Phenotypic and genotypic characterization of Brucella abortus biovar 4 isolates from cattle in Brazil / Caracterização fenotípica e genotípica de isolados de Brucella abortus biovar 4 em bovinos no Brasil

ABSTRACT: The aim of the present study was to characterize (phenotypically and genotypically) two strains of Brucella abortus identified as belonging to biovar 4 isolated from cattle in Brazil. The strains were isolated from cervical bursitis from cattle in the states of Pará and Rio Grande do Sul, respectively. In the phenotypic identification, the isolates were positive in CO2 requirement, produced H2S, were resistant to basic fuchsin (20 µg / mL) and sensitive to thionin (20 µg / mL and 40 µg / mL) and presented M surface antigen, but A surface antigen is absent. The isolates were positive in the PCR for the bcsp31 gene (genus-specific) and in the AMOS-enhanced PCR, both isolates showed a band profile consistent with B. abortus biovar 1, 2 or 4. Moreover, both isolates also showed restriction patterns identical to the reference strain when tested by the omp2b PCR-RFLP. In genotyping using Multiple Locus Variable Number of Tandem Repeat (VNTR) Analysis - MLVA (MLVA16), the isolates showed differences in several loci (Bruce42, Bruce19, Bruce04, Bruce16 and Bruce30); by Multiple Locus Sequence Typing (MLST), they also exhibited differences in sequence type (ST), strain 16/02 ST1 (2-1-1-2-1-3-1-1-1) and strain 128/11 ST (22-1-1 -8-9-3-1-1-1). The extensive typing of B. abortus strains isolated from cattle in Brazil using different approaches confirmed the occurrence of rare B. abortus biovar 4 in the country.

RESUMO: O objetivo do presente estudo foi caracterizar (fenotipicamente e genotipicamente) duas cepas de Brucella abortus identificadas como pertencentes ao biovar 4 isolada de bovinos no Brasil. As cepas foram isoladas de bursite cervical de bovinos dos estados do Pará e Rio Grande do Sul, respectivamente. Na identificação fenotípica, os isolados foram positivos na exigência de CO2, produziram H2S, foram resistentes à fucsina básica (20 µg / mL) e sensíveis à tionina (20 µg / mL e 40 µg / mL) e apresentaram antígeno de superfície M, mas o antígeno de superfície A foi ausente. Os isolados foram positivos na PCR para o gene bcsp31 (gênero específico) e na PCR - AMOS, ambos os isolados apresentaram perfil de banda consistente com B. abortus biovar 1, 2 ou 4. Além disso, ambos os isolados também apresentaram padrões de restrição idêntica à cepa de referência quando testada pelo omp2b PCR-RFLP. Na genotipagem usando Multiple Locus Variable Number of Tandem Repeat (VNTR) - MLVA (MLVA16), os isolados apresentaram diferenças em vários loci (Bruce42, Bruce19, Bruce04, Bruce16 e Bruce30); no Multiple Locus Sequence Typing (MLST), os isolados também exibiram diferenças na sequência tipo (ST), amostra 16/02 ST1 (2-1-1-2-1-3-1-1-1) e amostra 128/11 ST (22-1-1-8-9-3-1-1-1). A extensa tipagem de cepas de B. abortus isoladas de bovinos no Brasil por diferentes abordagens confirmou a rara ocorrência de B. abortus biovar 4 no país.

Genetic diversity and antimicrobial susceptibility of Staphylococcus aureus isolated from bovine mastitis in Minas Gerais, Brazil / Diversidade genética e susceptibilidade a antimicrobianos em Staphylococcus aureus isoladas de mastite bovina em Minas Gerais, Brasil

ABSTRACT: This study evaluated the genetic diversity and antimicrobial susceptibility of Staphylococcus aureus isolates from dairy cows in Minas Gerais, Brazil. Thirty-seven isolates from five municipalities (8 herds) were genotyped using multi-locus sequence typing (MLST) and susceptibility to 12 antimicrobial agents was tested using the disk diffusion method. High resistance rates for penicillin [75.68% (28/37)], ampicillin [70.27% (26/37)], and tetracycline [70.27% (26/37)] were detected. Multidrug resistance was observed in seven [18.92% (7/37)] isolates, and two were suggestive of Methicillin-resistant Staphylococcus aureus (MRSA). Among the 37 isolates, 33 novel sequence types (ST) and two known STs (ST126 and ST746) were identified in MLST. The clonal complexes more frequently observed were: CC97 [78.38%; (29/37)], CC1 [8.11%; (3/37)] and CC5 [5.40%; (2/37)]. Minimum‐spanning tree (MST) analysis according to data from municipalities, herds, and resistance patterns for all isolates did not show any clustering pattern. However, the MST comparing all Brazilian S. aureus isolates deposited in the PubMLST database and from this study depicted an association between the genotype and strain origin (clinical sample). Isolates from this study that belong to CC97 were close to database isolates from milk and dairy products, while those that belong to CC1 and CC5 were close to database isolates from human sources and the environment of dairy farms or industries. In conclusion, our results showed a high rate of resistance to penicillins and tetracyclines and great genetic diversity among the S. aureus isolates from bovine mastitis genotyped in the present study.

