala NCYC 434 was previously purified and characterized in our laboratory. The protein is glycosilated and has a pI value of 3,7 and molecular mass of 49 kDa, with exo &amp / #946 / -1,3-glucanase activity. Antibacterial activity of the pure K5 type yeast killer protein was tested against 19 clinical isolates of gram-positive bacteria causing skin infections and 2 quality control strains and found to have inhibitory activity on the isolates of Methicillin-sensitive Staphylococcus aureus (MSSA) and Enterococcus faecium. Toxin MIC and MBC ranges were 32 - 256 &micro / g/ml and 64 - &gt / 512 &micro / g/ml respectively. Cell killing analysis revealed that toxin has a bacteriostatic activity and the inhibitory effect starts between 8. and 12. hours. Regrowth of the bacteria is retarded with the increased dose of the toxin. K5 type yeast killer protein might be used as a topical antibacterial agent with its bacteriostatic activity for skin and wound infections caused by MSSA and Enterococcus faecium with appropriate formulation studies upon the antibacterial spectrum determination of the toxin in this study.

No description available.

Background: Clinical breakpoints and epidemiological cut-off values for N. gonorrhoeae azithromycin antimicrobial susceptibility testing have not been established. This study utilized existing minimum inhibitory concentration (MIC) data from CDC’s Gonococcal Isolate Surveillance Project (GISP) to establish epidemiological cut-off values for azithromycin and N. gonorrhoeae as determined by agar dilution. Methods: MIC distributions for the pooled dataset and each data year (2005-2012) were constructed. Epidemiological cut-off values were calculated using two methods. Method 1 considers the wild-type MIC distribution, the modal MIC for the distribution, and the inherent variability of the test (±1 twofold-dilution). Method 2 defines the epidemiological cut-off value as two twofold-dilutions higher than the MIC50. Results: Taking into consideration the wild-type MIC distributions and the inherent variability of the test, the epidemiological cut-off value chosen for the pooled dataset and each data year using Method 1 was ≤1.0 µg/mL. The MIC50 for the pooled dataset and each data year was 0.25 µg/mL. Two twofold-dilutions higher than the MIC50 (0.25 µg/mL) for the pooled dataset and each data year was 1.0 µg/mL. Discussion: The epidemiological cut-off values chosen using Methods 1 and 2 (≤1.0 µg/mL) were identical for the pooled dataset and each data year, indicating the epidemiological cut-off value has not changed from 2005-2012. The epidemiological cut-off value for N. gonorrhoeae azithromycin agar dilution antimicrobial susceptibility testing established during this study can be used to help set clinical breakpoints and identify isolates with reduced susceptibility to azithromycin.

Raw and processed foods are vulnerable to contamination during their production, distribution and sale. Thus, a wide variety of chemical preservatives are used in the food industry to prevent the growth of food spoilage and pathogenic bacteria. However, health and economic concerns have led to an intensive search for natural alternatives, such as plant extracts, that can safely be used as substitutes for synthetic antimicrobials and preservatives to partially or completely inhibit the growth of bacteria. This study evaluated the antimicrobial effects of natural phenolic compounds extracted from vegetables, fruits, herbs and spices. The main objective was to determine the lowest concentration of phenolics to inhibit the visible growth of the pathogenic bacteria which is defined as the minimum inhibitory concentration (MIC). Some of the most common Gram-positive and Gram-negative foodborne pathogens were treated with several natural phenolic compounds. Concentrations of 5, 10, 15, and 20 ppm (pH 5-6) of each compound were evaluated by broth micro-dilution method and the MICs were determined by using official density (OD) assay. The results demonstrated that the phenolic compounds have varying antimicrobial activities against foodborne pathogens. Natural sources of phenolic compounds contain major antibacterial components and have great potential to be used as natural antimicrobials and food preservatives.

