O Toxoplasma gondii apresenta uma estrutura populacional clonal. A análise genotípica do locus SAG2 foi realizada para determinar a ocorrência de diferentes linhagens de T. gondii (tipos I, II e III) em gatos domésticos. Amostras de soro de 237 gatos de 15 municípios no estado de São Paulo foram testadas para pesquisa de anticorpos anti-T. gondii através do teste de aglutinação modificado (MAT). Anticorpos (MAT ≥ 25) foram encontrados em 84 (35,4%) dos 237 gatos. Com os tecidos (cérebro, coração, língua e musculatura esquelética) de 71 gatos positivos foram realizados bioensaios em camundongos (cinco camundongos por grupo) sendo obtidos 47 isolados. A análise de polimorfismo de comprimento dos fragmentos de DNA gerados por enzimas de restrição (RFLP) sobre produtos do locus SAG2 amplificados pela PCR revelou que 34 isolados (72,4%) eram do tipo I, 12 (25,5%) eram do tipo III e um (2,1%) apresentava infecção mista (tipo I e tipo III). Não houve isolado do tipo II. A maioria dos isolados do tipo I (23/34) causou o óbito de todos os camundongos infectados e a maioria dos isolados do tipo III (7/12) não levou ao óbito nenhum camundongo infectado. Foram encontrados cistos no cérebro dos camundongos infectados em todos os 47 isolados. A determinação genotípica também foi feita diretamente das amostras primárias dos gatos (homogeneizados de tecidos) usando a nested-PCR-RFLP. A caracterização do locus SAG2 foi bem sucedida em 80,4% (37/46) das amostras testadas. Os genótipos obtidos das amostras primárias foram idênticos aos dos isolados correspondentes. O genótipo misto foi confirmado pelo seqüenciamento direto de DNA dos produtos da PCR obtidos do isolado e da amostra primária do gato. Amostras dos cinco camundongos infectados com este isolado foram seqüenciadas. Três camundongos se infectaram com o genótipo tipo III, um com o genótipo tipo I e o outro com o genótipo misto, demonstrando que infecções mistas podem originar diferentes padrões de infecção em um hospedeiro. / Toxoplasma gondii has a clonal population structure. Genotypic analysis of the SAG2 locus was performed to determine the occurrence of the different lineages of T. gondii (types I, II and III) in domestic cats. Antibodies to T. gondii were determined in serum samples of 237 cats from 15 counties in São Paulo state, Brazil, by the modified agglutination test (MAT). Antibodies (MAT ≥ 25) were found in 84 (35.4%) of 237 cats. Tissues (brain, heart, tongue and skeletal muscle) of 71 of the positive cats were bioassayed in mice (five mice per group). Forty-seven isolates were obtained. Restriction fragment length polymorphism (RFLP) in PCR-amplified SAG2 products revealed that 34 isolates (72.4%) were type I, 12 (25.5%) were type III and one (2.1%) was mixed with type I and type III. There was no type II isolate. Most of the type I isolates (23/34) killed all infected mice and most of the type III isolates (7/12) killed no infected mice. Tissue cysts were found in mice infected with all 47 isolates. The genotype determination was also made directly from primary samples from cats (tissue homogenates) using nested-PCR-RFLP analysis. Characterization of the SAG2 locus was successful in 80.4% (37/46) of the samples tested. Genotypes obtained from primary samples were the same as those from the corresponding isolates. The mixed genotype was confirmed by direct DNA sequencing of PCR products from the isolate and from the cat primary sample and samples from the five mice infected with this isolate were sequenced. Three had type III genotype, one had type I, and one had type I + type III, demonstrating that mixed infections can originate different patterns of infection in a host.

