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Biblioteca (s) : |
INIA Treinta y Tres. |
Fecha : |
04/11/2019 |
Actualizado : |
03/12/2019 |
Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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. |
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. |
Título : |
A cautionary report for pathogen identification using shotgun metagenomics; a comparison to aerobic culture and polymerase chain reaction for Salmonella enterica identification. |
Fecha de publicación : |
2019 |
Fuente / Imprenta : |
Frontier in Microbiology, 2019, 10:2499. doi: 10.3389/fmicb.2019.02499 |
Páginas : |
7 p. |
DOI : |
10.3389/fmicb.2019.02499 |
Idioma : |
Inglés |
Notas : |
Article history: received: 8 July 2019 // Accepted 16 October 2019 // Published 01 November 2019.
Open Access Journal. www.frontiersin.org |
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 |
Palabras claves : |
CULTURE; PATHOGEN IDENTIFICATION; PCR; SALMONELLA ENTERICA; SHOTGUN METAGENOMICS. |
Thesagro : |
CATTLE; FEEDLOT; VACAS. |
Asunto categoría : |
L73 Enfermedades de los animales |
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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INIA Treinta y Tres (TT) |
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Biblioteca (s) : |
INIA Tacuarembó. |
Fecha actual : |
21/02/2014 |
Actualizado : |
12/02/2019 |
Tipo de producción científica : |
Documentos |
Autor : |
MONTOSSI, F.; SAN JULIÁN, R.; MEDEROS, A.; BANCHERO, G.; BERRETTA, E.J.; RISSO, D.; DE MATTOS, D.; FERREIRA, G. |
Afiliación : |
FABIO MARCELO MONTOSSI PORCHILE, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ROBERTO SAN JULIAN SANCHEZ, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; AMERICA ESTHER MEDEROS SILVEIRA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; GEORGGET ELIZABETH BANCHERO HUNZIKER, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ELBIO JOAQUIN BERRETTA CARVALLO, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; DIEGO FERNANDO RISSO RIET, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; DANIEL DE MATTOS, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; GUSTAVO ALVARO FERREIRA DE MATTOS, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. |
Título : |
Avances tecnológicos para la región basáltica: 2. Producción ovina. |
Fecha de publicación : |
1997 |
Fuente / Imprenta : |
ln: INIA Tacuarembó. Unidad Experimental Glencoe. Tecnologías de producción ganadera para Basalto. Tacuarembó (Uruguay): INIA, 1997. |
Páginas : |
cap. 2, p. 1-6 |
Serie : |
(INIA Serie Actividades de Difusión ; 145) |
Idioma : |
Español |
Contenido : |
La investigación más reciente (1994 al presente) desarrollada por INIA en el rubro ovinos ha tenido como objetivo principal evaluar el efecto de diferentes
decisiones de manejo y estrategias de alimentación y control sanitario sobre la productividad de diferentes categoria ovinas, tanto para las razas Corriedale como
Merino, mayoritarias en la región. Dichos trabajos de investigación han estado orientados hacia la mejora de la eficiencia de la producción y la calidad de lana y
carne de los sistemas laneros de Basalto, a través del diseño y análisis de distintas estrategias que permitan mejorar los indices productivos de las diferentes etapas del
ciclo (cría, recría y engorde). Las estrategias han estado enfocadas hacia el uso del campo natural, mejoramientos extensivos y pasturas cultivadas y/o convencionales, desarrolladas sobre suelos medios a profundos, y más recientemente al uso de suplementos extraprediales. |
Palabras claves : |
ANIMAL PRODUCTION. |
Thesagro : |
CAMBIO TECNOLOGICO; ENGORDE; INVESTIGACION; MEJORAMIENTO ANIMAL; OVINOS; PRODUCCION ANIMAL; REPRODUCTIVIDAD; SUELO BASALTICO; URUGUAY. |
Asunto categoría : |
L01 Ganadería |
URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/9620/1/SAD145cap2p1-6.pdf
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Marc : |
LEADER 01968naa a2200349 a 4500 001 1020828 005 2019-02-12 008 1997 bl uuuu u00u1 u #d 100 1 $aMONTOSSI, F. 245 $aAvances tecnológicos para la región basáltica$b2. Producción ovina. 260 $c1997 300 $acap. 2, p. 1-6 490 $a(INIA Serie Actividades de Difusión ; 145) 520 $aLa investigación más reciente (1994 al presente) desarrollada por INIA en el rubro ovinos ha tenido como objetivo principal evaluar el efecto de diferentes decisiones de manejo y estrategias de alimentación y control sanitario sobre la productividad de diferentes categoria ovinas, tanto para las razas Corriedale como Merino, mayoritarias en la región. Dichos trabajos de investigación han estado orientados hacia la mejora de la eficiencia de la producción y la calidad de lana y carne de los sistemas laneros de Basalto, a través del diseño y análisis de distintas estrategias que permitan mejorar los indices productivos de las diferentes etapas del ciclo (cría, recría y engorde). Las estrategias han estado enfocadas hacia el uso del campo natural, mejoramientos extensivos y pasturas cultivadas y/o convencionales, desarrolladas sobre suelos medios a profundos, y más recientemente al uso de suplementos extraprediales. 650 $aCAMBIO TECNOLOGICO 650 $aENGORDE 650 $aINVESTIGACION 650 $aMEJORAMIENTO ANIMAL 650 $aOVINOS 650 $aPRODUCCION ANIMAL 650 $aREPRODUCTIVIDAD 650 $aSUELO BASALTICO 650 $aURUGUAY 653 $aANIMAL PRODUCTION 700 1 $aSAN JULIÁN, R. 700 1 $aMEDEROS, A. 700 1 $aBANCHERO, G. 700 1 $aBERRETTA, E.J. 700 1 $aRISSO, D. 700 1 $aDE MATTOS, D. 700 1 $aFERREIRA, G. 773 $tln: INIA Tacuarembó. Unidad Experimental Glencoe. Tecnologías de producción ganadera para Basalto. Tacuarembó (Uruguay): INIA, 1997.
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