Contamination from various sources has a huge impact on soil health and microbial community composition. Metal contamination of soil in mining scenarios is of concern and is not adequately addressed, particularly with respect to the microbial community. The mining industry is one of the largest contributors to heavy metal contamination of soil in South Africa, especially since the country is one of the major mining countries in the world. Platinum mining is of special importance, since the largest percentage of the world’s reserves of platinum group metals are found and mined in South Africa. Metals from mining activities become irreversibly immobilized in soil systems because they cannot be degraded and has a huge impact on soil systems. In this study, bacteria was isolated from soil samples collected from a platinum mine tailings dam outside Rustenburg. During the warm sampling season (March 2006) most isolates were found, especially in sites 3 and 4. During the colder and drier season (May 2006) there were less isolates. Most of the isolated cultures also displayed a wide temperature growth range, mostly between 24°C - 37°C. Paenibacillus lautus and Bacillus subtilus DN-10 had a growth range between 5°C - 40°C. Culturable metal tolerant bacteria were isolated, purified and identified using 16S rDNA sequences. Nine different species were found namely Paenibacillus lautus strain DS19, Paenibacillus lautus, Paenibacillus sp. C15, uncultured Paenibacillaceae, Bacillus subtilis strain DN-10, Bacillus sp. KDNB5, Bacillus cereus, Stenotrophomonas maltophilia and Alcaligenes sp. DJWH 146-2. The ability of these strains to tolerate metal concentrations were explored by determining their minimum inhibitory concentrations for a selection of metals e.g. aluminum, barium, cobalt, chromium, cadmium, copper, iron, lead, manganese, nickel and mercury. Most isolates were able to tolerate >5mM of the Al\Ni alloy and cobalt. Transmission electron microscopy was used to determine the location of metals inside bacterial cells and electron dispersive X-ray analysis was used to determine the levels of metals inside microbial cells. Bacillus subtilis DN-10 (LDK0306) showed a high MIC (>5mM) for most metals used, except Hg. This strain also had a high percentage (10.26%) of Pb detected in its cells by EDX. This was the highest percentage detected. Plasmids were extracted from the identified strains and can help gain a better understanding of metal tolerance mechanisms used by these isolates. / Thesis(MSc (Environmental Sciences))--North-West University, Potchefstroom Campus, 2013

Contamination from various sources has a huge impact on soil health and microbial community composition. Metal contamination of soil in mining scenarios is of concern and is not adequately addressed, particularly with respect to the microbial community. The mining industry is one of the largest contributors to heavy metal contamination of soil in South Africa, especially since the country is one of the major mining countries in the world. Platinum mining is of special importance, since the largest percentage of the world’s reserves of platinum group metals are found and mined in South Africa. Metals from mining activities become irreversibly immobilized in soil systems because they cannot be degraded and has a huge impact on soil systems. In this study, bacteria was isolated from soil samples collected from a platinum mine tailings dam outside Rustenburg. During the warm sampling season (March 2006) most isolates were found, especially in sites 3 and 4. During the colder and drier season (May 2006) there were less isolates. Most of the isolated cultures also displayed a wide temperature growth range, mostly between 24°C - 37°C. Paenibacillus lautus and Bacillus subtilus DN-10 had a growth range between 5°C - 40°C. Culturable metal tolerant bacteria were isolated, purified and identified using 16S rDNA sequences. Nine different species were found namely Paenibacillus lautus strain DS19, Paenibacillus lautus, Paenibacillus sp. C15, uncultured Paenibacillaceae, Bacillus subtilis strain DN-10, Bacillus sp. KDNB5, Bacillus cereus, Stenotrophomonas maltophilia and Alcaligenes sp. DJWH 146-2. The ability of these strains to tolerate metal concentrations were explored by determining their minimum inhibitory concentrations for a selection of metals e.g. aluminum, barium, cobalt, chromium, cadmium, copper, iron, lead, manganese, nickel and mercury. Most isolates were able to tolerate >5mM of the Al\Ni alloy and cobalt. Transmission electron microscopy was used to determine the location of metals inside bacterial cells and electron dispersive X-ray analysis was used to determine the levels of metals inside microbial cells. Bacillus subtilis DN-10 (LDK0306) showed a high MIC (>5mM) for most metals used, except Hg. This strain also had a high percentage (10.26%) of Pb detected in its cells by EDX. This was the highest percentage detected. Plasmids were extracted from the identified strains and can help gain a better understanding of metal tolerance mechanisms used by these isolates. / Thesis(MSc (Environmental Sciences))--North-West University, Potchefstroom Campus, 2013