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Registro completo
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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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Registros recuperados : 18 | |
1. | | BOSCHI, F.; SCHVARTZMAN, C.; MURCHIO, S.; FERREIRA, V.; SIRI, M.; GALVÁN, G.; SMOKER, M.; STRANSFEL, L.; ZYPFEL, C.; VILARÓ, F.; DALLA RIZZA, M. Enhanced bacterial wilt resistance in potato through expression of arabidopsis efr and introgression of quantitative resistance from solanum commersonii. Frontiers in Plant Sciences, Volume 8, 25 September 2017, Article number 1642. OPEN ACCESS. THIS ARTICLE IS PART OF THE RESEARCH TOPIC: Plant Pathogenic Ralstonia spp. From the Field to the Lab and Back Again: mechanisms of pathogen virulence and host resistance, population biology, community ecology and strategies for bacterial...Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Las Brujas. |
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2. | | BOSCHI, F.; SCHVARTZMAN, C.; MURCHIO, S.; FERREIRA, V.; SIRI, M.I.; GALVÁN, G.; SMOKER, M.; STRANSFEL, L.; ZIPFEL, C.; VILARÓ, F.; DALLA RIZZA, M. Resistencia a marchitez bacteriana en papa mediada por expression de EFR e introgression de genes de resistencia de Solanum commersonii. In: INIA (Instituto Nacional de Investigación Agropecuaria); INIA Las Brujas; Biotecnología. Jornada de Agrobiotecnología, X. Encuentro Nacional de REDBIO, II. Jornada técnica. Las Brujas, Canelones (UY): INIA, 2017. p.15-18. (Serie Actividades de Difusión; 780)Biblioteca(s): INIA Las Brujas. |
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3. | | BOSCHI, F.; VILARÓ, F.; GALVÁN, G.; SIRI, M. I.; FERREIRA, V.; MURCHIO, S.; SCHVARTZMAN, C.; DALLA RIZZA, M. Aspectos de bioseguridad en la evaluación de papa modificada genéticamente para el control de Ralstonia solanacearum. [p19]. Bloque 2: Mejoramiento por resistencia a enfermedades. In: Sociedad Uruguaya de Fitopatología Jornada Uruguaya de Fitopatología, 4., Jornada Uruguaya de Protección Vegetal, 2., 1° setiembre, 2017, Montevideo, Uruguay. Libro de resúmenes. Montevideo (UY): Sociedad Uruguay de Fitopatología (SUFIT), 2017. p. 39.Tipo: Abstracts/Resúmenes |
Biblioteca(s): INIA Las Brujas. |
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7. | | DALLA RIZZA, M.; SCHVARTZMAN, C.; MURCHIO, S.; BERRUETA, C.; BOSCHI, F.; LENZI, A.; GIMÉNEZ, G. Field performance of resistant potato genotypes transformed with the EFR receptor from Arabidopsis thaliana in the absence of bacterial wilt (Ralstonia solanacearum). Research article. The Plant Pathology Journal, 2022, vol.38 (3): 239-247. OPEN ACCESS. doi: https://doi.org/10.5423/PPJ.OA.01.2022.0008 Article history: Received 20 January 2022; Revised 9 May 2022; Accepted 10 May 2022. -- Corresponding author: Marco Dalla-Rizza, Email: mdallarizza@inia.org.uy -- Marco Dalla-Rizza and Claudia Schvartzman contributed equally to this...Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
Biblioteca(s): INIA Las Brujas. |
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8. | | FORT, S.; FERREIRA, V.; MURCHIO, S.; SCHVARTZMAN, C.; GALVÁN, G.A.; VILARÓ, F.; SIRI, M.I.; DALLA RIZZA, M. Potato plants transformed with the Arabidopsis EF-Tu receptor (EFR) show restricted pathogen colonization and enhanced bacterial with resistance under conditions resembling natural field infections. [Plantas de papa transformadas con el receptor de EF-Tu (EFR) de Arabidopsis presentan una colonización restringida del patógeno y mayor resistencia a la marchitez Bacteriana bajo condiciones semejantes a la infección natural de campo]. Special Issue X Encuentro Latinoamericano y del Caribe de Biotecnología Agropecuaria; XII Simposio REDBIO Argentina. Roca, William, Ed. 12 al 15 de noviembre de 2019, Montevideo, Uruguay. Agrociencia Uruguay 2020, v. 24, no. NE2, Article 413. DOI: 10.31285/AGRO.24.413 16 p. 2301-1548 Article history: Received 29 Jun. 2020 // Accepted 28 Sep. 2020 // Published 17 Dec 2020.
Comité científico editor:
Dra. Marisa López-Bilbao (INTA, Hurlingham, Provincia de Buenos Aires, Argentina); Dra. Sandra Sharry (Universidad...Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : -- - -- |
Biblioteca(s): INIA Treinta y Tres. |
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11. | | MAIDANA, M.; MURCHIO, S.; SCHVARTZMAN, C.; LEONI, C.; SEÑORALE, M.; MARÍN, M.; REGUERA, M.; BLUMWALD, E.; DALLA RIZZA, M. Herramientas para la expresión de pétptidos antimicrobianos. GGM 37 - COMUNICACIONES LIBRES - GGM. GENÓMICA Y GENÉTICA MOLECULAR In: JOURNAL OF BASIC & APPLIED GENETICS, 2016, Vol.27, Iss. 1 (Supp.). XVI LATIN AMERICAN CONGRESS OF GENETICS, IV CONGRESS OF THE URUGUAYAN SOCIETY OF GENETICS, XLIX ANNUAL MEETING OF THE GENETICS SOCIETY OF CHILE, XLV ARGENTINE CONGRESS OF GENETICS, 9-12 October 2016. PROCEEDINGS. Montevideo (Uruguay): SAG, 2016. p. 273Tipo: Trabajos en Congresos/Conferencias |
Biblioteca(s): INIA Las Brujas. |
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14. | | PERDOMO FERRANDO, E.; MURCHIO, S.; WALASEK, W.; SCHVARTZMAN, C.; MAESO, D.; DALLA RIZZA, M. Evaluación de eventos de tomate con el gen EFR para el control de bacterias patógenas. [p22]. Bloque 2: Mejoramiento por resistencia a enfermedades. In: Sociedad Uruguaya de Fitopatología Jornada Uruguaya de Fitopatología, 4., Jornada Uruguaya de Protección Vegetal, 2., 1° setiembre, 2017, Montevideo, Uruguay. Libro de resúmenes. Montevideo (UY): Sociedad Uruguay de Fitopatología (SUFIT), 2017. p. 42. Financiamiento: INIA. Proyecto BT _13.Tipo: Abstracts/Resúmenes |
Biblioteca(s): INIA Las Brujas. |
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Registros recuperados : 18 | |
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