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Registro completo
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Biblioteca (s) : |
INIA Treinta y Tres. |
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Fecha : |
17/04/2017 |
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Actualizado : |
11/10/2019 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
LAKIN, S.M.; DEAN, C.; NOYES, N.R.; DETTENWANGER, A.; ROSS, A. S.; DOSTER, E.; ROVIRA, P.J.; ABDO, Z.; JONES, K.L.; RUIZ, J.; BELK, K.E.; MORLEY, P.S.; BOUCHER, C. |
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Afiliación : |
STEVEN M. LAKIN; CHRIS DEAN; NOELLE R. NOYES; ADAM DETTENWANGER; ANNE SPENCER ROSS; ENRIQUE DOSTER; PABLO JUAN ROVIRA SANZ, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay. Department of Animal Sciences, Colorado State University, USA.; ZAID ABDO; KENNETH L. JONES; JAIME RUIZ; KEITH E. BELK; PAUL S. MORLEY; CHRISTINA BOUCHER. |
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Título : |
MEGARes: an antimicrobial resistance database for high throughput sequencing. |
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Fecha de publicación : |
2017 |
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Fuente / Imprenta : |
Nucleic Acids Research, 2017 v.45 p.574-580. |
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DOI : |
10.1093/nar/gkw1009 |
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Idioma : |
Inglés |
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Notas : |
Article History: Published online 2016 Nov 24.
DOI: https://doi.org/10.1093/nar/gkw1009 |
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Contenido : |
Antimicrobial resistance has become an imminent concern for public health. As methods for detection and characterization of antimicrobial resistance move from targeted culture and polymerase chain reaction to high throughput metagenomics, appropriate resources for the analysis of large-scale data are required. Currently, antimicrobial resistance databases are tailored to smaller-scale, functional profiling of genes using highly descriptive annotations. Such characteristics do not facilitate the analysis of large-scale, ecological sequence datasets such as those produced with the use of metagenomics for surveillance. In order to overcome these limitations, we present MEGARes (https://megares.meglab.org), a hand-curated antimicrobial resistance database and annotation structure that provides a foundation for the development of high throughput acyclical classifiers and hierarchical statistical analysis of big data. MEGARes can be browsed as a stand-alone resource through the website or can be easily integrated into sequence analysis pipelines through download. Also via the website, we provide documentation for AmrPlusPlus, a user-friendly Galaxy pipeline for the analysis of high throughput sequencing data that is pre-packaged for use with the MEGARes database. |
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Palabras claves : |
BASE DE DATOS; BIOINFORMÁTICA; DATASETS; DRUG RESISTANCE; GENES; METAGENÓMICA; METAGENOMICS; MICROBIAL; POLYMERASE CHAIN REACTION; PUBLIC HEALTH MEDICINE; RESISTENCIA ANTIMICROBIANA; SEQUENCE ANALYSIS. |
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Asunto categoría : |
L01 Ganadería |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/6677/1/Rovira-arb-2017-1.pdf
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210519/
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Marc : |
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245 $aMEGARes$ban antimicrobial resistance database for high throughput sequencing.$h[electronic resource]
260 $c2017
500 $aArticle History: Published online 2016 Nov 24. DOI: https://doi.org/10.1093/nar/gkw1009
520 $aAntimicrobial resistance has become an imminent concern for public health. As methods for detection and characterization of antimicrobial resistance move from targeted culture and polymerase chain reaction to high throughput metagenomics, appropriate resources for the analysis of large-scale data are required. Currently, antimicrobial resistance databases are tailored to smaller-scale, functional profiling of genes using highly descriptive annotations. Such characteristics do not facilitate the analysis of large-scale, ecological sequence datasets such as those produced with the use of metagenomics for surveillance. In order to overcome these limitations, we present MEGARes (https://megares.meglab.org), a hand-curated antimicrobial resistance database and annotation structure that provides a foundation for the development of high throughput acyclical classifiers and hierarchical statistical analysis of big data. MEGARes can be browsed as a stand-alone resource through the website or can be easily integrated into sequence analysis pipelines through download. Also via the website, we provide documentation for AmrPlusPlus, a user-friendly Galaxy pipeline for the analysis of high throughput sequencing data that is pre-packaged for use with the MEGARes database.
