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Registro completo
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Biblioteca (s) : |
INIA Treinta y Tres. |
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Fecha : |
04/11/2019 |
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Actualizado : |
03/12/2019 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
DOSTER, E.; ROVIRA, P.J.; NOYES, N.R.; BURGESS, B.A.; YANG, X.; WEINROTH, M.D.; LINKE, L.; MAGNUSON, R.; BOUCHER, C.; BELK, K.E.; MORLEY, P.S. |
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Afiliación : |
ENRIQUE DOSTER, Department in Microbiology, Immunology and Pathology, Colorado State University, USA.; PABLO JUAN ROVIRA SANZ, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; NOELLE R. NOYES, Department of Veterinary Population Medicine, University of Minnesota, USA.; BRANDY A. BURGESS, Department of Population Health, University of Georgia, USA.; XIANG YANG, Department of Animal Science, University of California, Davis, Davis, CA, USA.; MARGARET D. WEINROTH, Department of Animal Sciences, Colorado State University, USA.; LINDSEY LINKE, Department of Clinical Sciences, Colorado State University, USA.; ROBERTA MAGNUSON, Department of Clinical Sciences, Colorado State University, USA.; CHRISTINA BOUCHER, Department of Computer and Information Science and Engineering, University of Florida, Florida, USA.; KEITH E. BELK, Department of Animal Sciences, Colorado State University, Colorado, USA.; PAUL S. MORLEY, Veterinary Education, Research, and Outreach Center, West Texas A&M University, Texas, USA. |
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Título : |
A cautionary report for pathogen identification using shotgun metagenomics; a comparison to aerobic culture and polymerase chain reaction for Salmonella enterica identification. |
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Fecha de publicación : |
2019 |
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Fuente / Imprenta : |
Frontier in Microbiology, 2019, 10:2499. doi: 10.3389/fmicb.2019.02499 |
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Páginas : |
7 p. |
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DOI : |
10.3389/fmicb.2019.02499 |
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Idioma : |
Inglés |
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Notas : |
Article history: received: 8 July 2019 // Accepted 16 October 2019 // Published 01 November 2019.
Open Access Journal. www.frontiersin.org |
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Contenido : |
This study was conducted to compare aerobic culture, polymerase chain reaction (PCR), lateral flow immunoassay (LFI), and shotgun metagenomics for identification
of Salmonella enterica in feces collected from feedlot cattle. Samples were analyzed in parallel using all four tests. Results from aerobic culture and PCR were 100%
concordant and indicated low S. enterica prevalence (3/60 samples positive). Although low S. enterica prevalence restricted formal statistical comparisons, LFI and deep metagenomic sequencing results were discordant with these results. Specifically, metagenomic analysis using k-mer-based classification against the RefSeq database indicated that 11/60 of samples contained sequence reads that matched to the S. enterica genome and uniquely identified this species of bacteria within the sample. However, further examination revealed that plasmid sequences were often included with bacterial genomic sequence data submitted to NCBI, which can lead to incorrect taxonomic classification. To circumvent this classification problem, we separated all plasmid sequences included in bacterial RefSeq genomes and reassigned them to a unique taxon so that they would not be uniquely associated with specific bacterial species such as S. enterica. Using this revised database and taxonomic structure, we found that only 6/60 samples contained sequences specific for S. enterica, suggesting increased relative specificity. Reads identified as S. enterica in these six samples were further evaluated using BLAST and NCBI?s nr/nt database, which identified that only 2/60 samples contained reads exclusive to S. enterica chromosomal genomes. These two samples were culture- and PCR-negative, suggesting that even deep metagenomic sequencing suffers from lower sensitivity and specificity in comparison to more traditional pathogen detection methods. Additionally, no sample reads were taxonomically classified as S. enterica with two other metagenomic tools, Metagenomic Intra-species Diversity Analysis System (MIDAS) and Metagenomic Phylogenetic Analysis 2 (MetaPhlAn2). This study re-affirmed that the traditional techniques of aerobic culture and PCR provide similar results for S. enterica identification in cattle feces. On the other hand, metagenomic results are highly influenced by the classification method and reference database employed. These results highlight the nuances of computational detection of species-level sequences within short-read metagenomic sequence data, and emphasize the need for cautious interpretation of such results. MenosThis study was conducted to compare aerobic culture, polymerase chain reaction (PCR), lateral flow immunoassay (LFI), and shotgun metagenomics for identification