Neospora caninum é um protozoário parasita de grande importância em todo o mundo, sendo considerado a principal causa de abortamento bovino em algumas localidades. Enquanto a implicação deste parasita em distúrbios reprodutivos na espécie bovina seja conhecida, as informações disponíveis com a espécie bubalina são escassas. Este estudo avaliou e comparou as consequências da infecção experimental por N. caninum em búfalas e vacas, no estágio inicial da gestação, o de maior importância no que se refere à ocorrência de morte fetal. Protocolos de inseminação artificial em tempo fixo foram utilizados para maior controle da fecundação. Foram utilizados para inoculação dois isolados distintos, Nc-Bahia e Nc-1, possibilitando a comparação entre o isolado nacional e o isolado padrão. Todos os animais foram inoculados com 5 x 108 taquizoítos, pela via endovenosa, no 70º dia de gestação. Três búfalas e cinco vacas foram infectadas com o isolado Nc-Bahia, sendo detectado abortamento 42 dias pós-infecção (DPI) em somente uma das vacas inoculadas. Três búfalas e duas vacas foram inoculadas com o isolado Nc-1 e morte fetal foi detectada 35 DPI em todas as búfalas e vacas. Uma búfala e uma vaca permaneceram como controles negativos, sem infecção. A transmissão vertical foi verificada por semi-nested PCR nos animais infectados com Nc-Bahia e Nc-1. Diferentes graus de inflamação não-supurativa foram detectados em tecidos maternos, fetais e placentários. Todas as fêmeas inoculadas apresentaram resposta humoral frente à infecção. Embora a infecção estivesse mais disseminada pelo organismo das búfalas (p<0,05), a resposta humoral foi menor (p<0,05) e as lesões histológicas foram menos frequentes (p<0,05), indicando haver maior adaptação entre N. caninum e as búfalas, em comparação com os resultados obtidos nas vacas. O isolado Nc-Bahia foi menos patogênico que o Nc-1, por causar menos abortamentos (p<0,05) e menor frequência de lesões histológicas (p<0,05). A patogenicidade do agente na espécie bubalina foi confirmada, consideradas as lesões encontradas na análise histopatológica e a detecção da presença do agente por semi-nested PCR nos diversos tecidos estudados, além da positividade por imunoistoquímica em placenta e cérebro fetal bubalino. Esta é a primeira detecção de abortamento causado por N. caninum na espécie bubalina, em fêmeas infectadas experimentalmente com o protozoário, confirmando que problemas reprodutivos podem ser causados pelo N. caninum em búfalas. / Neospora caninum is a protozoan parasite with big importance all over the world, being considered the main cause of bovine abortion in some locations. While the implication of this parasite in bovine reproductive disorders is known, the available information within the buffalo species is scarce. This study evaluated and compared the consequences of experimental infection with N. caninum in buffaloes and cows on the initial stage of pregnancy, the most important regarding to the occurrence of fetal death. Protocols for fixed-time artificial insemination were used for greater control of fertilization. Two different isolates, Nc-Bahia and Nc-1, were utilized for inoculation, allowing the comparison between the national isolate and the standard isolate. All animals were inoculated with 5 x 108 tachyzoites, by endovenous route, at the 70th day of pregnancy. Three buffaloes and five cows were infected with the isolate Nc-Bahia and abortion was detected 42 days post-infection (DPI) in only one inoculated cow. Three buffaloes and two cows were inoculated with the isolate Nc-1 and fetal death was detected 35 DPI in all buffaloes and cows. A buffalo and a cow remained as negative controls, without infection. Vertical transmission was verified by semi-nested PCR in animals infected with Nc-Bahia and Nc-1. Different degrees of nonsuppurative inflamation were detected in maternal, foetal and placental tissues. All inoculated females showed humoral response against the infection. Although the infection was more disseminated withn the body of buffaloes (p <0.05), the humoral response was lower (p <0.05) and histological lesions were less frequent (p <0.05), indicating bigger adaptation between N. caninum and the buffaloes, in comparison with the results obtained in cows. Nc-Bahia isolate was less pathogenic than the Nc- 1, as it caused less abortions (p <0.05) and lower frequency of histological lesions (p<0.05). The pathogenicity of the agent in the bubaline species was confirmed, considering the lesions found on histopathology analysis and the detection of the agent´s presence by semi-nested PCR in the different studied tissues, in addition to the positivity by immunohistochemistry test in bubaline placenta and foetal brain. This is the first detection of abortion caused by N. caninum in buffalo species, in females experimentally infected with the protozoan, confirming that reproductive disorders can be caused by N. caninum in buffaloes.