653 $aBASE DE DATOS
653 $aBIOINFORMÁTICA
653 $aDATASETS
653 $aDRUG RESISTANCE
653 $aGENES
653 $aMETAGENÓMICA
653 $aMETAGENOMICS
653 $aMICROBIAL
653 $aPOLYMERASE CHAIN REACTION
653 $aPUBLIC HEALTH MEDICINE
653 $aRESISTENCIA ANTIMICROBIANA
653 $aSEQUENCE ANALYSIS
700 1 $aDEAN, C.
700 1 $aNOYES, N.R.
700 1 $aDETTENWANGER, A.
700 1 $aROSS, A. S.
700 1 $aDOSTER, E.
700 1 $aROVIRA, P.J.
700 1 $aABDO, Z.
700 1 $aJONES, K.L.
700 1 $aRUIZ, J.
700 1 $aBELK, K.E.
700 1 $aMORLEY, P.S.
700 1 $aBOUCHER, C.
773 $tNucleic Acids Research, 2017$gv.45 p.574-580.
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Registro original : |
INIA Treinta y Tres (TT) |
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| Registros recuperados : 17 | |
| 2. |  | 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. A cautionary report for pathogen identification using shotgun metagenomics; a comparison to aerobic culture and polymerase chain reaction for Salmonella enterica identification. Frontier in Microbiology, 2019, 10:2499. doi: 10.3389/fmicb.2019.02499 7 p. Article history: received: 8 July 2019 // Accepted 16 October 2019 // Published 01 November 2019.
Open Access Journal. www.frontiersin.org| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : -- - -- |
| Biblioteca(s): INIA Treinta y Tres. |
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| 3. | | NOYES, N. R.; ABDO, Z.; ROVIRA, P.J.; DOSTER, E.; YANG, X.; LINKE, L. M.; BURGESS, B. A.; MARTIN. J.; BOUCHER, C.; MORLEY, P. S.; BELK, K. E. A bayesian approach to investigating the effect of metaphylaxis on the microbiome-resistance of the commercial feedlot steers. Abstract. In: Plant and Animal Genome Conference, 24. San Diego, USA, 2016.| Tipo: Abstracts/Resúmenes |
| Biblioteca(s): INIA Treinta y Tres. |
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| 4. | | NOYES, N.; WEINROTH, M.; LAKIN, S.; DOSTER, E.; RAYMOND, R.; ROVIRA, P.J.; ABDO, Z.; RUIZ, J.; MARTIN, J.; BOUCHER, C.; JONES, K.; BELK, K.E. Comparing the resistome of poultry, swine, cattle and salmon production and nearby human waste water treatment plants. [Abstract]. In: Conference of Research Workers in Animal Diseases, 96th, 2015,Chicago (USA): CRWAD, 2015. p. 127.| Tipo: Abstracts/Resúmenes |
| Biblioteca(s): INIA Treinta y Tres. |
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| 5. | | DOSTER, E.; ROVIRA, P.J.; NOYES, N.R.; BURGESS, B.A.; YANG, X.; WEINROTH, M.; LINKE, L.; MAGNUSON, R.; PABILONIA, K.; BOUCHER, C. Comparing Salmonella enterica detection in feces using aerobic culture, targeted molecular tests, and shotgun metagenomics. In: SYMPOSIUM OF AMERICAN COLLEGE OF VETERINARY INTERNAL MEDICINE, 2017, GREENWOOD VILLAGE, CO, USA. Proceedings of ACVIM 2017, Greenwood Village, CO, USA. p. 338.| Tipo: Abstracts/Resúmenes |
| Biblioteca(s): INIA Treinta y Tres. |
