Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes.
Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes.
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靶富集长读段测序（TELSeq）将宏基因组中的抗菌素耐药基因置于背景中。
DOI：
10.1186/s40168-022-01368-y
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发表时间：
2022-11-02
期刊：
影响因子：
15.5
通讯作者：
Noyes, Noelle R.
中科院分区：
文献类型：
--
作者：
Slizovskiy, Ilya B.;Oliva, Marco;Settle, Jonathen K.;Zyskina, Lidiya, V;Prosperi, Mattia;Boucher, Christina;Noyes, Noelle R.
关键词：
宏基因组数据可用于分析微生物组内的高重要性基因。然而，目前的宏基因组工作流程产生的数据具有低灵敏度，并且不能准确地重建部分或全部基因组，特别是低丰度的那些。这些限制排除了共定位分析，即，表征宏基因组样品内基因和功能的基因组背景。基因组背景对于通过移动的遗传元件（MGE）与水平基因转移（HGT）相关的功能（例如抗微生物剂抗性（AMR））尤其重要。为了克服宏基因组学目前的局限性，我们提出了一种从宏基因组DNA中全面准确地重建抗菌素耐药基因（ARG）和MGE的方法，称为靶富集长读段测序（TELSeq）。使用不同样品类型的技术重复，我们将TELSeq的性能与非富集PacBio和短读段Illumina测序的性能进行了比较。TELSeq在不同的宏基因组中实现了比其他方法高得多的ARG回收率（>1,000倍）和灵敏度，揭示了广泛的耐药基因组谱，包括许多低丰度的ARG，包括一些具有公共卫生重要性的ARG。使用TELSeq产生的长读段，我们鉴定了位于低丰度ARG侧翼的许多MGE和货物基因，表明这些ARG可以通过HGT跨细菌分类群转移。TELSeq可以提供微生物耐药基因组背景的细微差别，因此在公共，动物和人类健康以及环境监测和AMR监测中具有广泛的应用。因此，这项技术代表了微生物组研究和应用的根本进步。视频摘要在线版本包含补充材料，可在10. 1186/s40168-022-01368-y获得。
Metagenomic data can be used to profile high-importance genes within microbiomes. However, current metagenomic workflows produce data that suffer from low sensitivity and an inability to accurately reconstruct partial or full genomes, particularly those in low abundance. These limitations preclude colocalization analysis, i.e., characterizing the genomic context of genes and functions within a metagenomic sample. Genomic context is especially crucial for functions associated with horizontal gene transfer (HGT) via mobile genetic elements (MGEs), for example antimicrobial resistance (AMR). To overcome this current limitation of metagenomics, we present a method for comprehensive and accurate reconstruction of antimicrobial resistance genes (ARGs) and MGEs from metagenomic DNA, termed target-enriched long-read sequencing (TELSeq). Using technical replicates of diverse sample types, we compared TELSeq performance to that of non-enriched PacBio and short-read Illumina sequencing. TELSeq achieved much higher ARG recovery (>1,000-fold) and sensitivity than the other methods across diverse metagenomes, revealing an extensive resistome profile comprising many low-abundance ARGs, including some with public health importance. Using the long reads generated by TELSeq, we identified numerous MGEs and cargo genes flanking the low-abundance ARGs, indicating that these ARGs could be transferred across bacterial taxa via HGT. TELSeq can provide a nuanced view of the genomic context of microbial resistomes and thus has wide-ranging applications in public, animal, and human health, as well as environmental surveillance and monitoring of AMR. Thus, this technique represents a fundamental advancement for microbiome research and application. Video abstract The online version contains supplementary material available at 10.1186/s40168-022-01368-y.
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影响因子：
5.2
作者：
Delmont TO;Eren AM;Maccario L;Prestat E;Esen ÖC;Pelletier E;Le Paslier D;Simonet P;Vogel TM
通讯作者：
Vogel TM
影响因子：
46.9
作者：
Bertrand, Denis;Shaw, Jim;Nagarajan, Niranjan
通讯作者：
Nagarajan, Niranjan
DOI：
10.1126/science.1220761
发表时间：
2012-08-31
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Forsberg KJ;Reyes A;Wang B;Selleck EM;Sommer MO;Dantas G
通讯作者：
Dantas G
影响因子：
16.6
作者：
Coutinho FH;Silveira CB;Gregoracci GB;Thompson CC;Edwards RA;Brussaard CPD;Dutilh BE;Thompson FL
通讯作者：
Thompson FL
影响因子：
4.6
作者：
Chung J;Son DS;Jeon HJ;Kim KM;Park G;Ryu GH;Park WY;Park D
通讯作者：
Park D