RESUMO: Este estudo teve como objetivo avaliar a diversidade genética e a suscetibilidade a antimicrobianos de cepas de Staphylococcus aureus isoladas de vacas leiteiras em Minas Gerais, Brasil. Trinta e sete cepas provenientes de cinco municípios (oito rebanhos) foram genotipadas usando a técnica multi-locus sequence typing (MLST) e a suscetibilidade a 12 antimicrobianos foi avaliada pelo método de difusão em disco. Foram detectadas altas taxas de resistência para penicilina [75,68% (28/37)], ampicilina [70,27% (26/37)] e tetraciclina [70,27% (26/37)] entre os isolados. A multirresistência foi observada em sete [18,92% (7/37)] isolados e dois foram classificados como sugestivos de Staphylococcus aureus resistente à meticilina (MRSA). Entre os 37 isolados, 33 novos sequence types (ST) e dois STs conhecidos (ST126 e ST746) foram identificados pelo MLST. Os complexos clonais mais frequentemente observados foram: CC97 [78,38%; (29/37)], CC1 [8,11%; (3/37)] e CC5 [5,40%; (2/37)]. Foi construída uma minimum‐spanning tree (MSTs) com todos isolados estudados e esta não mostrou padrão de agrupamento quando comparada com dados epidemiológicos como municípios e rebanho, do qual foi isolado, e perfis de resistência a antimicrobianos. Uma segunda MST foi construída comparando os isolados deste estudo e todas as cepas de S. aureus depositadas no banco de dados PubMLST provenientes do Brasil, que mostrou associação entre o genótipo, STs e a origem da cepa. Foi possível observar entre os isolados do estudo que, aqueles que pertenciam ao CC97, eram geneticamente mais próximos das cepas depositadas no PubMLST isoladas de leite e de produtos lácteos, enquanto aqueles que pertenciam aos CC1 e CC5 estavam mais próximos a cepas isoladas de humanos ou do ambiente de fazendas e indústrias de laticínios. Em conclusão, nossos resultados mostraram um alto índice de resistência às penicilinas e tetraciclinas e grande diversidade genética entre as cepas de S. aureus isoladas de casos de mastite bovina.

Molecular characterization of Astyanax species (Characiformes: Characidae) from the upper Paraguaçu River basin, a hydrographic system with high endemism

Molecular tools have been employed to improve the knowledge about freshwater Neotropical fishes. Such approaches supporting studies of groups including species complexes such as Astyanax, one of the most diversified and taxonomically complex genus of the family Characidae. Here, we employed species delimitation analyses in four Astyanax species described for the upper Paraguaçu River basin, a drainage within Northeastern Mata Atlântica freshwater ecoregion with high endemism. We implemented single and multilocus approaches based on two mitochondrial and one nuclear markers. Cytochrome c Oxidase I sequences previously available for Astyanax species were also added to our dataset. The single locus analyses showed A. epiagos, A. rupestris, and A. aff. rupestris as different Molecular Operational Taxonomic Units (MOTUs), while A. brucutu and A. lorien were grouped. However, the multilocus approach distinguished these two species and showed congruence for the remaining single locus results. Astyanax aff. rupestris was separated into two MOTUs using both approaches, highlighting the need for an integrative taxonomic revision including A. aff. rupestris. These findings contribute to a better understanding of the diversity of this fish group in the upper Paraguaçu, identifying hidden diversity and reinforcing the relevance of this hydrographic system as a notable hotspot for ichthyofauna biodiversity endemism.(AU)

Ferramentas moleculares têm sido empregadas para melhorar o conhecimento sobre os peixes Neotropicais. Tais abordagens apoiam estudos de grupos que incluem complexos de espécies, como Astyanax, um dos gêneros mais diversificados e taxonomicamente complexos dentro da família Characidae. Neste estudo, nós empregamos análises de delimitação de espécies em quatro espécies de Astyanax recentemente descritas da bacia do alto rio Paraguaçu, uma drenagem dentro da ecorregião Mata Atlântica Nordeste que apresenta alto endemismo. Nós realizamos abordagens de loco único e multilocos baseadas em dois marcadores mitocondriais e um nuclear. Sequências de Citocromo c Oxidase I anteriormente disponíveis para espécies de Astyanax foram adicionadas ao nosso conjunto de dados. As análises de loco único mostraram A. epiagos, A. rupestris e A. aff. rupestris como diferentes Unidades Taxonômicas Operacionais Moleculares (MOTUs), enquanto A. brucutu e A. lorien foram agrupadas. Entretanto, a abordagem multilocos distinguiu estas duas espécies e mostrou congruência com os demais resultados das análises de loco único. Astyanax aff. rupestris foi separada em duas MOTUs usando ambas as abordagens, sugerindo a necessidade de uma revisão taxonômica integrativa incluindo A. rupestris e ambas A. aff. rupestris. Esses achados contribuem para uma melhor compreensão da diversidade desse grupo de peixes na bacia do rio Paraguaçu, identificando diversidade oculta e reforçando a relevância desse sistema hidrográfico como um notável hotspot de endemismo da biodiversidade da ictiofauna.(AU)

Phenotypic and genotypic characterization of Brucella abortus biovar 4 isolates from cattle in Brazi / Caracterização fenotípica e genotípica de isolados de Brucella abortus biovar 4 em bovinos no Brasil

The aim of the present study was to characterize (phenotypically and genotypically) two strains of Brucella abortus identified as belonging to biovar 4 isolated from cattle in Brazil. The strains were isolated from cervical bursitis from cattle in the states of Pará and Rio Grande do Sul, respectively. In the phenotypic identification, the isolates were positive in CO2 requirement, produced H2S, were resistant to basic fuchsin (20 µg / mL) and sensitive to thionin (20 µg / mL and 40 µg / mL) and presented M surface antigen, but A surface antigen is absent. The isolates were positive in the PCR for the bcsp31 gene (genus-specific) and in the AMOS-enhanced PCR, both isolates showed a band profile consistent with B. abortus biovar 1, 2 or 4. Moreover, both isolates also showed restriction patterns identical to the reference strain when tested by the omp2b PCR-RFLP. In genotyping using Multiple Locus Variable Number of Tandem Repeat (VNTR) Analysis - MLVA (MLVA16), the isolates showed differences in several loci (Bruce42, Bruce19, Bruce04, Bruce16 and Bruce30); by Multiple Locus Sequence Typing (MLST), they also exhibited differences in sequence type (ST), strain 16/02 ST1 (2-1-1-2-1-3-1-1-1) and strain 128/11 ST (22-1-1 -8-9-3-1-1-1). The extensive typing of B. abortus strains isolated from cattle in Brazil using different approaches confirmed the occurrence of rare B. abortus biovar 4 in the country.