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| 6. | | LAKIN, S.M.; DEAN, C.J.; DETTENWANGER, A.; ROSS, A.; DOSTER, E.; ROVIRA, P.J.; ABDO, Z.; JONES, K.L.; BELK, K.E.; MORLEY, P.S.; BOUCHER, C. MEGaRES and AmrPlusPlus, a comprehensive database of antimicrobial resistance genes and user-friendly pipeline for analysis of high-throughput sequencing data.[Abstract]. In: PROCEEDINGS OF THE 96TH ANNUAL CONFERENCE OF RESEARCH WORKERS IN ANIMAL DEISEASES, CHICAGO, USA. 2016. Session Ecology and Management of Foodborne Agents. 065.| Tipo: Abstracts/Resúmenes |
| Biblioteca(s): INIA Treinta y Tres. |
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| 7. | | DOSTER, E.; ROVIRA, P.J.; NOYES, NOELLE R.; BURGESS, B.A.; MAGNUSON, R.; JONES, KENNETH; BOUCHER, C.; RUIZ, JAIME; BELK, K. E. Investigating the effect of tulathromycin exposure on potential microbial community function in feedlot cattle during the early feeding period using shotgun metagenomics. [Abstract]. In: Scientific Annual Research Day, 17. Fort Collins. 2016. Proceedings. Fort Collins: Colorado State University, 2016 p. 18.| Tipo: Abstracts/Resúmenes |
| Biblioteca(s): INIA Treinta y Tres. |
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| 8. | | DOSTER, E.; ROVIRA, P.J.; NOYES, N.; BURGES, B.; YANG, X.; WEINROTH, M.; LINKE, L.; MAGNUSON, R.; JONES, K.; BOUCHER, C.; RUIZ, J.; MORLEY, P.; BELK, K. Shotgun metagenomic detection of Salmonella enterica in feedlot cattle compared to aerobic culture and PCR techniques. [Abstract]. In: Conference of Research Workers in Animal Diseases, 2016. Chicago (USA): En línea| Tipo: Abstracts/Resúmenes |
| Biblioteca(s): INIA Treinta y Tres. |
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| 9. | | ROVIRA, P.J.; MCALLISTER, T.; LAKIN, S.M.; COOK, S.R.; DOSTER, E.; NOYES, N. R.; WEINROTH, M.D.; YANG, X.; PARKER, J. K.; BOUCHER, C.; BOOKER, C. W.; WOENER, D. R.; BELK, K. E.; MORLEY, P. S. Characterization of the microbial resistome in conventional and "raised without antibiotics" beef and dairy production systems. Frontier in Microbiology, September 2019. v. 10, article 1980, 11 p. OPEN ACCESS. Received 18 March 2019 // Accepted 12 August 2019 // Published 4 September 2019.| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : -- - -- |
| Biblioteca(s): INIA Treinta y Tres. |
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| 10. | | WEINROTH, M.D.; SCOTT, H.M.; NORBY, B.; LONERAGAN, G.H.; NOYES, N.R.; ROVIRA, P.J.; DOSTER, E.; YANG, X.; WOERNER, D.R.; MORLEY, P.S.; BELK, K.E. Effects of ceftiofur and chlortetracycline on the resistomes of feedlot cattle. Applied and Environmental Microbiology, July 2018, vol. 84, no.13, e00610-18. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Article history: Received 15 March 2018. / Accepted 24 April 2018. / Accepted manuscript posted online 4 May 2018. OPEN ACCESS.| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas; INIA Treinta y Tres. |
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| 11. | | LAKIN, S.M.; DEAN, C.; NOYES, N.R.; DETTENWANGER, A.; ROSS, A. S.; DOSTER, E.; ROVIRA, P.J.; ABDO, Z.; JONES, K.L.; RUIZ, J.; BELK, K.E.; MORLEY, P.S.; BOUCHER, C. MEGARes: an antimicrobial resistance database for high throughput sequencing. Nucleic Acids Research, 2017 v.45 p.574-580. Article History: Published online 2016 Nov 24.