A Diarréia Viral Bovina (BVD) provoca grandes perdas econômicas na pecuária mundial, é causada pelo vírus da diarréia viral bovina (BVDV), vírus que apresenta diversidade genética e antigênica entre as estirpes o que provavelmente influencia no diagnóstico. Com a proposta de verificar a presença de anticorpos, sua mensuração e neutralização cruzada frente quatro estirpes do vírus, amostras de 1500 bovinos não vacinados contra BVDV, sendo 519 de 15 rebanhos do Estado de Minas Gerais (MG), 499 de cinco rebanhos do Mato Grosso do Sul (MS) e 482 de cinco rebanhos de São Paulo (SP), foram testadas pela técnica de virusneutralização (VN) com as seguintes estirpes citopatogênicas: BVDV-1 (NADL estirpe americana e IBSP-11 isolado nacional) e BVDV-2 (VS-253 estirpe americana e IBSP-1020 isolado nacional). Dos 1500 animais, a variação da frequência de sororreagentes ao BVDV foi de 66,07% a 68,67%, ao analisar os diferentes grupos de animais, de acordo com o estado, a maior frequência de anticorpos foi obtida no MS, seguida por MG e SP, independente da estirpe utilizada na VN. O isolado nacional do genótipo 2, IBSP-1020 foi a estirpe que resultou em maior detecção de reagentes em MG e MS, enquanto que em SP foram as estirpes do genótipo 1. A avaliação dos resultados com as quatro estirpes revelou 73,27% (1099/1500) de animais reagentes a pelo menos um dos vírus, enquanto que, 57,60% (864/1500) foram reagentes aos quatro vírus, simultaneamente, ou seja, estes animais produziram anticorpos que reagiram com todas as estirpes em questão. Os títulos de anticorpos variaram de 10, valor mínimo de detecção da prova, a 5120, sendo que a maior parte dos animais apresentou títulos entre 40 e 160, os títulos observados nos animais de SP foram mais baixos com relação aos animais dos outros estados. A avaliação dos títulos de anticorpos de cada animal, comparando o resultado das estirpes duas a duas, revelou diferença na maioria das situações. Conclui-se que, houve alta frequência de ocorrência de bovinos reagentes ao BVDV, que variou de acordo com o sistema de criação e manejo dos rebanhos. Além disso, a utilização de mais de uma estirpe viral, independente do genótipo ou do local de origem do isolado, aumentou a sensibilidade de detecção de animais sororreagentes na VN. Foi evidenciada neutralização cruzada entre todas as estirpes estudadas. Os resultados reforçam a importância de selecionar estirpes representativas das regiões a serem estudadas para inclusão na VN, visando aumentar a sensibilidade do diagnóstico. / The bovine viral diarrhea (BVD) causes great economic losses in livestock worldwide, is caused by bovine viral diarrhea virus (BVDV), which presents genetic and antigenic diversity among strains which probably influences the serological diagnosis. For the proposal to verify the presence and titers of antibodies and cross-neutralization against four strains of virus, samples from 1,500 bovines naturally infected with BVDV, from the States of Minas Gerais (MG), Mato Grosso do Sul (MS) and São Paulo (SP) were tested by the virus-neutralization test (VN), against four cytopathic strains: BVDV-1 (NADL - American strain and IBSP-11 Brazilian isolate) and BVDV-2 (VS-253 - American strain and IBSP-1020 - Brazilian isolate). Of the 1,500 animals, the range from 66.07% to 68.67%, were reactive to BVDV, and the increased frequency of antibodies was obtained in the state of MS, followed by MG and SP, independent of the BVDV strain used in the VN. The national isolate of the genotype 2, IBSP-1020 strain showed highest detection of reagents in MG and MS states, while in SP were the strains of genotype 1. The results with the four strains showed that 73.27% (1,099/1,500) of animals positive to at least one virus, whereas 57.60% (864/1,500) were simultaneously reactive to the four viruses, in other words that is, these animals produced antibodies that cross reacted against all strains in question. The titers of antibodies ranged from 10, the minimum value of detection of VN, to 5120, and that most animals were between 40 and 160 titers. In comparison of antibodies titers among states was observed that animals in SP presented lowest antibody titer that other states. The evaluation of titers of antibodies in each animal, comparing the results of two by two strains showed statistical difference in most situations. It is concluded that there was a high frequency of occurrence of bovine reagents to BVDV, which varied according to the system of rasing and management of herds. Moreover, the use of different viral strains, independently of genotype or place of origin of isolate, increased the sensitivity of detection of seropositive animals in the VN. Cross-neutralization was observed among all strains studied. To increase the sensitivity of diagnosis it is important to select for VN the strains representative of the regions to be studied.