O objetivo do presente estudo foi caracterizar (fenotipicamente e genotipicamente) duas cepas de Brucella abortus identificadas como pertencentes ao biovar 4 isolada de bovinos no Brasil. As cepas foram isoladas de bursite cervical de bovinos dos estados do Pará e Rio Grande do Sul, respectivamente. Na identificação fenotípica, os isolados foram positivos na exigência de CO2, produziram H2S, foram resistentes à fucsina básica (20 µg / mL) e sensíveis à tionina (20 µg / mL e 40 µg / mL) e apresentaram antígeno de superfície M, mas o antígeno de superfície A foi ausente. Os isolados foram positivos na PCR para o gene bcsp31 (gênero específico) e na PCR - AMOS, ambos os isolados apresentaram perfil de banda consistente com B. abortus biovar 1, 2 ou 4. Além disso, ambos os isolados também apresentaram padrões de restrição idêntica à cepa de referência quando testada pelo omp2b PCR-RFLP. Na genotipagem usando Multiple Locus Variable Number of Tandem Repeat (VNTR) - MLVA (MLVA16), os isolados apresentaram diferenças em vários loci (Bruce42, Bruce19, Bruce04, Bruce16 e Bruce30); no Multiple Locus Sequence Typing (MLST), os isolados também exibiram diferenças na sequência tipo (ST), amostra 16/02 ST1 (2-1-1-2-1-3-1-1-1) e amostra 128/11 ST (22-1-1-8-9-3-1-1-1). A extensa tipagem de cepas de B. abortus isoladas de bovinos no Brasil por diferentes abordagens confirmou a rara ocorrência de B. abortus biovar 4 no país.

Ribosomal, mitochondrial and bacterial (Wolbachia) reference sequences for Dipetalonema gracile obtained from a wild pied tamarin (Saguinus bicolor) host in Manaus, Brazil / Sequências ribossômicas, mitocondriais e bacterianas (Wolbachia) de referência para Dipetalonema gracile obtidas de um hospedeiro sauim-de-coleira (Saguinus bicolor) em Manaus, Brasil

The primates that inhabit the rainforest surrounding the city of Manaus (Amazonas, Brazil) have long been recognised as potentially important reservoirs of emerging and re-emerging infectious diseases (ERIDs). PCR amplification of filarial sequences from wild-caught Simulium oyapockense has been used to incriminate potentially important Amazon-region ERID bridge vectors by showing they had previously fed on non-human primates. The broader use of filarial parasite sequences for the incrimination of biting insects as potentially important zoonotic disease vectors is limited by a paucity of primate-derived filarial parasite reference sequences which can be matched to the PCR amplified sequences obtained from insect-vector vectors. Here we have used shotgun sequencing to obtain reference data from an adult Dipetalonema gracile parasite which was found infecting a wild pied tamarin (Saguinus bicolor) in a peripheral region of Manaus. We report the parasite´s complete mitochondrial genome (which is 13,647 base pairs in length), 894,846 base pairs of its Wolbachia genome and 6,426 base pairs of its ribosomal DNA locus (spanning from the start of its 18S subunit to the end of its 28S subunit). Despite being critically endangered, S. bicolor is commonly encountered around the periphery of Manaus and in urban forest fragments. The reported sequences may be a useful reference tool for identifying ERID bridge vectors and potentially provide some insights into the amount and the nature of contact between primate pathogen reservoirs and the residents of Manaus.(AU)

Os primatas que habitam a floresta tropical ao redor da cidade de Manaus (Amazonas, Brasil) há muito são reconhecidos como reservatórios potencialmente importantes de doenças infecciosas emergentes e reemergentes. Sequências de DNA de parasitas filariais detectadas por PCR em amostras de Simulium oyapockense foram usadas para demonstrar que eles haviam se alimentado anteriormente de primatas não humanos e, dessa maneira, incriminar vetores-ponte da região amazônica. O uso mais amplo de detecção de parasitas filariais para a incriminação de vetores-ponte é limitado por uma escassez de sequências referência de parasitas filarias obtidas de hospedeiros. Aqui nós usamos o sequenciamento tipo shotgun para obter dados de referência de um parasita adulto Dipetalonema gracile encontrado infectando um sauim-de-coleira, Saguinus bicolor no entorno de Manaus. Relatamos o genoma mitocondrial completo do parasita (que tem 13.647 pares de bases de comprimento), 894.846 pares de bases de seu genoma de Wolbachia e 6.426 pares de bases de seu locus de DNA ribossômico (desde o início de sua subunidade 18S até o final de sua subunidade 28S). Apesar de criticamente ameaçado, S. bicolor é comumente encontrado no entorno de Manaus e em fragmentos florestais urbanos. As sequências relatadas podem ser uma ferramenta de referência útil para identificar vetores ponte e potencialmente fornecer algumas informações sobre o contato entre reservatórios de patógenos de primatas e os moradores de Manaus.(AU)

Identification of Polymorphism in the MC1R Gene and Its Association with the Melanin Content in Feathers of Chinese Yellow Quails

MC1R plays a crucial role in controlling the type of melanin synthesized in the melanocytes, which greatly affects plumage color in birds. One g.16796362G/T SNP was found in the MC1R gene coding region, which caused a Met120Ile mutation in the amino acid sequence. The Met120Ile mutation was located in the third transmembrane domain of the MC1R protein and decreased protein stability. The g.16796362G/T locus achieved medium polymorphism and had significant association with feather melanin content in Chinese yellow quails. The contents of total melanin and pheomelanin with AA genotype were significant lower than those with AB or BB genotypes in skin tissues, while the expression levels of MC1R mRNA had no significant difference in feathers with different genotypes. This experiment indicated that the Met120Ile mutation could affect the function of the MC1R protein and change the biosynthesis of melanin in Chinese yellow quails.(AU)

Genetic diversity and antimicrobial susceptibility of Staphylococcus aureus isolated from bovine mastitis in Minas Gerais, Brazil / Diversidade genética e susceptibilidade a antimicrobianos em Staphylococcus aureus isoladas de mastite bovina em Minas Gerais, Brasil

