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Registro Completo |
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Biblioteca(s): |
Embrapa Gado de Corte. |
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Data corrente: |
27/11/2023 |
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Data da última atualização: |
28/11/2023 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
SUNIGA, P. A. P.; MANTOVANI, C.; SANTOS, M. G. dos; EGITO, A. A. do; VERBISCK, N. V.; SANTOS, L. R. dos; DÁVILA, A. M. R.; ZIMPEL, C. K.; ZERPA, M. C. S.; CHIEBAO, D. P.; GUIMARÃES, A. M. DE S.; NASSAR, A. F. DE C.; ARAUJO, F. R. |
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Afiliação: |
PAULA ADAS PEREIRA SUNIGA, UNIVERSIDADE FEDERAL DE MATO GROSSO DO SUL; CYNTHIA MANTOVANI, CNPGC; MARIA GORETTI DOS SANTOS, CNPGC; ANDREA ALVES DO EGITO, CNPGC; NEWTON VALERIO VERBISCK, CNPGC; LENITA RAMIRES DOS SANTOS, CNPGC; ALBERTO MARTÍN RIVERA DÁVILA, INSTITUTO OSWALDO CRUZ; CRISTINA KRAEMER ZIMPEL, MICHIGAN STATE UNIVERSITY; MARIA CAROLINA SISCO ZERPA, UNIVERSIDASDE DE SÃO PAULO; DANIELA PONTES CHIEBAO, ANIMAL HEALTH RESEARCH CENTER; ANA MÁRCIA DE SÁ GUIMARÃES, UNIVERSIDADE DE SÃO PAULO; ALESSANDRA FIGUEIREDO DE CASTRO NASSAR, ANIMAL HEALTH RESEARCH CENTER; FLABIO RIBEIRO DE ARAUJO, CNPGC. |
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Título: |
Glanders Diagnosis in an Asymptomatic Mare from Brazil: Insights from Serology, Microbiological Culture, Mass Spectrometry, and Genome Sequencing. |
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Ano de publicação: |
2023 |
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Fonte/Imprenta: |
Pathogens, v. 12, e1250, 2023. |
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DOI: |
https://doi.org/10.3390/pathogens12101250 |
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Idioma: |
Inglês |
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Conteúdo: |
ABSTRACT - This manuscript elucidates the occurrence of glanders in an asymptomatic mare from Brazil presenting positive Burkholderia mallei antibody titers. The diagnosis was established through a multi-pronged approach encompassing microbiological culture, mass spectrometry, and genome sequencing. The outbreak occurred in 2019 in Tatuí, São Paulo, Brazil, and the infected mare, despite displaying no clinical symptoms, had multiple miliary lesions in the liver, as well as intense catarrhal discharge in the trachea. Samples were collected from various organs and subjected to bacterial isolation, molecular detection, and identification. The strain was identified as B. mallei using PCR and confirmed by MALDI-TOF mass spectrometry. Whole-genome sequencing revealed a genome size of 5.51 Mb with a GC content of 65.8%, 5871 genes (including 4 rRNA and 53 tRNA genes), and 5583 coding DNA sequences (CDSs). Additionally, 227 predicted pseudogenes were detected. In silico analysis of different genomic loci that allow for differentiation with Burkholderia pseudomallei confirmed the identity of the isolate as B. mallei, in addition to the characteristic genome size. The BAC 86/19 strain was identified as lineage 3, sublineage 2, which includes other strains from Brazil, India, and Iran. The genome sequencing of this strain provides valuable information that can be used to better understand the pathogen and its epidemiology, as well as to develop diagnostic tools for glanders. |
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Thesagro: |
Doença Animal; Patogenicidade. |
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Thesaurus Nal: |
Animal diseases; Burkholderia mallei; Genome; Glanders; Mass spectrometry; Pathogenicity. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/doc/1158739/1/Glanders-diagnosis-Asymptomatic-Mare-2023.pdf
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Marc: |
LEADER 02616naa a2200373 a 4500
001 2158739
005 2023-11-28
008 2023 bl uuuu u00u1 u #d
024 7 $ahttps://doi.org/10.3390/pathogens12101250$2DOI
100 1 $aSUNIGA, P. A. P.
