Os rotavírus do grupo A (RVA) são importantes causadores de diarreias virais em crianças e animais jovens de diferentes espécies, com impactos na saúde pública e animal. Visando contribuir para o entendimento e prevenção das rotaviroses assim como suas possíveis relações zoonóticas, caracterizou-se os 11 segmentos de dsRNA de rotavírus codificadores das proteínas estruturais e não estruturais presentes em amostras fecais positivas de suínos coletadas nos anos de 2012-2013, em 2 estados brasileiros. Mediante o emprego de RT-PCR, sequenciamento nucleotídico e análises filogenéticas, todos os segmentos genéticos oriundos de 12 amostras de RVA detectados em suínos foram analisados e comparados com os de outras amostras descritas previamente. As sequências obtidas para os genes codificadores das proteínas NSP2, NSP3 e VP6 contemplaram a open reading frame (ORF) completa do gene, enquanto que a ORF parcial foi determinada para os genes codificadores das proteínas VP1, VP2, VP3, VP4, VP7, NSP1, NSP4, NSP5 e NSP6. Os genotipos de rotavírus suíno provenientes das regiões amostradas concordam com os mais frequentemente descritos nesta espécie animal, apresentando, assim, uma matriz genética suína com a maioria dos segmentos pertencentes à constelação genotípica 1, com exceção dos genes codificadores das proteínas VP6 e NSP1, os quais foram os genotipos I5 e A8, respectivamente. Apesar de predominar o genotipo 1 (Wa-like) nas sequências deste estudo, a análise genômica sugere a existência de uma variação intragenotípica no genoma do rotavírus do grupo A atualmente circulante nas populações suína amostradas dos estados de São Paulo e Mato Grosso. Adicionalmente, buscou-se identificar os aminoácidos relacionados com a adaptação dos rotavírus no hospedeiro e assinaturas genéticas que distinguissem RVA suíno e humano. Para isso, as sequências obtidas neste estudo foram comparadas com outras cepas de RVA detectadas nestas duas espécies e pertencentes ao genotipo 1 (Wa-like) disponíveis no Genbank. Como resultados foram encontrados mais de 75 sítios de mudanças deaminoácidos que diferenciam RVA suíno e humano além de sítios de substituiçãopresentes em algumas proteínas virais que frequentemente covariaram entre elas. Estes resultados proporcionam um maior entendimento da diversidade viral circulante em unidades de produção suína e uma melhor compreensão dos animaiscomo reservatórios genéticos de cepas de rotavírus emergentes em humanos. / Group A rotaviruses (RVA) are leading causes of viral diarrhea in children and in the young of many animals species with impacts on public and animal health. To contribute to the understanding and prevention of rotaviruses as well as its possible zoonotic relationships, it was characterized the 11 segments of dsRNA rotavirus encoding the structural and nonstructural proteins present in positive fecal samples from pigs collected in the years 2012-2013 in 2 Brazilian states. Using RT-PCR, nucleotide sequencing, and phylogenetic analyses, all gene segments from 12 RVA samples detected in pigs were analyzed and compared with the other samples as described previously. The sequences obtained for the NSP2, NSP3, and VP6 coding genes covered the complete open reading frame (ORF), while the partial ORF was determined for the VP1, VP2, VP3, VP4, VP7, NSP1, NSP4, NSP5 and NSP6 coding genes. The genotypes of porcine rotavirus from the sampled regions agree with the most frequently reported in this species, presenting thus a porcine-RVA-like backbone with most segments being designated as constellation genotype 1, with the exception of the VP6 and NSP1 coding genes, which were genotypes I5 and A8, respectively. Although genotype 1 (Wa-like) sequences were predominant in this study, the genomic analysis suggests the existence of a intragenotypic variation in group A rotavirus genome currently circulating in swine populations sampled in the states of São Paulo and Mato Grosso. In addition, we sought to identify the amino acids related to the adaptation of rotavirus in the host and genetic signatures that distinguish RVA pig and human. For this, the sequences obtained in this study were compared with other strains of RVA detected in these two species, belonging to genotype 1 (Wa-like) available in Genbank. The following results were found more than 75 sites of amino acid changes that differentiate RVA pig and human as well as substitution sites present in some viral proteins that often covaried between them. These results provide a greater understanding of the current viral diversity in swine production units and a better understanding of animals as genetic reservoirs emerging rotavirus strains in humans.