of Salmonella enterica in feces collected from feedlot cattle. Samples were analyzed in parallel using all four tests. Results from aerobic culture and PCR were 100%
concordant and indicated low S. enterica prevalence (3/60 samples positive). Although low S. enterica prevalence restricted formal statistical comparisons, LFI and deep metagenomic sequencing results were discordant with these results. Specifically, metagenomic analysis using k-mer-based classification against the RefSeq database indicated that 11/60 of samples contained sequence reads that matched to the S. enterica genome and uniquely identified this species of bacteria within the sample. However, further examination revealed that plasmid sequences were often included with bacterial genomic sequence data submitted to NCBI, which can lead to incorrect taxonomic classification. To circumvent this classification problem, we separated all plasmid sequences included in bacterial RefSeq genomes and reassigned them to a unique taxon so that they would not be uniquely associated with specific bacterial species such as S. enterica. Using this revised database and taxonomic structure, we found that only 6/60 samples contained sequences specific for S. enterica, suggesting increased relative specificity. Reads identified as S. enterica in these six samples were ... Presentar Todo |
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Palabras claves : |
CULTURE; PATHOGEN IDENTIFICATION; PCR; SALMONELLA ENTERICA; SHOTGUN METAGENOMICS. |
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Thesagro : |
CATTLE; FEEDLOT; VACAS. |
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Asunto categoría : |
L73 Enfermedades de los animales |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/13700/1/Rovira-arb-2019-Frontiers-Microbiology.pdf
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Marc : |
LEADER 03789naa a2200373 a 4500
001 1060378
005 2019-12-03
008 2019 bl uuuu u00u1 u #d
024 7 $a10.3389/fmicb.2019.02499$2DOI
100 1 $aDOSTER, E.
245 $aA cautionary report for pathogen identification using shotgun metagenomics; a comparison to aerobic culture and polymerase chain reaction for Salmonella enterica identification.$h[electronic resource]
260 $c2019
300 $a7 p.
500 $aArticle history: received: 8 July 2019 // Accepted 16 October 2019 // Published 01 November 2019. Open Access Journal. www.frontiersin.org
520 $aThis study was conducted to compare aerobic culture, polymerase chain reaction (PCR), lateral flow immunoassay (LFI), and shotgun metagenomics for identification of Salmonella enterica in feces collected from feedlot cattle. Samples were analyzed in parallel using all four tests. Results from aerobic culture and PCR were 100% concordant and indicated low S. enterica prevalence (3/60 samples positive). Although low S. enterica prevalence restricted formal statistical comparisons, LFI and deep metagenomic sequencing results were discordant with these results. Specifically, metagenomic analysis using k-mer-based classification against the RefSeq database indicated that 11/60 of samples contained sequence reads that matched to the S. enterica genome and uniquely identified this species of bacteria within the sample. However, further examination revealed that plasmid sequences were often included with bacterial genomic sequence data submitted to NCBI, which can lead to incorrect taxonomic classification. To circumvent this classification problem, we separated all plasmid sequences included in bacterial RefSeq genomes and reassigned them to a unique taxon so that they would not be uniquely associated with specific bacterial species such as S. enterica. Using this revised database and taxonomic structure, we found that only 6/60 samples contained sequences specific for S. enterica, suggesting increased relative specificity. Reads identified as S. enterica in these six samples were further evaluated using BLAST and NCBI?s nr/nt database, which identified that only 2/60 samples contained reads exclusive to S. enterica chromosomal genomes. These two samples were culture- and PCR-negative, suggesting that even deep metagenomic sequencing suffers from lower sensitivity and specificity in comparison to more traditional pathogen detection methods. Additionally, no sample reads were taxonomically classified as S. enterica with two other metagenomic tools, Metagenomic Intra-species Diversity Analysis System (MIDAS) and Metagenomic Phylogenetic Analysis 2 (MetaPhlAn2). This study re-affirmed that the traditional techniques of aerobic culture and PCR provide similar results for S. enterica identification in cattle feces. On the other hand, metagenomic results are highly influenced by the classification method and reference database employed. These results highlight the nuances of computational detection of species-level sequences within short-read metagenomic sequence data, and emphasize the need for cautious interpretation of such results.
650 $aCATTLE
650 $aFEEDLOT
650 $aVACAS
653 $aCULTURE
653 $aPATHOGEN IDENTIFICATION
653 $aPCR
653 $aSALMONELLA ENTERICA
653 $aSHOTGUN METAGENOMICS
700 1 $aROVIRA, P.J.