This study evaluated the genetic diversity and antimicrobial susceptibility of Staphylococcus aureus isolates from dairy cows in Minas Gerais, Brazil. Thirty-seven isolates from five municipalities (8 herds) were genotyped using multi-locus sequence typing (MLST) and susceptibility to 12 antimicrobial agents was tested using the disk diffusion method. High resistance rates for penicillin [75.68% (28/37)], ampicillin [70.27% (26/37)], and tetracycline [70.27% (26/37)] were detected. Multidrug resistance was observed in seven [18.92% (7/37)] isolates, and two were suggestive of Methicillin-resistant Staphylococcus aureus (MRSA). Among the 37 isolates, 33 novel sequence types (ST) and two known STs (ST126 and ST746) were identified in MLST. The clonal complexes more frequently observed were: CC97 [78.38%; (29/37)], CC1 [8.11%; (3/37)] and CC5 [5.40%; (2/37)]. Minimum­spanning tree (MST) analysis according to data from municipalities, herds, and resistance patterns for all isolates did not show any clustering pattern. However, the MST comparing all Brazilian S. aureus isolates deposited in the PubMLST database and from this study depicted an association between the genotype and strain origin (clinical sample). Isolates from this study that belong to CC97 were close to database isolates from milk and dairy products, while those that belong to CC1 and CC5 were close to database isolates from human sources and the environment of dairy farms or industries. In conclusion, our results showed a high rate of resistance to penicillins and tetracyclines and great genetic diversity among the S. aureus isolates from bovine mastitis genotyped in the present study.

Este estudo teve como objetivo avaliar a diversidade genética e a suscetibilidade a antimicrobianos de cepas de Staphylococcus aureus isoladas de vacas leiteiras em Minas Gerais, Brasil. Trinta e sete cepas provenientes de cinco municípios (oito rebanhos) foram genotipadas usando a técnica multi-locus sequence typing (MLST) e a suscetibilidade a 12 antimicrobianos foi avaliada pelo método de difusão em disco. Foram detectadas altas taxas de resistência para penicilina [75,68% (28/37)], ampicilina [70,27% (26/37)] e tetraciclina [70,27% (26/37)] entre os isolados. A multirresistência foi observada em sete [18,92% (7/37)] isolados e dois foram classificados como sugestivos de Staphylococcus aureus resistente à meticilina (MRSA). Entre os 37 isolados, 33 novos sequence types (ST) e dois STs conhecidos (ST126 e ST746) foram identificados pelo MLST. Os complexos clonais mais frequentemente observados foram: CC97 [78,38%; (29/37)], CC1 [8,11%; (3/37)] e CC5 [5,40%; (2/37)]. Foi construída uma minimum­spanning tree (MSTs) com todos isolados estudados e esta não mostrou padrão de agrupamento quando comparada com dados epidemiológicos como municípios e rebanho, do qual foi isolado, e perfis de resistência a antimicrobianos. Uma segunda MST foi construída comparando os isolados deste estudo e todas as cepas de S. aureus depositadas no banco de dados PubMLST provenientes do Brasil, que mostrou associação entre o genótipo, STs e a origem da cepa. Foi possível observar entre os isolados do estudo que, aqueles que pertenciam ao CC97, eram geneticamente mais próximos das cepas depositadas no PubMLST isoladas de leite e de produtos lácteos, enquanto aqueles que pertenciam aos CC1 e CC5 estavam mais próximos a cepas isoladas de humanos ou do ambiente de fazendas e indústrias de laticínios. Em conclusão, nossos resultados mostraram um alto índice de resistência às penicilinas e tetraciclinas e grande diversidade genética entre as cepas de S. aureus isoladas de casos de mastite bovina.

Evaluation of Bayesian methods of genomic association via chromosomic regions using simulated data

The development of efficient methods for genome-wide association studies (GWAS) between quantitative trait loci (QTL) and genetic values is extremely important to animal and plant breeding programs. Bayesian approaches that aim to select regions of single nucleotide polymorphisms (SNPs) proved to be efficient, indicating genes with important effects. Among the selection criteria for SNPs or regions, selection criterion by percentage of variance can be explained by genomic regions (%var), selection of tag SNPs, and selection based on the window posterior probability of association (WPPA). To also detect potentially associated regions, we proposed measuring posterior probability of the interval PPint), which aims to select regions based on the markers of greatest effects. Therefore, the objective of this work was to evaluate these approaches, in terms of efficiency in selecting and identifying markers or regions located within or close to genes associated with traits. This study also aimed to compare these methodologies with single-marker analyses. To accomplish this, simulated data were used in six scenarios, with SNPs allocated in non-overlapping genomic regions. Considering traits with oligogenic inheritance, WPPA criterion followed by %var and PPint criteria were shown to be superior, presenting higher values of detection power, capturing higher percentages of genetic variance and larger areas. For traits with polygenic inheritance, PPint and WPPA criteria were considered superior. Single-marker analyses identified SNPs associated only in oligogenic inheritance scenarios and was lower than the other criteria.(AU)

Genome-wide association mapping for heading date in oats under subtropical environments

Selection for heading date has been a decisive factor to increase areas cropped with oats in Brazil. Although important to oat breeders, genomic regions controlling heading date have not been completely identified. The objective of this study was to identify genomic regions controlling oat heading date in subtropical environments. A set of 412 oat genotypes, developed from 1974 to 2015, was assessed for heading date in contrasting environments and genotyped using genotyping-by-sequencing (GBS). Phenotypic and genotypic data were used in single and multi-environment association models. Quantitative trait loci (QTL) associated to heading date were identified on oat consensus groups Mrg02, Mrg05, Mrg06, Mrg12, and Mrg21. Some of the findings confirmed the association of genomic regions with heading date, while others emerge as new candidate regions associated to the trait. The genomic regions identified on Mrg02 and Mrg12 were associated to Vernalization 3 (Vrn3), while the genomic region identified on Mrg21 is associated with Vernalization 1 (Vrn1). The Vrn1 region was detected in Londrina, an environment with reduced vernalization condition, and in the multi-environment model. The results reveal that some genotypes of the panel are responsive to vernalization, increasing the days to heading without this environmental stimulus. Our results provide important contribution for a better understanding of heading date in subtropical environments and a strong basis for marker-assisted selection in oats.