Os rotavírus do grupo A (RVA) são importantes causadores de diarreias virais em crianças e animais jovens de diferentes espécies, com impactos na saúde pública e animal. Visando contribuir para o entendimento e prevenção das rotaviroses assim como suas possíveis relações zoonóticas, caracterizou-se os 11 segmentos de dsRNA de rotavírus codificadores das proteínas estruturais e não estruturais presentes em amostras fecais positivas de suínos coletadas nos anos de 2012-2013, em 2 estados brasileiros. Mediante o emprego de RT-PCR, sequenciamento nucleotídico e análises filogenéticas, todos os segmentos genéticos oriundos de 12 amostras de RVA detectados em suínos foram analisados e comparados com os de outras amostras descritas previamente. As sequências obtidas para os genes codificadores das proteínas NSP2, NSP3 e VP6 contemplaram a open reading frame (ORF) completa do gene, enquanto que a ORF parcial foi determinada para os genes codificadores das proteínas VP1, VP2, VP3, VP4, VP7, NSP1, NSP4, NSP5 e NSP6. Os genotipos de rotavírus suíno provenientes das regiões amostradas concordam com os mais frequentemente descritos nesta espécie animal, apresentando, assim, uma matriz genética suína com a maioria dos segmentos pertencentes à constelação genotípica 1, com exceção dos genes codificadores das proteínas VP6 e NSP1, os quais foram os genotipos I5 e A8, respectivamente. Apesar de predominar o genotipo 1 (Wa-like) nas sequências deste estudo, a análise genômica sugere a existência de uma variação intragenotípica no genoma do rotavírus do grupo A atualmente circulante nas populações suína amostradas dos estados de São Paulo e Mato Grosso. Adicionalmente, buscou-se identificar os aminoácidos relacionados com a adaptação dos rotavírus no hospedeiro e assinaturas genéticas que distinguissem RVA suíno e humano. Para isso, as sequências obtidas neste estudo foram comparadas com outras cepas de RVA detectadas nestas duas espécies e pertencentes ao genotipo 1 (Wa-like) disponíveis no Genbank. Como resultados foram encontrados mais de 75 sítios de mudanças deaminoácidos que diferenciam RVA suíno e humano além de sítios de substituiçãopresentes em algumas proteínas virais que frequentemente covariaram entre elas. Estes resultados proporcionam um maior entendimento da diversidade viral circulante em unidades de produção suína e uma melhor compreensão dos animaiscomo reservatórios genéticos de cepas de rotavírus emergentes em humanos. / Group A rotaviruses (RVA) are leading causes of viral diarrhea in children and in the young of many animals species with impacts on public and animal health. To contribute to the understanding and prevention of rotaviruses as well as its possible zoonotic relationships, it was characterized the 11 segments of dsRNA rotavirus encoding the structural and nonstructural proteins present in positive fecal samples from pigs collected in the years 2012-2013 in 2 Brazilian states. Using RT-PCR, nucleotide sequencing, and phylogenetic analyses, all gene segments from 12 RVA samples detected in pigs were analyzed and compared with the other samples as described previously. The sequences obtained for the NSP2, NSP3, and VP6 coding genes covered the complete open reading frame (ORF), while the partial ORF was determined for the VP1, VP2, VP3, VP4, VP7, NSP1, NSP4, NSP5 and NSP6 coding genes. The genotypes of porcine rotavirus from the sampled regions agree with the most frequently reported in this species, presenting thus a porcine-RVA-like backbone with most segments being designated as constellation genotype 1, with the exception of the VP6 and NSP1 coding genes, which were genotypes I5 and A8, respectively. Although genotype 1 (Wa-like) sequences were predominant in this study, the genomic analysis suggests the existence of a intragenotypic variation in group A rotavirus genome currently circulating in swine populations sampled in the states of São Paulo and Mato Grosso. In addition, we sought to identify the amino acids related to the adaptation of rotavirus in the host and genetic signatures that distinguish RVA pig and human. For this, the sequences obtained in this study were compared with other strains of RVA detected in these two species, belonging to genotype 1 (Wa-like) available in Genbank. The following results were found more than 75 sites of amino acid changes that differentiate RVA pig and human as well as substitution sites present in some viral proteins that often covaried between them. These results provide a greater understanding of the current viral diversity in swine production units and a better understanding of animals as genetic reservoirs emerging rotavirus strains in humans.

