Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines
ABSTRACT: Candida auris is a multidrug-resistant pathogen that represents a serious public health threat due to its rapid global emergence, increasing incidence of healthcare-associated outbreaks, and high rates of antifungal resistance. Whole-genome sequencing and genomic surveillance have the pote...
- Autores:
-
Misas Rivas, Elizabeth
Welsh, Rory
Forsberg, Kaitlin
Lyman, Meghan
Chow, Nancy
- Tipo de recurso:
- Article of investigation
- Fecha de publicación:
- 2021
- Institución:
- Universidad de Antioquia
- Repositorio:
- Repositorio UdeA
- Idioma:
- eng
- OAI Identifier:
- oai:bibliotecadigital.udea.edu.co:10495/43332
- Acceso en línea:
- https://hdl.handle.net/10495/43332
- Palabra clave:
- Candida auris
Micosis
Mycoses
Farmacorresistencia Fúngica
Drug Resistance, Fungal
Genómica
Genomics
Secuenciación Completa del Genoma
Whole Genome Sequencing
https://id.nlm.nih.gov/mesh/D000088063
https://id.nlm.nih.gov/mesh/D009181
https://id.nlm.nih.gov/mesh/D025141
https://id.nlm.nih.gov/mesh/D023281
https://id.nlm.nih.gov/mesh/D000073336
- Rights
- openAccess
- License
- http://creativecommons.org/licenses/by/2.5/co/
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| dc.title.spa.fl_str_mv |
Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines |
| title |
Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines |
| spellingShingle |
Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines Candida auris Micosis Mycoses Farmacorresistencia Fúngica Drug Resistance, Fungal Genómica Genomics Secuenciación Completa del Genoma Whole Genome Sequencing https://id.nlm.nih.gov/mesh/D000088063 https://id.nlm.nih.gov/mesh/D009181 https://id.nlm.nih.gov/mesh/D025141 https://id.nlm.nih.gov/mesh/D023281 https://id.nlm.nih.gov/mesh/D000073336 |
| title_short |
Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines |
| title_full |
Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines |
| title_fullStr |
Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines |
| title_full_unstemmed |
Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines |
| title_sort |
Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines |
| dc.creator.fl_str_mv |
Misas Rivas, Elizabeth Welsh, Rory Forsberg, Kaitlin Lyman, Meghan Chow, Nancy |
| dc.contributor.author.none.fl_str_mv |
Misas Rivas, Elizabeth Welsh, Rory Forsberg, Kaitlin Lyman, Meghan Chow, Nancy |
| dc.contributor.researchgroup.spa.fl_str_mv |
Biología Celular y Molecular CIB U. de A. U. del Rosario |
| dc.subject.decs.none.fl_str_mv |
Candida auris Micosis Mycoses Farmacorresistencia Fúngica Drug Resistance, Fungal Genómica Genomics Secuenciación Completa del Genoma Whole Genome Sequencing |
| topic |
Candida auris Micosis Mycoses Farmacorresistencia Fúngica Drug Resistance, Fungal Genómica Genomics Secuenciación Completa del Genoma Whole Genome Sequencing https://id.nlm.nih.gov/mesh/D000088063 https://id.nlm.nih.gov/mesh/D009181 https://id.nlm.nih.gov/mesh/D025141 https://id.nlm.nih.gov/mesh/D023281 https://id.nlm.nih.gov/mesh/D000073336 |
| dc.subject.meshuri.none.fl_str_mv |
https://id.nlm.nih.gov/mesh/D000088063 https://id.nlm.nih.gov/mesh/D009181 https://id.nlm.nih.gov/mesh/D025141 https://id.nlm.nih.gov/mesh/D023281 https://id.nlm.nih.gov/mesh/D000073336 |
| description |
ABSTRACT: Candida auris is a multidrug-resistant pathogen that represents a serious public health threat due to its rapid global emergence, increasing incidence of healthcare-associated outbreaks, and high rates of antifungal resistance. Whole-genome sequencing and genomic surveillance have the potential to bolster C. auris surveillance networks moving forward. Laboratories conducting genomic surveillance need to be able to compare analyses from various national and international surveillance partners to ensure that results are mutually trusted and understood. Therefore, we established an empirical outbreak benchmark dataset consisting of 23 C. auris genomes to help validate comparisons of genomic analyses and facilitate communication among surveillance networks. Our outbreak benchmark dataset represents a polyclonal ¿ phylogeny with three subclades. The genomes in this dataset are from well-vetted studies that are supported by multiple lines of evidence, which demonstrate that the whole-genome sequencing data, phylogenetic tree, and epidemiological data are all in agreement. This C. auris benchmark set allows for standardized comparisons of phylogenomic pipelines, ultimately promoting effective C. auris collaborations. |
| publishDate |
2021 |
| dc.date.issued.none.fl_str_mv |
2021 |
| dc.date.accessioned.none.fl_str_mv |
2024-11-10T12:54:09Z |
| dc.date.available.none.fl_str_mv |
2024-11-10T12:54:09Z |
| dc.type.spa.fl_str_mv |