700 1 $aNOYES, N.R.
700 1 $aBURGESS, B.A.
700 1 $aYANG, X.
700 1 $aWEINROTH, M.D.
700 1 $aLINKE, L.
700 1 $aMAGNUSON, R.
700 1 $aBOUCHER, C.
700 1 $aBELK, K.E.
700 1 $aMORLEY, P.S.
773 $tFrontier in Microbiology, 2019, 10:2499. doi: 10.3389/fmicb.2019.02499
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Registro original : |
INIA Treinta y Tres (TT) |
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Registro completo
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Biblioteca (s) : |
INIA La Estanzuela; INIA Las Brujas; INIA Treinta y Tres. |
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Fecha actual : |
21/09/2018 |
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Actualizado : |
25/10/2019 |
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Tipo de producción científica : |
Serie Técnica |
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Autor : |
ARBOLEYA, J. (Ed.). |
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Afiliación : |
JORGE EDUARDO ARBOLEYA DUFOUR, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. |
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Título : |
Solarización: una técnica de manejo integrado de malezas y plagas en horticultura. |
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Fecha de publicación : |
2018 |
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Fuente / Imprenta : |
Montevideo (UY): INIA, 2018. |
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Páginas : |
84 p. |
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Serie : |
(INIA Serie Técnica; 245) |
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ISBN : |
978-9974-38-400-2 |
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ISSN : |
1688-9266 |
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DOI : |
http://doi.org/10.35676/INIA/ST.245 |
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Idioma : |
Español |
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Contenido : |
El manejo y control de malezas en cultivos hortícolas ha sido una línea de investigación llevada adelante desde hace mucho tiempo. Desde la década del 90, en Bella Unión, se llevaron adelante trabajos de solarización de canteros para el control de malezas con excelentes resultados. A partir de ese momento la solarización se fue adoptando en el litoral norte para el control de malezas en los almácigos de cebolla.
La solarización consiste en la cobertura hermética del suelo húmedo con plástico transparente UV, durante un tiempo determinado, contribuyendo al manejo integrado de los almácigos en dos importantes aspectos: disminuir el banco de semillas de malezas existente en el suelo y reducir/controlar algunas enfermedades (tales como mal de almácigos, podredumbre blanca y otros) y nematodos.
En esta publicación se pone a disposición de técnicos y productores la información generada en esta temática. |
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Thesagro : |
CEBOLLA; CONTROL DE MALEZAS; CONTROL DE PLAGAS; MANEJO INTEGRADO DE PLAGAS; SOLARIZACION; SOLARIZACION DE SUELOS. |
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Asunto categoría : |
F01 Cultivo |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/11245/1/st-245-2018.pdf
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Marc : |
LEADER 01628nam a2200241 a 4500
001 1059034
005 2019-10-25
008 2018 bl uuuu u00u1 u #d
020 $a978-9974-38-400-2
022 $a1688-9266
024 7 $ahttp://doi.org/10.35676/INIA/ST.245$2DOI
100 1 $aARBOLEYA, J.
245 $aSolarización$buna técnica de manejo integrado de malezas y plagas en horticultura.
260 $aMontevideo (UY): INIA$c2018
300 $a84 p.
490 $a(INIA Serie Técnica; 245)
520 $aEl manejo y control de malezas en cultivos hortícolas ha sido una línea de investigación llevada adelante desde hace mucho tiempo. Desde la década del 90, en Bella Unión, se llevaron adelante trabajos de solarización de canteros para el control de malezas con excelentes resultados. A partir de ese momento la solarización se fue adoptando en el litoral norte para el control de malezas en los almácigos de cebolla. La solarización consiste en la cobertura hermética del suelo húmedo con plástico transparente UV, durante un tiempo determinado, contribuyendo al manejo integrado de los almácigos en dos importantes aspectos: disminuir el banco de semillas de malezas existente en el suelo y reducir/controlar algunas enfermedades (tales como mal de almácigos, podredumbre blanca y otros) y nematodos. En esta publicación se pone a disposición de técnicos y productores la información generada en esta temática.
650 $aCEBOLLA
650 $aCONTROL DE MALEZAS
650 $aCONTROL DE PLAGAS
650 $aMANEJO INTEGRADO DE PLAGAS
650 $aSOLARIZACION
650 $aSOLARIZACION DE SUELOS
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INIA Las Brujas (LB) |
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