Uncertainties and risks in delimiting species of Cambeva (Siluriformes: Trichomycteridae) with single-locus methods and geographically restricted data

Cambeva contains species with complex taxonomy or poorly delimitated in terms of morphology and geopraphic distribution. We conducted an extensive review of Cambeva populations from coastal drainages of Southern to Southeastern Brazil to evaluate species geographic limits with an integrative analysis including morphological and molecular data (COI). We test if two single-locus methods, Bayesian Poisson Tree Processes (bPTP) and Generalized Mixed Yule Coalescent (GMYC), are efficient to delimit species boundaries in Cambeva by the comparison with the diagnosable morphological units. Using GMYC, we also evaluated the combination of tree and molecular clock priors to reconstruct the input phylogeny and assessed how well the implemented model fitted our empirical data. Eleven species were identified using a morphological diagnosability criterion: Cambeva balios, C. barbosae, C. botuvera, C. cubataonis, C. davisi, C. guaraquessaba, C. iheringi, C. tupinamba, and C. zonata and two treated as undescribed species. In contrast with previous knowledge, many of them have wider distribution and high intraspecific variation. Species delimitation based on single-locus demonstrated incongruences between the methods and strongly differed from the morphological delimitation. These disagreements and the violation of the GMYC model suggest that a single-locus data is insufficient to delimit Cambeva species and the failure may be attributable to events of mitochondrial introgression and incomplete lineage sorting.(AU)

Cambeva contém espécies com taxonomia complexa ou mal delimitadas em termos morfológicos e de distribuição geográfica. Realizamos uma extensa revisão de populações de Cambeva das drenagens costeiras do Sul ao Sudeste do Brasil para avaliar os limites das espécies com uma análise integrativa incluindo dados morfológicos e moleculares (COI). Testamos se dois métodos de locus único, Implementação Bayesiana dos Processos da Árvore de Poisson (bPTP) e Coalescente de Yule Misto Generalizado (GMYC), são eficientes para delimitar os limites das espécies em Cambeva pela comparação com as unidades morfológicas diagnosticáveis. Usando o GMYC, também avaliamos a combinação de árvores e relógios moleculares para reconstruir a filogenia e avaliamos o quão bem o modelo implementado se ajustava aos nossos dados empíricos. Foram identificadas 11 espécies usando o critério morfológico: Cambeva balios, C. barbosae, C. botuvera, C. cubataonis, C. davisi, C. guaraquessaba, C. iheringi, C. tupinamba e C. zonata e duas tratadas como espécies não-descritas. Em contraste com o conhecimento prévio, muitas delas têm distribuição mais ampla e alta variação intraespecífica. A delimitação das espécies baseada em locus único demonstrou incongruências entre os métodos e diferiu fortemente da delimitação morfológica. Essas discordâncias e a violação do modelo GMYC sugerem que os dados de locus único são insuficientes para delimitar as espécies de Cambeva e a falha pode ser atribuída a eventos de introgressão mitocondrial e sorteio incompleto da linhagem.(AU)

Diagnostic locus for identification of silverside hybrids (Odontesthes humensis and Odontesthes bonariensis) in a natural population / Locus diagnóstico para identificação de híbridos de peixe-rei (Odontesthes humensis and Odontesthes bonariensis) em população natural

Hybridization is a natural phenomenon that occurs more often in fish than in other vertebrates. The use of nuclear and mitochondrial molecular markers provides valuable results in the detection of these events. The aim of this study was to investigate the occurrence of interspecific hybrids in natural populations of silverside. The samples of Odontesthes humensis, Odontesthes bonariensis, and indivi-duals that were morphologically different from pure species were collected in the Mangueira lagoon, located in southern Brazil. Result: Six tetranucleotide microsatellite loci were synthesized and tested. The UFPEL_OH3 locus proved to be diagnostic for the detection of silverside hybrids, and it was possi-ble to distinguish between pure and hybrid species. The mitochondrial marker gene cytb synthesized from conserved Odontesthes sequences in the GenBank genetic database showed no differences in the genetic sequence of the samples, needing further studies to confirm the hypothesis.(AU)

A hibridação é um fenômeno natural que ocorre mais frequentemente em peixes do que em outros vertebrados. Para detectá-la, são utilizados marcadores moleculares nucleares e mitocondriais, os quais fornecem resultados valiosos. O objetivo deste estudo foi investigar a ocorrência de híbridos in-terespecíficos em populações naturais de peixe-rei. As amostras de Odontesthes humensis, Odontesthes bonariensis e de indivíduos morfologicamente diferentes das espécies puras foram coletadas na lagoa Mangueira, localizada no Sul do Brasil. Foram sintetizados e testados seis loci microssatélites tetranu-cleotídeos. O locus UFPEL_OH3 mostrou-se um diagnóstico para detectar híbridos de peixe-rei, pos-sibilitando a distinção de espécies puras de híbridas. O marcador mitocondrial gene cytb, sintetizado com base nas sequências conservadas de Odontesthes no banco de dados genéticos do GenBank, não apresentou diferenças na sequência genética das amostras, portanto, são necessários mais estudos para confirmar a hipótese de hibridação.(AU)

Genomic characterization, antimicrobial resistance profiles, enterotoxin, and biofilm production of methicillin-resistant Staphylococcus aureus isolated from clinical and animal products origins in Eastern Turkey

ABSTRACT: Staphylococcus aureus is an opportunistic and ubiquitous pathogen found in the skin, nares, and mucosal membranes of mammals. Increasing resistance to antimicrobials including methicillin has become an important public concern. One hundred and eight (108) S. aureus strains isolated from a total of 572 clinical and animal products samples, were investigated for their biofilm capability, methicillin resistance, enterotoxin genes, and genetic diversity. Although only one strain isolated from raw retail was found as a strong biofilm producer, the percentage of antimicrobial resistance pattern was relatively higher. 17.59% of S. aureus strains tested in this study were resistant to cefoxitin and identified as methicillin-resistant S. aureus (MRSA) isolates. mecA and mecC harboring S. aureus strains were detected at a rate of 2.79% and 0.93%, respectively. In addition, staphylococcal enterotoxin genes including Sea, Seb, Sec, and Sed genes were found to be 18.5%, 32.4%, 6.5% and 3.7%, respectively. The phylogenetic relationship among the isolates showed relationship between joint calf and cow milk isolates. Multi locus sequence typing (MLST) revealed three different sequence types (STs) including ST84, ST829, and ST6238. These findings highlight the development and spread of MRSA strains with zoonotic potential in animals and the food chain throughout the world.