Os fungos entomopatogênicos do gênero Metarhizium e Beauveria compreendem um importante grupo de patógenos de artrópodes-praga. A seleção de isolados de fungos promissores é a primeira e uma das mais importantes etapas no desenvolvimento de um biopesticida, pois alguns isolados podem apresentar alta virulência e não necessariamente boa produção em substrato e vice-versa, sendo interessante a combinação desses dois parâmetros para a viabilidade comercial de um produto. A dificuldade de criação ou manutenção de algumas espécies de pragas em laboratório é um limitante para a condução de testes de virulência, tornando-se interessante a utilização de espécies modelo, de fácil criação, nas etapas preliminares de seleção. Nesse sentido, este estudo objetivou selecionar isolados com alta produção de conídios e virulência, comparando a eficiência de controle de M. anisopliae e B. bassiana às pragas alvo Mahanarva fimbriolata e Bemisia tabaci Biótipo B, respectivamente, com a mortalidade em Tenebrio molitor. Inicialmente, foram selecionados 50 isolados a partir de 100 isolados de cada gênero, baseado em avaliações visuais do crescimento e esporulação em meio de cultivo em placas de Petri. Estes isolados selecionados foram cultivados em arroz parboilizado para quantificação do rendimento produtivo de conídios. Os 25 isolados mais produtivos de cada espécie de fungo foram utilizados nos bioensaios com T. molitor. Posteriormente, os cinco isolados que causaram maior e menor mortalidade de cada gênero, foram utilizados nos bioensaios com as respectivas pragas-alvo. A variação no rendimento de conídios de Beauveria spp., foi de 0,3 a 7,7 x 109 conídios.grama de arroz-1 e de Metarhizium spp. foi de 0,1 a 2,5 x 109 conídios.grama de arroz-1. A mortalidade confirmada de larvas de T. molitor por Beauveria spp., variou de 5,5 a 96,4% e por M. anisopliae variou de 29,1 a 89,1%. Alguns isolados causaram mortalidade elevada tanto no inseto modelo quanto na praga-alvo, porém, não foi verificada uma relação entre a virulência para as duas espécies. Da mesma forma, não foi observada associação entre os parâmetros produção de conídios e virulência. O isolado ESALQ 4958 de B. bassiana se destacou nos dois bioensaios apresentando mortalidades elevadas de ninfas de B. tabaci Biótipo B. Nos bioensaios utilizando ninfas de M. fimbriolata, ESALQ 1641 foi o isolado que apresentou os maiores percentuais de mortalidade nos dois bioensaios. Analisando conjuntamente as variáveis produção de conídios e virulência a T. molitor e a espécie alvo, os isolados ESALQ 540 (B. bassiana) e ESALQ 1116 (M. anisopliae) se destacaram por apresentarem valores elevados para todas as variáveis de interesse. Os resultados reforçam a necessidade de uma análise conjunta destas variáveis com um peso diferenciado para cada variável na seleção de isolados para utilização em produtos microbianos para o controle de pragas. / The genus Metarhizium spp. and Beauveria spp. are important entomopathogenic fungi used to control arthropod pests. The selection of promising fungal isolates is the first and one of the most important steps on the development of a biopesticide, since some isolates may present high virulence and not necessarily good production in substrate and vice-versa, being the combination of these two parameters important for the commercial viability. Difficulties of rearing or maintaining some species of pests in laboratory are limitations for the conduction of virulence tests, justifying the use of easy to breed model species on the preliminary steps of selection. Therefore, this study aimed to select isolates with high conidia production and virulence, comparing the control efficiency of M. anisopliae and B. bassiana to the target pests, Mahanarva fimbriolata and Bemisia tabaci biotype B, respectively, with mortality in Tenebrio molitor. At first, 50 isolates were selected from 100 isolates of each genus, based on growth and sporulation in culture medium on Petri dishes. These isolates were grown in parboiled rice to quantify the yield