Burkholderia contaminans MS14 shows excellent antimicrobial activities against a wide range of pathogens. Complete sequence analysis reveals that the MS14 genome harbors multiple gene loci that contribute to its antimicrobial activities and lacks key virulence features commonly found in pathogenic Burkholderia species. A mutagenesis study identified the genes required for MS14 antibacterial activities and gene expression profiling targeted a polyketide synthase (PKS) gene cluster. Site-specific mutagenesis confirmed the PKS gene cluster is directly related to MS14 antibacterial activities and the PKS gene product is predicted to be the MS14 antibacterial compound. Strain UFB2 isolated from Mississippi shows significant antifungal and antibacterial activities. UFB2 was classified to be Pseudomonas chlororaphis and its complete genome sequence was reported in this study. Green house trails showed P. chlororaphis strain UFB2 could efficiently reduce the disease severity of bacterial canker of tomato, by significantly inhibiting the growth of the pathogen Clavibacter michiganensis subsp. michiganensis. The research findings of B. contaminans MS14 and P. chlororaphis UFB2 have provided insights into the development of MS14 antibacterial compound for agricultural application and potential use of strain UFB2 as a biocontrol agent.

Salmonella est un agent pathogène animal et zoonotique d'importance mondiale. Les infections causées par cette bactérie chez les animaux d’élevage peuvent être asymptomatiques ou se traduire par une gastro-entérite ou une maladie invasive. Chez les humains, les maladies d’origines alimentaires associées à Salmonella sont principalement causées par l'ingestion de produits d'origine animale contaminés. Cependant, aucune étude n’a déterminé la prévalence ou caractérisé le profil de virulence et d’antibiorésistance de Salmonella provenant des fermes ovines du Québec, alors que cette province détient le 2ème plus grand cheptel ovin canadien. Ainsi, cette étude visait à estimer la prévalence des fermes ovines positives à Salmonella dans la province du Québec, à identifier les sérotypes circulant dans ces troupeaux, à caractériser le profil de virulence et de résistance aux antimicrobiens de souches de Salmonella isolées dans ces fermes et à évaluer l'influence de certains facteurs de risque (ex. la saisonnalité, la taille des troupeaux et le type de production) sur la prévalence de fermes ovines positives à Salmonella au Québec. Pour cela, 61 fermes ovines du Québec ont été sélectionnées aléatoirement et ont été échantillonnées. Un pool fécal provenant de 10 animaux a été prélevé par ferme. Des milieux sélectifs ont été utilisés pour isoler Salmonella dans chaque échantillon. La confirmation de Salmonella a été faite par des tests biochimiques suivis par la détection du gène invA par PCR et les sous-espèces ont été identifiées par PCR multiplex. Le rapport de prévalence a été calculé pour évaluer l’association entre les facteurs de risque et la présence de Salmonella dans les fermes. Le séquençage du génome complet de 76 isolats a permis d’identifier les sérotypes et de déterminer le profil de virulence et de résistance génotypique de ces isolats. La confirmation de la résistance phénotypique de différentes souches a été effectuée en utilisant la méthode de diffusion en milieu solide (antibiogramme) et la méthode de dilution en milieu liquide. Les résultats indiquent que 83,6% (95% CI 74,3%-92,9%) des troupeaux sont porteurs de Salmonella. Le sérotype Salmonella enterica sous-espèce diarizonae 61 k:1, 5, (7) (Sheep