245 $aGlanders Diagnosis in an Asymptomatic Mare from Brazil$bInsights from Serology, Microbiological Culture, Mass Spectrometry, and Genome Sequencing.$h[electronic resource]
260 $c2023
520 $aABSTRACT - This manuscript elucidates the occurrence of glanders in an asymptomatic mare from Brazil presenting positive Burkholderia mallei antibody titers. The diagnosis was established through a multi-pronged approach encompassing microbiological culture, mass spectrometry, and genome sequencing. The outbreak occurred in 2019 in Tatuí, São Paulo, Brazil, and the infected mare, despite displaying no clinical symptoms, had multiple miliary lesions in the liver, as well as intense catarrhal discharge in the trachea. Samples were collected from various organs and subjected to bacterial isolation, molecular detection, and identification. The strain was identified as B. mallei using PCR and confirmed by MALDI-TOF mass spectrometry. Whole-genome sequencing revealed a genome size of 5.51 Mb with a GC content of 65.8%, 5871 genes (including 4 rRNA and 53 tRNA genes), and 5583 coding DNA sequences (CDSs). Additionally, 227 predicted pseudogenes were detected. In silico analysis of different genomic loci that allow for differentiation with Burkholderia pseudomallei confirmed the identity of the isolate as B. mallei, in addition to the characteristic genome size. The BAC 86/19 strain was identified as lineage 3, sublineage 2, which includes other strains from Brazil, India, and Iran. The genome sequencing of this strain provides valuable information that can be used to better understand the pathogen and its epidemiology, as well as to develop diagnostic tools for glanders.
650 $aAnimal diseases
650 $aBurkholderia mallei
650 $aGenome
650 $aGlanders
650 $aMass spectrometry
650 $aPathogenicity
650 $aDoença Animal
650 $aPatogenicidade
700 1 $aMANTOVANI, C.
700 1 $aSANTOS, M. G. dos
700 1 $aEGITO, A. A. do
700 1 $aVERBISCK, N. V.
700 1 $aSANTOS, L. R. dos
700 1 $aDÁVILA, A. M. R.
700 1 $aZIMPEL, C. K.
700 1 $aZERPA, M. C. S.
700 1 $aCHIEBAO, D. P.
700 1 $aGUIMARÃES, A. M. DE S.
700 1 $aNASSAR, A. F. DE C.
700 1 $aARAUJO, F. R.
773 $tPathogens$gv. 12, e1250, 2023.
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Registro original: |
Embrapa Gado de Corte (CNPGC) |
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Registro Completo
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
02/12/2010 |
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Data da última atualização: |
27/01/2020 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
HERAI, R. H.; COSTA, G. G. D. L.; R. JÚNIOR, O.; VIDAL, R. O.; NASCIMENTO, L. C.; PARIZZI, L. P.; PEREIRA, G. G. A.; CARAZZOLLE, M. F. |
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Afiliação: |
LGE/IB/UNICAMP, LBA/CNPTIA; LGE/UNICAMP; LGE/IB/UNICAMP; LGE/IB/UNICAMP, LNBio; LGE/IB/UNICAMP; LGE/IB/UNICAMP; LGE/IB/UNICAMP, LNBio; LGE/IB/UNICAMP, CENAPAD. |
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Título: |
TORNADO: an automated pipeline for de novo hybrid genome assembly based on free software packages for sanger and next generation sequencing technologies (NGS). |
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Ano de publicação: |
2010 |
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Fonte/Imprenta: |
In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 6., 2010, Ouro Preto. Abstracts... [S.l.: s.n.], 2010. |
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Páginas: |
p. 119. |
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Idioma: |
Inglês |
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Notas: |
X-meeting 2010. |
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Conteúdo: |
Next generation sequence technologies (NGS) made possible to sequence entirely genomes in a fast way and low cost, from unicellular to complex organisms, like plants and mammals. These sequences can be assembled (i ) using a reference genome or by some de novo bioinformatics method, such as Velvet, SOAPDenovo, Edena, ABYSS, GS Assembler 454, Mira and ZORRO. They are mainly based on de Bruijin graphs or, in a few softwares, reads overlapping to form contigs and scaffolds. The involved filtering and assembly step are very sensitive for each type of tool, and can be a key factor to generate the best assembly results. This way, when a set of sequences from distinct technologies exists, from Sanger to NGS, it is necessary the use of distinct assembly strategies for each type of data. Actually, at our knowledge, there is no automated hybrid strategies based on in-use of distinct assembly softwares that can be applied to assembly hybrid data generated by NGS or Sanger platforms. This works presents TORNADO, and automated pipeline for hybrid genome assembly based on free software packages. TORNADO did not proposed new methods for genome assembly. It just uses the best described software strategies for each type of genomic data to perform the hybrid assembly. It was organized in two main modules that are configured by XML file. In the first module, input data are filtered for trimming and experimental artifacts clipping. In the second module, based on sequence type, TORNADO automatically performs the assembly task using Mira for 454 and Sanger reads, Velvet for Illumina/Solexa or Solid/Life Tech reads. Finally, each assembled data are merged in a single assembly using ZORRO. If there are paired-end (mate pairs data) reads, an additional step involves