RESUMO: Staphylococcus aureus é um patógeno dúctil e ubíquo encontrado na pele, narinas e membranas mucosas de mamíferos. O aumento da resistência aos antimicrobianos, incluindo a meticilina, tornou-se uma importante preocupação pública. Cento e oito (108) cepas de S. aureus isoladas de um total de 572 amostras clínicas e de produtos animais foram investigadas por sua capacidade de biofilme, resistência à meticilina, genes de enterotoxinas e diversidade genética. Embora apenas uma cepa isolada do cru tenha sido encontrada como forte produtora de biofilme, a porcentagem do padrão de resistência antimicrobiana foi relativamente maior. Parte das cepas (17,59%) de S. aureus testadas neste estudo eram resistentes à cefoxitina e identificadas como isolados de MRSA. mecA e mecC abrigando cepas de S. aureus foram detectados a uma taxa de 2,79% e 0,93%, respectivamente. Além disso, verificou-se que os genes da enterotoxina estafilocócica, incluindo os genes Sea, Seb, Sec e Sed, eram 18,5%, 32,4%, 6,5% e 3,7%, respectivamente. A relação filogenética entre os isolados mostrou relação entre os isolados de bezerro e leite de vaca. A tipagem de sequência multiloco (MLST) revelou três tipos de sequência diferentes (STs), incluindo ST84, ST829 e ST6238. Essas descobertas destacam o desenvolvimento e a disseminação de cepas de MRSA com potencial zoonótico em animais e na cadeia alimentar em todo o mundo.

Evaluation of a new additive-dominance genomic model and implications for quantitative genetics and genomic selection

The Fisher's infinitesimal model is traditionally used in quantitative genetics and genomic selection, and it attributes most genetic variance to additive variance. Recently, the dominance maximization model was proposed and it prioritizes the dominance variance based on alternative parameterizations. In this model, the additive effects at the locus level are introduced into the model after the dominance variance is maximized. In this study, the new parameterizations of additive and dominance effects on quantitative genetics and genomic selection were evaluated and compared with the parameterizations traditionally applied using the genomic best linear unbiased prediction method. As the parametric relative magnitude of the additive and dominance effects vary with allelic frequencies of populations, we considered different minor allele frequencies to compare the relative magnitudes. We also proposed and evaluated two indices that combine the additive and dominance variances estimated by both models. The dominance maximization model, along with the two indices, offers alternatives to improve the estimates of additive and dominance variances and their respective proportions and can be successfully used in genetic evaluation.

Genome-Wide Association Study on Two Immune-Related Traits in Jinghai Yellow Chicken

This study was designed to discover molecular marker associated with the interferon INF-γ and avian influenza (AI) antibody titer traits in Jinghai Yellow chicken (Gallus gallus). Serum samples were taken from 400 female chickens and the INF-γ concentrations and AI antibody titer levels were measured. A genome-wide association study was carried out using specific-locus amplified fragment (SLAF) sequencing. Bioinformatics analysis was applied to detect single-nucleotide polymorphisms (SNPs) associated with the two traits. After sequencing and quality control, 103,680 SLAFs and 90,961 SNPs were obtained. The 400 samples were divided into 10 subgroups to reduce the effects of group stratification. The Bonferroni adjusted P-value of genome-wide significance was set at 1.87E−06 according to the number of independent SNP markers and linkage disequilibrium blocks. A SNP that was significantly associated with INF-γ concentration was detected in the myomesin 1 (MYOM1) gene on chromosome 2, and another SNPthat was significantly associated with the AI antibody titer level was detected in an RNA methyltransferase gene (Nsun7), which was found to have an important biological function. We propose that MYOM1 and Nsun7 are valuable candidate genes that influence the disease resistance characters of chicken. However, in-depth investigations are needed to determine the essential roles of these genes in poultry disease resistance and their possible application in breeding disease resistant poultry.(AU)

Genome-Wide Association Study of Abdominal Fat in Wenshang Barred Chicken Based on the Slaf-Seq Technology

Chicken abdominal fat (AF) is an economically important trait, and many studies have been conducted on genetic selection for AF. However, previous studies have focused on detecting functional chromosome mutations or regions using gene chips. The present study used the specific-locus amplified fragment sequencing (SLAF-seq) technology to perform a genome-wide association study (GWAS) on purebred Wengshang Barred chicken. A total of 1,286,715 single-nucleotide polymorphisms (SNPs) were detected, and 175,211 SNPs were selected as candidate SNPs for genome-wide association analysis using TASSEL general linear models. Two SNPs markers reached genome-wide significance. Of these, rs7943847, rs127627362 were significantly associated with AF at 120 days. These SNPs are close to eight genes (SLC16A6, ARSG, WIPI1, PRKAR1A, FAM20A, ABCA8, ABCA9, CPQ,). These results would enrich the studies on AF and promote the use of Chinese chicken, especially the Wenshang Barred chicken.(AU)

Genomic characterization, antimicrobial resistance profiles, enterotoxin, and biofilm production of methicillin-resistant Staphylococcus aureus isolated from clinical and animal products origins in Eastern Turkey / Caracterização genômica perfis de resistência antimicrobiana, produção de enterotoxinas e biofilme Staphylococcus aureus resistente à meticilina isolado de origem clínica e de produtos de origem animal no leste da Turquia