of conidia. The 25 most productive isolates of each fungus species were used in the bioassays with T. molitor. After, the five isolates that caused higher and lower mortality of each genus were used in the bioassays with the respective target pests. Beauveria spp. conidia yield ranged from 0.3 to 7.7 x 109 conidia.grams of rice-1 and Metarhizium spp. from 0.1 to 2.5 x 109 conidia.gram of rice-1. The confirmed mortality of T. molitor larvae by Beauveria spp. varied from 5.5 to 96.4% and M. anisopliae varied from 29.1 to 89.1%. Some isolates caused high mortality in both, model insect and the target pest; however, no relationship between the virulence of both species was observed. Similarly, there was no association between the parameters conidia production and virulence. The B. bassiana isolate ESALQ 4958 in both bioassays presented high mortalities of B. tabaci Biotype B. In bioassays using M. fimbriolata nymphs, ESALQ 1641 was the isolate that presented the highest mortalities in both bioassays. Analyzing the variables, conidia production and virulence to T. molitor and the target species, the isolates ESALQ 540 (B. bassiana) and ESALQ 1116 (M. anisopliae) showed high values for all variables of interest. The results reinforce the necessity of a joint analysis of these variables with different weight for each one in the selection of isolates, aiming to use them in microbial products for pest control.

Foi realizada a pesquisa de anticorpos anti-Toxoplasma gondii, através do teste de aglutinação modificado (MAT), em 68 amostras de soros de capivaras de seis municípios no estado de São Paulo. Anticorpos (MAT?25) foram encontrados em 51 (75%) capivaras examinadas. Dentre estas realizou-se o bioensaio em camundongos, com tecidos do cérebro, coração e língua, de 40 capivaras, sendo obtidos 36 isolados (90%). Não houve associação entre o número de isolados e idade das capivaras (p=0,21), sexo (p=0,58) ou tipo de criação (p=0,62), isto é, criadouros e vida livre, bem como a freqüência de isolamentos e os títulos de anticorpos (p=0,99). A análise de polimorfismo de comprimento dos fragmentos de DNA gerados por enzimas de restrição (RFLP) sobre produtos do locus SAG2 amplificados pela reação em cadeia pela polimerase (PCR) revelou que 20 isolados (55,5%) pertenciam ao genótipo I, 14 (38,9%) ao genótipo III e dois (5,6%) que apresentaram genótipo misto (tipos I e III). Não foi encontrado isolado tipo II. A proporção de isolados tipo I entre as capivaras de vida livre foi maior (p=0,049) do que entre as capivaras provenientes de criadouros. Por outro lado, entre as capivaras de criadouros, a proporção de isolados tipo III foi maior (p=0,041). A maioria dos isolados tipo I (12/20) causou óbito em todos os camundongos infectados e, em nenhum grupo com este isolado, 100% dos camundongos sobreviveram. A maioria dos isolados tipo III (8/14) não matou nenhum camundongo infectado. A freqüência de óbitos em camundongos com genótipo I (86%) foi maior do que o tipo III (44,9%) (p<0,001), enquanto a sobrevida dos camundongos com genótipo III foi significativamente maior que a dos camundongos com genótipo I (p<0,001). Foram encontrados cistos nos cérebros dos camundongos infectados em todos os 36 isolados. A análise genotípica também foi realizada diretamente dos tecidos de 35 das 36 capivaras (homogeneizados de tecidos) das quais houve isolamento pelo bioensaio, usando nestedPCR-RFLP no locus SAG2. Foram caracterizadas 22 amostras (62,8%), 21 delas idênticas aos dos isolados correspondentes. Em uma amostra genótipo misto foi obtido dos tecidos primários e tipo I no isolado. Os genótipos mistos foram confirmados pelo seqüenciamento de DNA dos produtos da nestedPCR obtidos das amostras primárias das capivaras. / Antibodies to Toxoplasma gondii were assayed by the modified agglutination test (MAT) in serum samples of 68 capybaras from six counties in São Paulo state, Brazil. Antibodies (MAT?25) were found in 51 (75%) capybaras examined. Tissues (brain, heart and tongue) of 40 of the seropositive capybaras