CloseGaps software, which closes the gaps between assembled scaffolds. TORNADO was already applied to assembly hybrid genomic reads from Moniliophthora perniciosa fungi, Witche's broom causal in plant cacao. Results showed that our strategy can works like an useful method to automatically assembly hybrid genome data. TORNADO's was implemented using Java and PERL programming language technologies. MenosNext generation sequence technologies (NGS) made possible to sequence entirely genomes in a fast way and low cost, from unicellular to complex organisms, like plants and mammals. These sequences can be assembled (i ) using a reference genome or by some de novo bioinformatics method, such as Velvet, SOAPDenovo, Edena, ABYSS, GS Assembler 454, Mira and ZORRO. They are mainly based on de Bruijin graphs or, in a few softwares, reads overlapping to form contigs and scaffolds. The involved filtering and assembly step are very sensitive for each type of tool, and can be a key factor to generate the best assembly results. This way, when a set of sequences from distinct technologies exists, from Sanger to NGS, it is necessary the use of distinct assembly strategies for each type of data. Actually, at our knowledge, there is no automated hybrid strategies based on in-use of distinct assembly softwares that can be applied to assembly hybrid data generated by NGS or Sanger platforms. This works presents TORNADO, and automated pipeline for hybrid genome assembly based on free software packages. TORNADO did not proposed new methods for genome assembly. It just uses the best described software strategies for each type of genomic data to perform the hybrid assembly. It was organized in two main modules that are configured by XML file. In the first module, input data are filtered for trimming and experimental artifacts clipping. In the second module, based on sequence type, TORNADO automatic... Mostrar Tudo |
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Palavras-Chave: |
Bases de dados; Bioinformática. |
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Thesagro: |
Genoma. |
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Thesaurus NAL: |
Bioinformatics; Computer software; Databases; Genome; Moniliophthora perniciosa. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/23820/1/p119.pdf
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Marc: |
LEADER 03238nam a2200313 a 4500
001 1868519
005 2020-01-27
008 2010 bl uuuu u00u1 u #d
100 1 $aHERAI, R. H.
245 $aTORNADO$ban automated pipeline for de novo hybrid genome assembly based on free software packages for sanger and next generation sequencing technologies (NGS).$h[electronic resource]
260 $aIn: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 6., 2010, Ouro Preto. Abstracts... [S.l.: s.n.]$c2010
300 $ap. 119.
500 $aX-meeting 2010.
520 $aNext generation sequence technologies (NGS) made possible to sequence entirely genomes in a fast way and low cost, from unicellular to complex organisms, like plants and mammals. These sequences can be assembled (i ) using a reference genome or by some de novo bioinformatics method, such as Velvet, SOAPDenovo, Edena, ABYSS, GS Assembler 454, Mira and ZORRO. They are mainly based on de Bruijin graphs or, in a few softwares, reads overlapping to form contigs and scaffolds. The involved filtering and assembly step are very sensitive for each type of tool, and can be a key factor to generate the best assembly results. This way, when a set of sequences from distinct technologies exists, from Sanger to NGS, it is necessary the use of distinct assembly strategies for each type of data. Actually, at our knowledge, there is no automated hybrid strategies based on in-use of distinct assembly softwares that can be applied to assembly hybrid data generated by NGS or Sanger platforms. This works presents TORNADO, and automated pipeline for hybrid genome assembly based on free software packages. TORNADO did not proposed new methods for genome assembly. It just uses the best described software strategies for each type of genomic data to perform the hybrid assembly. It was organized in two main modules that are configured by XML file. In the first module, input data are filtered for trimming and experimental artifacts clipping. In the second module, based on sequence type, TORNADO automatically performs the assembly task using Mira for 454 and Sanger reads, Velvet for Illumina/Solexa or Solid/Life Tech reads. Finally, each assembled data are merged in a single assembly using ZORRO. If there are paired-end (mate pairs data) reads, an additional step involves CloseGaps software, which closes the gaps between assembled scaffolds. TORNADO was already applied to assembly hybrid genomic reads from Moniliophthora perniciosa fungi, Witche's broom causal in plant cacao. Results showed that our strategy can works like an useful method to automatically assembly hybrid genome data. TORNADO's was implemented using Java and PERL programming language technologies.
650 $aBioinformatics
650 $aComputer software
650 $aDatabases
650 $aGenome
650 $aMoniliophthora perniciosa
650 $aGenoma
653 $aBases de dados
653 $aBioinformática
700 1 $aCOSTA, G. G. D. L.
700 1 $aR. JÚNIOR, O.
700 1 $aVIDAL, R. O.
700 1 $aNASCIMENTO, L. C.
700 1 $aPARIZZI, L. P.
700 1 $aPEREIRA, G. G. A.
700 1 $aCARAZZOLLE, M. F.
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Embrapa Agricultura Digital (CNPTIA) |
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