Staphylococcus aureus is an opportunistic and ubiquitous pathogen found in the skin, nares, and mucosal membranes of mammals. Increasing resistance to antimicrobials including methicillin has become an important public concern. One hundred and eight (108) S. aureus strains isolated from a total of 572 clinical and animal products samples, were investigated for their biofilm capability, methicillin resistance, enterotoxin genes, and genetic diversity. Although only one strain isolated from raw retail was found as a strong biofilm producer, the percentage of antimicrobial resistance pattern was relatively higher. 17.59% of S. aureus strains tested in this study were resistant to cefoxitin and identified as methicillin-resistant S. aureus (MRSA) isolates. mecA and mecC harboring S. aureus strains were detected at a rate of 2.79% and 0.93%, respectively. In addition, staphylococcal enterotoxin genes including Sea, Seb, Sec, and Sed genes were found to be 18.5%, 32.4%, 6.5% and 3.7%, respectively. The phylogenetic relationship among the isolates showed relationship between joint calf and cow milk isolates. Multi locus sequence typing (MLST) revealed three different sequence types (STs) including ST84, ST829, and ST6238. These findings highlight the development and spread of MRSA strains with zoonotic potential in animals and the food chain throughout the world.

Staphylococcus aureus é um patógeno dúctil e ubíquo encontrado na pele, narinas e membranas mucosas de mamíferos. O aumento da resistência aos antimicrobianos, incluindo a meticilina, tornou-se uma importante preocupação pública. Cento e oito (108) cepas de S. aureus isoladas de um total de 572 amostras clínicas e de produtos animais foram investigadas por sua capacidade de biofilme, resistência à meticilina, genes de enterotoxinas e diversidade genética. Embora apenas uma cepa isolada do cru tenha sido encontrada como forte produtora de biofilme, a porcentagem do padrão de resistência antimicrobiana foi relativamente maior. Parte das cepas (17,59%) de S. aureus testadas neste estudo eram resistentes à cefoxitina e identificadas como isolados de MRSA. mecA e mecC abrigando cepas de S. aureus foram detectados a uma taxa de 2,79% e 0,93%, respectivamente. Além disso, verificou-se que os genes da enterotoxina estafilocócica, incluindo os genes Sea, Seb, Sec e Sed, eram 18,5%, 32,4%, 6,5% e 3,7%, respectivamente. A relação filogenética entre os isolados mostrou relação entre os isolados de bezerro e leite de vaca. A tipagem de sequência multiloco (MLST) revelou três tipos de sequência diferentes (STs), incluindo ST84, ST829 e ST6238. Essas descobertas destacam o desenvolvimento e a disseminação de cepas de MRSA com potencial zoonótico em animais e na cadeia alimentar em todo o mundo.

Investigation of Genetic Diversity of Pasteurella multocida Isolated from Diseased Poultry in Korea

ABSTRACT Pasteurella multocida causes fowl cholera which is an economically important disease in poultry industries around the world. In this study, we analyzed the capsular genotype, lipopolysaccharide (LPS) genotype, virulence-associated genes (VAGs) patterns, antimicrobial resistance and genetic diversity in a total of 9 P. multocida isolates from poultry with fowl cholera between 2014 and 2019 in Korea. When combining the capsular types with the LPS genotypes, two isolates of the 9 isolates were A:L3, and the others were non-typeable (NT): L3. Of the 23 VAGs, all the isolates harbored ptfA, fimA, hsf-1, hsf-2, pfhA, exbB, exbD, tonB, hgbA, hgbB, fur, sodA, sodC, pmHAS, ompA, ompH, oma87, plpB, psl, and nanH, whereas toxA gene was not detected in any of the 9 isolates. In addition, among the 11 antimicrobials, most of the isolates except for one isolate resistant to florfenicol, exhibited susceptibility to all the antimicrobials. Multi-locus sequence typing (MLST) analysis revealed 5 different sequence types (ST): ST8, ST351, ST352, ST353, and ST368. The ST351, ST352, ST353, and ST368 were identified for the first time in this study, and ST352 and ST353 isolates were largely prevalent nationwide. These STs isolates should be monitored continuously because in some cases, ST352 and ST353 isolates demonstrated high mortality rates. Although only limited numbers of isolates have been analyzed, our findings provide overall characteristics and epidemiological information of the P. multocida strains recently prevalent in Korea.

Sistema CRISPR/Cas9 e perspectivas de aplicações na cadeia produtiva animal / CRISPR/Cas9 system and perspectives for applications in the animal production chain

O melhoramento genético tem papel fundamental no aumento da eficiência da produção pecuária. Entretanto, programas tradicionais de melhoramento podem levar vários anos para atingir um determinado objetivo. Novas abordagens genômicas permitem acelerar esse processo e recentemente a edição gênica surgiu como nova alternativa, além de ter potencial para induzir outras modificações genéticas de interesse comercial e biomédico. A possibilidade de editar o genoma de diferentes espécies, de maneira simples e eficaz, tornou-se possível com a tecnologia do sistema CRISPR/Cas9. Esse sistema biológico foi identificado em bactérias e funciona como um mecanismo natural de defesa desses organismos. Baseando-se nos princípios biológicos, cientistas adaptaram esse sistema para atuar em células de mamíferos, incluindo humanas. Trabalhos científicos demonstraram a aplicabilidade da técnica, que permite novas abordagens na condução de estudos da função gênica, além de permitir diferentes experimentos de alteração específica da sequência do DNA. Do ponto de vista da produção animal, a utilização do sistema CRISPR traz novos conceitos e possibilidades para o melhoramento genético. O objetivo desta revisão é discutir os princípios da metodologia, associando resultados previamente conhecidos à possíveis aplicações com enfoque na cadeia produtiva animal.(AU)

