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| Registros recuperados : 17 | |
| 2. |  | 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.| Biblioteca(s): INIA Treinta y Tres. |
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| 3. | | 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.| Biblioteca(s): INIA Treinta y Tres. |
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| 4. | | 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.| 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.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| Biblioteca(s): INIA Treinta y Tres. |
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| 6. | | 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.| Biblioteca(s): INIA Treinta y Tres. |
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| 7. | | 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.| 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| 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.| 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.| Biblioteca(s): INIA Las Brujas; INIA Treinta y Tres. |
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| 11. | | 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| Biblioteca(s): INIA Treinta y Tres. |
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| 12. | | 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| Biblioteca(s): INIA Treinta y Tres. |
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| 13. | | 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.| Biblioteca(s): INIA Treinta y Tres. |
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| 14. | | 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.| Biblioteca(s): INIA Treinta y Tres. |
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| 15. | | 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| 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.| 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| Biblioteca(s): INIA Treinta y Tres. |
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| Registros recuperados : 17 | |
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 | Acceso al texto completo restringido a Biblioteca INIA Treinta y Tres. Por información adicional contacte bibliott@inia.org.uy. |
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Registro completo
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Biblioteca (s) : |
INIA Treinta y Tres. |
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Fecha actual : |
21/02/2014 |
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Actualizado : |
13/09/2018 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Circulación / Nivel : |
Internacional - A |
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Autor : |
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. |
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Afiliación : |
NOELLE R. NOYES; MAGGIE E. WEINROTH; JENNIFER K. PARKER; CHRIS J. DEAN; STEVEN M. LAKIN; ROBERT A. RAYMOND; PABLO JUAN ROVIRA SANZ, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ENRIQUE DOSTER; ZAID ABDO; JENNIFER N. MARTIN; KENNETH L. JONES; JAIME RUIZ; CHRISTINA A. BOUCHER; KEITH E. BELK; PAUL S. MORLEY. |
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Título : |
Enrichment allows identification of diverse, rate elements in metagenomic resistome-virulome sequencing. |
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Fecha de publicación : |
2017 |
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Fuente / Imprenta : |
Microbiome, 2017, 5, p. 142 |
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Páginas : |
13 p. |
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DOI : |
10.1186/s40168-017-0361-8 |
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Idioma : |
Inglés |
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Notas : |
Article History: Received: 29 May 2017, Accepted: 5 October 2017, Published: 17 October 2017 |
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Contenido : |
Background: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to imitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias.
Results: The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional
metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins.
Conclusions: These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistomevirulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of
microbiome-resistome dynamics. MenosBackground: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to imitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias.
Results: The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional
metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistan... Presentar Todo |
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Palabras claves : |
ANTIMICROBIAL RESISTANCE; METAGENÓMICA; MICROBIAL ECOLOGY; MOLECULAR ENRICHMENT; RARE MICROBIOME; RESISTOME. |
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Thesagro : |
ANALISIS BIOLOGICO; ECOLOGIA MICROBIANA; RESISTENCIA A AGENTES DANINOS. |
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Asunto categoría : |
U30 Métodos de investigación |
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Marc : |
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024 7 $a10.1186/s40168-017-0361-8$2DOI
100 1 $aNOYES, N.R.
245 $aEnrichment allows identification of diverse, rate elements in metagenomic resistome-virulome sequencing.$h[electronic resource]
260 $c2017
300 $a13 p.
500 $aArticle History: Received: 29 May 2017, Accepted: 5 October 2017, Published: 17 October 2017
520 $aBackground: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to imitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias. Results: The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins. Conclusions: These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistomevirulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of microbiome-resistome dynamics.
650 $aANALISIS BIOLOGICO
650 $aECOLOGIA MICROBIANA
650 $aRESISTENCIA A AGENTES DANINOS
653 $aANTIMICROBIAL RESISTANCE
653 $aMETAGENÓMICA
653 $aMICROBIAL ECOLOGY
653 $aMOLECULAR ENRICHMENT
653 $aRARE MICROBIOME
653 $aRESISTOME
700 1 $aWEINROTH, M.E.
700 1 $aPARKER, J.K.
700 1 $aDEAN, C.J.
700 1 $aLAKIN, S.M.
700 1 $aRAYMOND, R.A.
700 1 $aROVIRA, P.J.
700 1 $aDOSTER, E.
700 1 $aABDO, Z.
700 1 $aMARTIN, J.N.
700 1 $aJONES, K.L.
700 1 $aRUIZ, J.
700 1 $aBOUCHER, C.A.
700 1 $aBELK, K.E.
700 1 $aMORLEY, P.S.
773 $tMicrobiome, 2017, 5, p. 142
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