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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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 | Acceso al texto completo restringido a Biblioteca INIA Las Brujas. Por información adicional contacte bibliolb@inia.org.uy. |
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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha actual : |
20/03/2024 |
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Actualizado : |
20/03/2024 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Circulación / Nivel : |
Internacional - -- |
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Autor : |
MACÊDO, I.L. DE; SOUSA, D.E.R. DE; SOUZA, A.D.R.; ARMIÉN, A.G.; MACHADO, M.; CASTRO, M.B. DE |
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Afiliación : |
ISABEL LUANA DE MACÊDO, Veterinary Pathology and Forensic Laboratory, Veterinary Teaching Hospital, University of Brasilia, Distrito Federal, Brazil; Graduate Program in Animal Science, University of Brasilia, Distrito Federal, Brazil; DAVI EMANUEL RIBEIRO DE SOUSA, Veterinary Pathology and Forensic Laboratory, Veterinary Teaching Hospital, University of Brasilia, Distrito Federal, Brazil; Graduate Program in Animal Science, University of Brasilia, Distrito Federal, Brazil; ANTONIZETE DOS REIS SOUZA, Primatology Center, Fazenda Água Limpa, University of Brasilia, Distrito Federal, Brazil; ANÍBAL G. ARMIÉN, California Animal Health & Food Safety Laboratory System (CAHFS), School of Veterinary Medicine, University of California, Davis, USA; MIZAEL MACHADO DA COSTA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; MÁRCIO BOTELHO DE CASTRO, Veterinary Pathology and Forensic Laboratory, Veterinary Teaching Hospital, University of Brasilia, Distrito Federal, Brazil; Graduate Program in Animal Science, University of Brasilia, Distrito Federal, Brazil. |
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Título : |
Fatal Africanized bee attack in captive non-human primates (Saimiri ustus and Sapajus libidinosus). |
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Complemento del título : |
Short communication. |
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Fecha de publicación : |
2024 |
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Fuente / Imprenta : |
Toxicon. 2024, Volume 241, Article 107666. https://doi.org/10.1016/j.toxicon.2024.107666 |
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ISSN : |
0041-0101 |
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DOI : |
10.1016/j.toxicon.2024.107666 |
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Idioma : |
Inglés |
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Notas : |
Article history: Received 8 February 2024, Revised 26 February 2024, Accepted 27 February 2024, Available online 28 February 2024, Version of Record 8 March 2024. -- Correspondence: Castro, M.B.D.; Veterinary Pathology and Forensic Laboratory, Veterinary Teaching Hospital, University of Brasilia, Distrito Federal, Brazil; email:mbcastro@unb.br --Funding: This research was partly financed by the Coordination for the Improvement of Higher Education Personnel - Brazil (CAPES) - Finance Code 001 (ILM, DERS). We thank the National Council for Scientific and Technological Development ( CNPq ) for the Research Productivity grant (PQ), process n. 307909/2021-2 (MBC). |
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Contenido : |
ABSTRACT.- Bee stings (BS) are a life-threatening issue and a growing concern for public health and animals in the Americas. We describe the clinical, pathological, and ultrastructural findings of a massive lethal bee attack in two non-human primates (NHPs). Both animals showed BS scattered throughout the skin, surrounded by a local reaction, diffuse pulmonary congestion, edema, hemorrhage, and remarkable degeneration and necrosis of renal epithelial cells from the proximal and distal tubules, characterizing a systemic bee envenomation reaction. © 2024 Elsevier Ltd |
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Palabras claves : |
Bee venom; Envenomation; Kidney injury; Macaques; PLATAFORMA DE INVESTIGACIÓN EN SALUD ANIMAL - INIA; Systemic reaction. |
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Asunto categoría : |
L40 Estructura animal |
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Marc : |
LEADER 02135naa a2200289 a 4500
001 1064505
005 2024-03-20
008 2024 bl uuuu u00u1 u #d
022 $a0041-0101
024 7 $a10.1016/j.toxicon.2024.107666$2DOI
100 1 $aMACÊDO, I.L. DE
245 $aFatal Africanized bee attack in captive non-human primates (Saimiri ustus and Sapajus libidinosus).$h[electronic resource]
260 $c2024
500 $aArticle history: Received 8 February 2024, Revised 26 February 2024, Accepted 27 February 2024, Available online 28 February 2024, Version of Record 8 March 2024. -- Correspondence: Castro, M.B.D.; Veterinary Pathology and Forensic Laboratory, Veterinary Teaching Hospital, University of Brasilia, Distrito Federal, Brazil; email:mbcastro@unb.br --Funding: This research was partly financed by the Coordination for the Improvement of Higher Education Personnel - Brazil (CAPES) - Finance Code 001 (ILM, DERS). We thank the National Council for Scientific and Technological Development ( CNPq ) for the Research Productivity grant (PQ), process n. 307909/2021-2 (MBC).
520 $aABSTRACT.- Bee stings (BS) are a life-threatening issue and a growing concern for public health and animals in the Americas. We describe the clinical, pathological, and ultrastructural findings of a massive lethal bee attack in two non-human primates (NHPs). Both animals showed BS scattered throughout the skin, surrounded by a local reaction, diffuse pulmonary congestion, edema, hemorrhage, and remarkable degeneration and necrosis of renal epithelial cells from the proximal and distal tubules, characterizing a systemic bee envenomation reaction. © 2024 Elsevier Ltd
653 $aBee venom
653 $aEnvenomation
653 $aKidney injury
653 $aMacaques
653 $aPLATAFORMA DE INVESTIGACIÓN EN SALUD ANIMAL - INIA
653 $aSystemic reaction
700 1 $aSOUSA, D.E.R. DE
700 1 $aSOUZA, A.D.R.
700 1 $aARMIÉN, A.G.
700 1 $aMACHADO, M.
700 1 $aCASTRO, M.B. DE
773 $tToxicon. 2024, Volume 241, Article 107666. https://doi.org/10.1016/j.toxicon.2024.107666
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