were bioassayed in mice and 36 (90%) isolates were obtained. There was no statistical association between number of isolates and age (p=0.21), gender (p=0.58) and type of rearing (p=0.62), as well as no association with frequency of isolations and antibody titer distribution (p=0.99). Restriction fragment length polymorphism (RFLP) analysis in PCR-amplified SAG2 locus products revealed that 20 isolates (55.5%) were genotype I, 14 (38.9%) were genotype III and two (5.6%) were mixed genotypes (types I and III). Type II isolate was not found. The proportion of type I isolates in the group of wildlife capybaras was higher (p=0.049) than in the captive rearing group. On the other hand, the proportion of type III isolates was significantly higher in the captive rearing group (p=0.041). Most of the type I isolates (12/20) killed all infected mice and none of those groups had 100% of surviving mice. Most of the mice infected with genotype III isolate survived. The mortality rate in mice infected with genotype I (86%) was higher than the type III (44.9%) (p<0.001) and mice infected with type III isolates survived for longer periods than type I isolates (p<0.001). Tissue cysts were found in mice infected with all 36 isolates. Genotyping was also done directly from the tissue homogenates from the 35 of 36 capybaras using nested-PCR-RFLP analysis on the SAG2 locus. Twenty?two samples (62.8%) were characterized and in 21 the genotypes found were the same as those from the corresponding isolates. In one sample, mixed genotype was detected directly from the primary sample and type I from the mice isolate. The mixed genotype was confirmed by direct DNA sequencing of the nestedPCR products from the capybaras primary samples.

Aspergillus fumigatus has long been a focus of research, as it is the cause of the majority of Aspergillus infections. A. fumigatus is widely distributed in the environment and mainly distributed in air as conidia and is the main source of lung infection. A. fumigatus airborne counts were determined monthly during two years from the outside air environment at the University of Manchester campus and compared to total fungal airborne counts. Total fungal airborne counts were strongly seasonally associated with peak counts occurring during the summer months reaching 1,100-1400 CFU m-3and were correlated positively with mean temperature (R2=0.697). In contrast, Aspergillus fumigatus counts were not seasonally associated and gave persistent low levels of between 3-20 CFU m-3and were not correlated with mean temperature. A random selection of Manchester environmental isolates collected over one year along with clinical patient isolates and environmental isolates from the air from Dublin were analysed for genetic diversity using two combined RAPD primers. RAPD analysis revealed that the Manchester environmental isolates represented a genetically diverse population while the clinical isolates were less diverse and formed three major clusters. The Dublin isolates were the least diverse, probably due to their isolation at a single time point. When the pathogenicity of clinical and Dublin isolates were compared with a random selection of Manchester isolates in a wax moth model, as a group, clinical isolates were significantly more pathogenic than environmental isolates. Moreover, when relative pathogenicity of individual isolates was compared, clinical isolates were the most pathogenic, Dublin isolates the least pathogenic and Manchester isolates showed a range of pathogenicities suggesting that selection for the most pathogenic isolates from the environment occurs during patient infection. When the expression of secreted phospholipases in vitro during wax moth larvae of a range of isolates displaying varying degrees of pathogenicity was compared, two phospholipase C genes, AfplcA and AfplcC were strongly correlated with pathogenicity. AfplcC was by far the most highly expressed, however a ΔAfplcC knockout strain did not show attenuated virulence compared to the wild type in wax moth larvae.

