Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes

Abstract In the fight to limit the global spread of antibiotic resistance, the assembly of environmental metagenomes has the potential to provide rich contextual information (e.g., taxonomic hosts, carriage on mobile genetic elements) about antibiotic resistance genes (ARG) in the environment. Howev...

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Autores principales:	Connor L. Brown, Ishi M. Keenum, Dongjuan Dai, Liqing Zhang, Peter J. Vikesland, Amy Pruden
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2b75f9d0f0ba43eebd37b5e835d68635
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spelling	oai:doaj.org-article:2b75f9d0f0ba43eebd37b5e835d686352021-12-02T13:30:17ZCritical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes10.1038/s41598-021-83081-82045-2322https://doaj.org/article/2b75f9d0f0ba43eebd37b5e835d686352021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83081-8https://doaj.org/toc/2045-2322Abstract In the fight to limit the global spread of antibiotic resistance, the assembly of environmental metagenomes has the potential to provide rich contextual information (e.g., taxonomic hosts, carriage on mobile genetic elements) about antibiotic resistance genes (ARG) in the environment. However, computational challenges associated with assembly can impact the accuracy of downstream analyses. This work critically evaluates the impact of assembly leveraging short reads, nanopore MinION long-reads, and a combination of the two (hybrid) on ARG contextualization for ten environmental metagenomes using seven prominent assemblers (IDBA-UD, MEGAHIT, Canu, Flye, Opera-MS, metaSpades and HybridSpades). While short-read and hybrid assemblies produced similar patterns of ARG contextualization, raw or assembled long nanopore reads produced distinct patterns. Based on an in-silico spike-in experiment using real and simulated reads, we show that low to intermediate coverage species are more likely to be incorporated into chimeric contigs across all assemblers and sequencing technologies, while more abundant species produce assemblies with a greater frequency of inversions and insertion/deletions (indels). In sum, our analyses support hybrid assembly as a valuable technique for boosting the reliability and accuracy of assembly-based analyses of ARGs and neighboring genes at environmentally-relevant coverages, provided that sufficient short-read sequencing depth is achieved.Connor L. BrownIshi M. KeenumDongjuan DaiLiqing ZhangPeter J. VikeslandAmy PrudenNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Connor L. Brown Ishi M. Keenum Dongjuan Dai Liqing Zhang Peter J. Vikesland Amy Pruden Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes
description	Abstract In the fight to limit the global spread of antibiotic resistance, the assembly of environmental metagenomes has the potential to provide rich contextual information (e.g., taxonomic hosts, carriage on mobile genetic elements) about antibiotic resistance genes (ARG) in the environment. However, computational challenges associated with assembly can impact the accuracy of downstream analyses. This work critically evaluates the impact of assembly leveraging short reads, nanopore MinION long-reads, and a combination of the two (hybrid) on ARG contextualization for ten environmental metagenomes using seven prominent assemblers (IDBA-UD, MEGAHIT, Canu, Flye, Opera-MS, metaSpades and HybridSpades). While short-read and hybrid assemblies produced similar patterns of ARG contextualization, raw or assembled long nanopore reads produced distinct patterns. Based on an in-silico spike-in experiment using real and simulated reads, we show that low to intermediate coverage species are more likely to be incorporated into chimeric contigs across all assemblers and sequencing technologies, while more abundant species produce assemblies with a greater frequency of inversions and insertion/deletions (indels). In sum, our analyses support hybrid assembly as a valuable technique for boosting the reliability and accuracy of assembly-based analyses of ARGs and neighboring genes at environmentally-relevant coverages, provided that sufficient short-read sequencing depth is achieved.
format	article
author	Connor L. Brown Ishi M. Keenum Dongjuan Dai Liqing Zhang Peter J. Vikesland Amy Pruden
author_facet	Connor L. Brown Ishi M. Keenum Dongjuan Dai Liqing Zhang Peter J. Vikesland Amy Pruden
author_sort	Connor L. Brown
title	Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes
title_short	Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes
title_full	Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes
title_fullStr	Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes
title_full_unstemmed	Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes
title_sort	critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/2b75f9d0f0ba43eebd37b5e835d68635
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Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes

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