Genetic improvement has a prominent role in increasing the efficiency of livestock production systems. However, traditional breeding programs may take several years to achieve a specific goal. New genomic approaches could accelerate this process and recently gene editing appeared as an alternative and still holds the potential to induce genetic alterations of commercial and biomedical interest. The possibility of editing the genome of different species, in a simple and effective way, became possible with the technology of the CRISPR / Cas9 system. This biological system was identified in bacteria and works as a natural defense mechanism for these organisms. Based on biological principles, scientists adapted this system to act on mammalian cells, including humans. Scientific studies demonstrated the applicability of the technique, which allows new approaches in conducting studies of gene function, in addition to different experiments of targeted modification of the DNA sequence. From the point of view of animal production, the use of the CRISPR brings new concepts and possibilities for genetic improvement. The purpose of this review is to discuss the principles of the methodology, associating previously known results to possible applications focusing on the animal production chain.(AU)

Sistema CRISPR/Cas9 e perspectivas de aplicações na cadeia produtiva animal / CRISPR/Cas9 system and perspectives for applications in the animal production chain

O melhoramento genético tem papel fundamental no aumento da eficiência da produção pecuária. Entretanto, programas tradicionais de melhoramento podem levar vários anos para atingir um determinado objetivo. Novas abordagens genômicas permitem acelerar esse processo e recentemente a edição gênica surgiu como nova alternativa, além de ter potencial para induzir outras modificações genéticas de interesse comercial e biomédico. A possibilidade de editar o genoma de diferentes espécies, de maneira simples e eficaz, tornou-se possível com a tecnologia do sistema CRISPR/Cas9. Esse sistema biológico foi identificado em bactérias e funciona como um mecanismo natural de defesa desses organismos. Baseando-se nos princípios biológicos, cientistas adaptaram esse sistema para atuar em células de mamíferos, incluindo humanas. Trabalhos científicos demonstraram a aplicabilidade da técnica, que permite novas abordagens na condução de estudos da função gênica, além de permitir diferentes experimentos de alteração específica da sequência do DNA. Do ponto de vista da produção animal, a utilização do sistema CRISPR traz novos conceitos e possibilidades para o melhoramento genético. O objetivo desta revisão é discutir os princípios da metodologia, associando resultados previamente conhecidos à possíveis aplicações com enfoque na cadeia produtiva animal.

Genetic improvement has a prominent role in increasing the efficiency of livestock production systems. However, traditional breeding programs may take several years to achieve a specific goal. New genomic approaches could accelerate this process and recently gene editing appeared as an alternative and still holds the potential to induce genetic alterations of commercial and biomedical interest. The possibility of editing the genome of different species, in a simple and effective way, became possible with the technology of the CRISPR / Cas9 system. This biological system was identified in bacteria and works as a natural defense mechanism for these organisms. Based on biological principles, scientists adapted this system to act on mammalian cells, including humans. Scientific studies demonstrated the applicability of the technique, which allows new approaches in conducting studies of gene function, in addition to different experiments of targeted modification of the DNA sequence. From the point of view of animal production, the use of the CRISPR brings new concepts and possibilities for genetic improvement. The purpose of this review is to discuss the principles of the methodology, associating previously known results to possible applications focusing on the animal production chain.

Genetic variability in Tambaqui generations of the breeding program in the Central-West Region of Brazil / Variabilidade genética em gerações de Tambaqui do programa de melhoramento da Região Centro-Oeste do Brasil

The implementation of fish breeding programs in Brazil has brought significant results in the productivity of tilapia. However, the insertion of native species with great potential (such as Tambaqui Colossoma macropomum) in these programs is still recent, and thus requires genetic information for monitoring and enabling their consolidation into the programs. The objective of the present study was to evaluate the genetic diversity of the parental generation (G0) and two consecutive generations (G1 and G2) in the C. macropomum genetic improvement program, located in the municipality of Sorriso, Mato Grosso, Brazil. Ninety caudal fin samples were collected (30 samples per generation) for DNA extraction. The genetic study implemented seven microsatellite markers (Cm1A8, Cm1A11, Cm1D1, Cm1E3, Cm1F4, Cm1F5, and Cm1H8). A total of 17 alleles were amplified, with variations in the mean number between four to two alleles per locus. The size per locus ranged from 170 to 360 bp. The average inbreeding coefficient was 0.126 (G0), -0.040 (G1), and 0.131 (G2). No null or exclusive alleles were found. The observed heterozygosity values for G1 and G2 demonstrated the preservation of genetic variability (0.453 and 0.409, respectively). In conclusion, the genetic diversity of the parental generation (G0) and the two progenies generations (G1 and G2) were adequate, which demonstrates that the genetic improvement program was conducted correctly; however, it is important to continue to evaluations the genetic diversity of the future progeny.

A implantação de programas de melhoramento genético de peixes do Brasil tem trazido resultados significativos na produtividade de peixes como na Tilápia. No entanto, a inserção desses programas em espécies nativas de grande potencial como o Tambaqui (Colossoma macropomum) ainda é recente, sendo necessárias informações genéticas que permitam seu monitoramento e viabilizem sua consolidação. O objetivo do presente estudo foi avaliar a diversidade genética da geração parental (G0) e duas gerações consecutivas (G1 e G2) do programa de melhoramento genético de Colossoma macropomum, localizado no município de Sorriso Mato Grosso, Brasil. Noventa amostras de nadadeira caudal foram coletadas (30 amostras por geração) para a extração do DNA. O estudo genético foi conduzido implementando-se um total de sete loci microssatélites (Cm1A8, Cm1A11, Cm1D1, Cm1E3, Cm1F4, Cm1F5 e Cm1H8). Um total de 17 alelos foram amplificados, com variações no número médio entre quatro a dois alelos por locus. O tamanho por loci variou entre 170 a 360 pares de bases. O coeficiente de endogamia médio foi 0,126 (G0), -0,040 (G1) e 0,131 (G2). Não foram encontrados alelos nulos nem alelos exclusivos. Os valores de heterozigosidade observada para G1 e G2 demonstraram preservação da variabilidade genética (0,453 e 0,409, respectivamente). Em conclusão a diversidade genética tanto da geração parental (G0) como das duas gerações (G1 e G2) foi adequada, o que demostra que o programa de melhoramento genético está sendo conduzido de maneira correta sendo importante dar continuidade com avaliações de diversidade genética nas progênies futuras.