Antimicrobial resistance (AMR) is concerning because it limits antimicrobial drug treatment options. AMR occurs by the overuse and misuse of antimicrobial drugs. In environmental settings, AMR can disseminate from places of high use, which leads to increased exposure to humans and animals. A previous study from our laboratory group showed extended-spectrum cephalosporinase-producing Escherichia coli/Klebsiella pneumoniae were isolated from fecal samples obtained in rural Cambodian community settings. Based on these isolates, this study has two aims. The first aim was characterization of selected Cambodian isolates with random amplification polymorphic DNA (RAPD) and antibiotic susceptibility test. From RAPD, the selected six isolates are diverse, except for C61 and C66 bacteria isolates with potential clonality. Additionally, the selected isolates are multidrug resistant (MDR) with reduced susceptibility to beta-lactams and fluoroquinolones. The second aim was to assess two developed methodologies, multiplex automated genome engineering (MAGE) and One-Step Curing Plasmid, by validation in bacteria laboratory strain and development for six Cambodian isolates. To modify AMR genetic elements, MAGE uses pMA7-SacB for homologous recombination with oligos for chromosomal gene disruption. Meanwhile, One-Step Curing Plasmid uses pFREE with the CRISPR/Cas9 system for plasmid and self-curing. Validation showed that MAGE can modify 8% of E. coli MG1655 with lacZ control screening oligos and almost 90% are cured from pFREE. Selected Cambodian isolates have antibiotic-resistance plasmids of IncR or IncFII replicon. For usage in Cambodian isolates, pFREE was modified to be pCAM-FREE by cloning IncR and IncFII plasmid as gRNA1 and gRNA5, respectively. Sequencing results showed pCAM-FREE have gRNA5. In conclusion, our study managed to characterize selected Cambodian isolates as MDR and diverse. In a laboratory strain, MAGE and One-Step Curing Plasmid are functional methods. Furthermore, pCAM-FREE was constructed to target IncFII and in the future, MAGE and pCAM-FREE could be tested in Cambodian isolates.

The ultimate goal of this research is to develop an efficient, reproducible and low cost method for analysis of VOCs in complex mixtures such as those in exhaled breath and in headspace of fungi cultures. In Chapter I; analytical methods for volatile biomarkers identification is reviewed In Chapter II, active SPME GCMS was employed to analyze VOCs in the breath of a single healthy male and a single female. The goal was to determine the extent of intra-individual variations in the VOC profiles. In Chapter III, a preliminary study was carried out in a greenhouse to determine the pathogenicity of different isolates of M. phaseolina on soybeans. This will allow, in future studies, the matching of VOC profiles of different isolates of M. phaseolina with their relative pathogenicity. This is a key step towards the development of an early warning system for the detection of pathogenic M. phaseolina fungus contaminations.

Campylobacter est l’agent pathogène zoonotique responsable de la majorité des gastro-entérites d’origine bactérienne chez l’homme. Les produits de volaille représentent la principale source d’infection; toutefois, l’exposition peut également découler de contacts directs avec les animaux ou avec l’eau. Une forte variation saisonnière est présente dans les cas rapportés, qui n’est toujours pas élucidée : les eaux environnementales, sources d’infection connues, sont soupçonnées. Cette étude transversale a été réalisée dans la région Sud-Est du Québec (Canada) où Campylobacter fut quantifié et génotypé à partir de différentes sources d’eau (eaux de captage, récréatives et usées) et de cas cliniques afin d’évaluer les risques potentiels posé par l’eau environnementale. Différents essais PCR en temps réel furent appliqués à l’eau environnementale et comparés: 2 ont été sélectionnés pour leur spécificité et sensibilité de quantification. Les courbes standards ont été calibrées en utilisant la PCR digitale pour déterminer précisément les concentrations. Les isolats environnementaux et cliniques furent comparés génétiquement en utilisant le CGF (« comparative genomic fingerprinting »). Les eaux usées étaient plus contaminées que les eaux de captage et récréatives (3.9Log, 1.7Log et 1.0Log cellules/L en moyenne, respectivement). Six pour cent des isolats d’eaux environnementales étaient génétiquement similaires (100 % homologie) aux isolats cliniques. Les cas cliniques de campylobactériose d’été montraient des isolats avec davantage de similarités génétiques avec les isolats retrouvés dans l’eau environnementale comparativement aux autres saisons (p<0.01). Les faibles concentrations et similarités génétiques entre les isolats d’eau et cliniques suggèrent un risque de transmission possible, mais faible. / Campylobacter is a zoonotic pathogen that is responsible for the majority of cases of bacterial gastroenteritis. Among the numerous Campylobacter transmission routes including direct contact, food