DOI: https://doi.org/10.1093/nar/gkw1009| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : A - A |
| Biblioteca(s): INIA Treinta y Tres. |
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| 12. | | NOYES, N.R.; PARKER, J.K.; DEAN, C.J.; RAYMOND, R.A.; WEINROTH, M.E.; ROVIRA, P.J.; DOSTER, E.; ABDO, Z.; MARTIN, J.; JONES, K.L.; RUIZ, J.; BOUCHER, C.A.; BELK, K.E.; MORLEY, P.S. Megarich, a pre-sequencing capture system for enriching and counting resistance genes within metagenomic samples. [Abstract]. In: PROCEEDINGS OF THE 96TH ANNUAL CONFERENCE OF RESEARCH WORKERS IN ANIMAL DEISEASES, CHICAGO, USA. 2016. Session Ecology and Management of Foodborne Agents. - 064.| Tipo: Abstracts/Resúmenes |
| Biblioteca(s): INIA Treinta y Tres. |
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| 13. | | WEINROTH, M.D.; LANKIN, S.M.; NOYES, N.R.; YANG, X.; ROVIRA, P.J.; DOSTER, E.; DEAN, C.; PARKER, J.K.; ANDERSON, C.; ABDO, Z.; BOUCHER, C.; RUIZ, J.; BELK, K.E.; MORLEY, P.S. Metagenomic investigations of antimicrobial resistance in beef, pork, and broiler production systems. [Abstract]. ln: Conference of Research Workers in Animal Disease. (3-5 Dec., 2017, Chicago, Illinois, USA) Presentation Abstracts. Chicago, Illinois (USA): CRWAD, 2017. p. 27.| Tipo: Abstracts/Resúmenes |
| Biblioteca(s): INIA Treinta y Tres. |
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| 14. | | MORLEY, P.; BELK, K.; DOSTER, E.; LAKIN, S.; DEAN, C.; MUGGLI, M.; NOYES, N.; ROVIRA, P.J.; WEINROTH, M.; YANG, X.; ABDO, Z.; BOUCHER, C.; RUIZ, J.; SCOTT, H.M.; VAN METRE, D.C.; WOERNER, D.E. Metagnomic investigations of antimicrobial resitance in food animal populations. In: USDA NIFA Antimicrobial Resistance Program Project. 2017, Florida, USA. p. 14-15| Tipo: Abstracts/Resúmenes |
| Biblioteca(s): INIA Treinta y Tres. |
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| 15. | | DOSTER, E.; ROVIRA, P.J.; NOYES, N.R.; BURGESS, B. A.; YANG, X.; WEINROTH, M.D.; LAKIN, S.M.; DEAN, C.J.; LINKE, L.; MAGNUSON, R.; JONES, K.I.; BOUCHER, C.; RUIZ, J.; BELK, K.E.; MORLEY, P.S. Investigating effects of tulathromycin metaphylaxis on the fecal resistome and microbiome of commercial feedlot cattle early in the feeding period. Frontier in Microbiology, 2018, 9:1715. 14 p. Article history: Received: 14 April 2018; Accepted: 09 July 2018; Published: 30 July 2018.
Open Access journal.
https://doi.org/10.3389/fmicb.2018.01715| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Treinta y Tres. |
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| 16. | | DOSTER, E.; ROVIRA, P.J.; NOYES, N. R.; BURGESS, B.A.; YANG, X.; WEINROTH, M.; LINKE, L.; MAGNUSON, R.; JONES, K.; BOUCHER, C.; RUIZ, J.; MORLEY, P.S.; BELK, K.E. Use of shotgun metagenomic to evaluate the microbiome in cattle feces following tulathromycin metaphylaxis. [Abstract]. In: Conference of Research Workers in Animal Diseases, 96th, 2015,Chicago (USA): CRWAD, 2015. p. 128.| Tipo: Abstracts/Resúmenes |
| Biblioteca(s): INIA Treinta y Tres. |
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| 17. | | NOYES, N.R.; WEINROTH, M.E.; PARKER, J.K.; DEAN, C.J.; LAKIN, S.M.; RAYMOND, R.A.; ROVIRA, P.J.; DOSTER, E.; ABDO, Z.; MARTIN, J.N.; JONES, K.L.; RUIZ, J.; BOUCHER, C.A.; BELK, K.E.; MORLEY, P.S. Enrichment allows identification of diverse, rate elements in metagenomic resistome-virulome sequencing. Microbiome, 2017, 5, p. 142 13 p. Article History: Received: 29 May 2017, Accepted: 5 October 2017, Published: 17 October 2017| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - A |
| Biblioteca(s): INIA Treinta y Tres. |
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| Registros recuperados : 17 | |
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