associated Salmonella diarizonae (SASd) a été le seul sérotype identifié dans tous les isolats qui ont été séquencés. Aucun des facteurs de risque évalués n’était associée à la présence de Salmonella. En outre, aucun gène de résistance aux antimicrobiens n’a été identifié à partir de l’analyse des génomes séquencés et toutes les souches ont été révélées comme étant phénotypiquement sensibles aux différents antimicrobiens testés. De plus, des facteurs de virulence, comme les ilots de pathogénicité (SPI-1, SPI-2, SPI-3, SPI-5, SPI-9 et SPI-13) et le plasmide (IncX1), ont été identifiés chez les 84 SASd. Cette étude est la première à rapporter que la prévalence des fermes ovines positives à Salmonella est élevée au Québec (83,6%). Seule la présence du sérotype 61 k:1, 5, (7) a été détectée. Finalement, toutes les souches de Salmonella isolées dans le cadre de cette étude étaient sensibles aux antimicrobiens testés. / Salmonella is a world-known animal and zoonotic pathogen. Infections caused by this bacterium in livestock can be asymptomatic or result in gastroenteritis or an invasive disease. In humans, food-related diseases associated with Salmonella are mainly caused by the ingestion of contaminated products of animal origin. However, no studies have determined the prevalence or characterized the virulence and antimicrobial resistance (AMR) profiles of Salmonella from sheep farms in Quebec, where the province holds the second largest sheep population in Canada. This study aimed to estimate the prevalence of Salmonella-positive sheep farms in the province of Quebec, to identify the serotypes circulating in these flocks, to characterize the virulence and AMR profiles of Salmonella strains isolated from these farms and to assess the influence of some potential risk factors on the prevalence of Salmonella-positive sheep farms in the province of Quebec. For this purpose, 61 sheep farms in Quebec were randomly selected and sampled. A fecal pool including samples from 10 animals was collected per farm. Selective culture media were used to isolate Salmonella in each sample. Salmonella was confirmed by biochemical tests followed by the detection of invA gene by PCR and the subspecies were identified by multiplex PCR. The prevalence ratio was calculated to assess the association between risk factors and the presence of Salmonella in farms. The Whole genome sequencing (WGS) of 76 isolates was used to determine the serotypes, the virulence and the AMR profile of these isolates. The confirmation of the phenotypic AMR of these isolates (n=76) was carried out using the Kirby–Bauer disk diffusion method (antibiogram) or the broth microdilution method. The results indicated that 83.6% (95% CI 74.3%-92.9%) of the flocks are carrier of Salmonella and only the Salmonella enterica subspecies diarizonae serotype 61: k: 1, 5, (7) (sheep associated S. diarizonae, SASd) was identified. None of the tested risk factors was associated with Salmonella positivity at the flock level. In addition, no AMR genes were identified from the WGS data, and all strains were phenotypically sensitive to the various antimicrobials tested. In addition, virulence factors such as pathogenicity islands (SPI-1, SPI-2, SPI-3, SPI-5, SPI-9 and SPI-13) and plasmid (IncX1) have been identified in the sequenced strains. This study was the first to report a high prevalence of Salmonella-positive sheep farms in Quebec (83.6%). Only the presence of serotype 61 k:1, 5, (7) was detected. Interestingly, all Salmonella strains isolated in this study were sensitive to the tested antimicrobials.