and water, poultry consumption has been recognized as the major route. A strong seasonal variation in campylobacteriosis cases exists for reasons that are not well understood; environmental water is suspected to be involved. This cross-sectional study was conducted in the Southeastern region of Quebec (Canada), wherein Campylobacter from different waters (drinking water source, recreational and sewage) and clinical sources was quantified and genotyped in order to evaluate the potential risks posed by environmental water. Several real-time PCR assays were compared for specific application to environmental water: two were selected for their specificity and sensitivity of quantification. Standard curves were calibrated using digital PCR to accurately determine concentrations. Campylobacter isolates from clinical and water sources were genetically compared using CGF (comparative genomic fingerprinting). Sewage waters showed the highest Campylobacter concentrations, while drinking water source and recreational waters showed the lowest (average of 3.9Log, 1.7Log and 1.0Log cells/L, respectively). CGF revealed that 6% of water isolates were genetically similar (100% homology) to clinical isolates. Summer cases of campylobacteriosis revealed isolates showing more genetic similarities with environmental water isolates compared to other seasons (p<0.01). The low Campylobacter concentrations and genetic similarities between water and clinical isolates from the same region, suggests that these environmental waters pose a real, but low risk of transmission.

Fusarium oxysporum Schl. var. vanillae (Tucker) Gondon is known to cause root rot in Vanilla planifolia Andrews in most regions where it is grown, including the major plantations in Xishuangbanna, Yunnan Province of China. This is of serious economic concern to the Province since the vanilla flavouring extractable from the beans of the plant is a valuable food product and an important export commodity. There are no fungicides registered for the control of Fusarium root rot and the only available chemical control methods are ineffective and cause serious contamination of the soil. Breeding for resistance is difficult when no dominant gene is known or where little information is available on fungal pathogenicity. Biocontrol is the main alternative for disease control in this crop, an attractive approach because of increasing concerns for environmental protection. The investigation considers two biocontrol strategies: first the introduction of virulent, antagonistic, non-pathogenic strains, closely-related to the pathogen, to overcome pathogenic populations in infected soils; second the use of essential oils with antimicrobial properties when applied to infected soils. Pathogenicity tests have been done on 81 out of 87 F. oxysporum isolates collected in Yunnan Province. Among these, 32 isolates were non-pathogenic and 49 were pathogenic. The pathogenicity results showed the complexity of F. oxysporum in Yunnan. Seventeen isolates were recovered from the Daluo plantation, of which 14 were pathogenic isolates and 3 non-pathogenic isolates; 26 from the Menglun plantation, in which 12 were pathogenic and 14 were non-pathogenic; 18 isolates from the Manjingdai plantation, in which 12 isolates were pathogenic, whilst the other 6 were non-pathogenic and 20 were obtained from the plantation in Hekou i County, of which 11 were pathogenic isolates and 9 were non-pathogenic. Genetic diversity within this population of F. oxysporum has been investigated with respect to vegetative compatibility and to determine the relationship between VCGs and virulence. The VCG results showed that the 87 strains of Fusarium oxysporum f.sp vanillae isolated from Yunnan Province were complex. They could be distributed into 12 different VCGs and that a direct relationship between VCGs group and virulence could not be drawn. Two non-pathogenic strains, ML-5-2 and HK-5b-4-1, have been screened from 87 strains as candidate biocontrol agents by pathogenicity and VCG, which are self-incompatible and closely related to the pathogens. These two strains were effective in vanilla root rot control in controlled environments, but their effects in field experiments were less conclusive. Seven essential oils, which have long been regarded as having inhibitory effects on pathogens in nature, have also been investigated as biocontrol agents. Three oils, cinnamon oil, thyme oil and clove oil, were effective in inhibiting the growth of pathogen in vitro. These oils may develop into useful components of different management strategies with non-pathogenic strains. For the future, consideration will need to be given to the mechanism(s) of the interaction of the antagonistic components with the soil microbe population and host plant and also to appropriate formulation, to take account of soil type, crop status, cultural practices, environmental and economic factors. Biocontrol methods have considerable potential but must be acceptable to farmers as part of an overall crop management programme.