Artículo de investigación |
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http://purl.org/coar/resource_type/c_2df8fbb1 |
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https://purl.org/redcol/resource_type/ART |
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http://purl.org/coar/version/c_970fb48d4fbd8a85 |
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info:eu-repo/semantics/article |
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info:eu-repo/semantics/publishedVersion |
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http://purl.org/coar/resource_type/c_2df8fbb1 |
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publishedVersion |
| dc.identifier.citation.spa.fl_str_mv |
Welsh RM, Misas E, Forsberg K, Lyman M, Chow NA. Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines. J Fungi (Basel). 2021 Mar 16;7(3):214. doi: 10.3390/jof7030214. |
| dc.identifier.uri.none.fl_str_mv |
https://hdl.handle.net/10495/43332 |
| dc.identifier.doi.none.fl_str_mv |
10.3390/jof7030214 |
| dc.identifier.eissn.none.fl_str_mv |
2309-608X |
| identifier_str_mv |
Welsh RM, Misas E, Forsberg K, Lyman M, Chow NA. Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines. J Fungi (Basel). 2021 Mar 16;7(3):214. doi: 10.3390/jof7030214. 10.3390/jof7030214 2309-608X |
| url |
https://hdl.handle.net/10495/43332 |
| dc.language.iso.spa.fl_str_mv |
eng |
| language |
eng |
| dc.relation.ispartofjournalabbrev.spa.fl_str_mv |
J. Fungi. |
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7 |
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3 |
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Journal of Fungi |
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http://creativecommons.org/licenses/by/2.5/co/ |
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https://creativecommons.org/licenses/by/4.0/ |
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info:eu-repo/semantics/openAccess |
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openAccess |
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7 páginas |
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application/pdf |
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MDPI |
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Basilea, Suiza |
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Universidad de Antioquia |
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Misas Rivas, ElizabethWelsh, RoryForsberg, KaitlinLyman, MeghanChow, NancyBiología Celular y Molecular CIB U. de A. U. del Rosario2024-11-10T12:54:09Z2024-11-10T12:54:09Z2021Welsh RM, Misas E, Forsberg K, Lyman M, Chow NA. Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines. J Fungi (Basel). 2021 Mar 16;7(3):214. doi: 10.3390/jof7030214.https://hdl.handle.net/10495/4333210.3390/jof70302142309-608XABSTRACT: Candida auris is a multidrug-resistant pathogen that represents a serious public health threat due to its rapid global emergence, increasing incidence of healthcare-associated outbreaks, and high rates of antifungal resistance. Whole-genome sequencing and genomic surveillance have the potential to bolster C. auris surveillance networks moving forward. Laboratories conducting genomic surveillance need to be able to compare analyses from various national and international surveillance partners to ensure that results are mutually trusted and understood. Therefore, we established an empirical outbreak benchmark dataset consisting of 23 C. auris genomes to help validate comparisons of genomic analyses and facilitate communication among surveillance networks. Our outbreak benchmark dataset represents a polyclonal ¿ phylogeny with three subclades. The genomes in this dataset are from well-vetted studies that are supported by multiple lines of evidence, which demonstrate that the whole-genome sequencing data, phylogenetic tree, and epidemiological data are all in agreement. This C. auris benchmark set allows for standardized comparisons of phylogenomic pipelines, ultimately promoting effective C. auris collaborations.COL00009627 páginasapplication/pdfengMDPIBasilea, Suizahttp://creativecommons.org/licenses/by/2.5/co/https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic PipelinesArtículo de investigaciónhttp://purl.org/coar/resource_type/c_2df8fbb1https://purl.org/redcol/resource_type/ARThttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionCandida aurisMicosisMycosesFarmacorresistencia FúngicaDrug Resistance, FungalGenómicaGenomicsSecuenciación Completa del GenomaWhole Genome Sequencinghttps://id.nlm.nih.gov/mesh/D000088063https://id.nlm.nih.gov/mesh/D009181https://id.nlm.nih.gov/mesh/D025141https://id.nlm.nih.gov/mesh/D023281https://id.nlm.nih.gov/mesh/D000073336J. 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