Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing.
Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing.
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DOI：
10.1186/s40168-017-0361-8
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发表时间：
2017-10-17
期刊：
影响因子：
15.5
通讯作者：
Morley PS
中科院分区：
文献类型：
--
作者：
Noyes NR;Weinroth ME;Parker JK;Dean CJ;Lakin SM;Raymond RA;Rovira P;Doster E;Abdo Z;Martin JN;Jones KL;Ruiz J;Boucher CA;Belk KE;Morley PS
鸟枪式元基因组测序越来越多地被用作评估抗菌素耐药性和毒力的生态水平动态的工具，并与微生物组分析相结合。人们对使用这种方法对抗菌素耐药性和病原微生物进行环境监测的兴趣也在增加。在已发表的元基因组数据集中，所有与抗性和毒力相关的序列的总数占所有测序的1%，这导致了对低丰度抗病毒体元件的检测受到限制。这项研究描述了抗性毒素体低丰度部分的范围和组成，使用了诱饵捕获和浓缩系统，该系统结合了独特的分子指数来计数DNA分子并校正浓缩偏差。诱饵捕获和浓缩系统的使用显著增加了抗病毒体的靶标测序，能够检测到额外的1441个基因材料，并揭示了抗病毒体的低丰度部分，与更传统的元基因组分析检测到的抗病毒体更加多样化和成分不同。抗病毒体的低丰度部分还含有对公众健康有重要意义的抗病基因，如超广谱β-内酰胺酶，这是传统的鸟枪式元基因组测序无法检测到的。此外，诱饵捕获和浓缩系统的使用使得能够识别用于区分样品来源的稀有抗性基因单倍型。这些结果表明，稀有的抗性-病毒体包含有价值和独特的信息，可用于抗性监测和群体遗传学研究。使用本研究中验证的诱饵捕获和浓缩系统获取稀有的抗药性-病毒体可以极大地促进我们对微生物抗药性动力学的理解。本文的在线版本(10.1186/s401680170361-8)包含向授权用户提供的补充材料。
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 limitations 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. 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. 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 resistome-virulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of microbiome-resistome dynamics. The online version of this article (10.1186/s40168-017-0361-8) contains supplementary material, which is available to authorized users.
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影响因子：
12.3
作者：
Fournier PE;Dubourg G;Raoult D
通讯作者：
Raoult D
影响因子：
64.8
作者：
Beaber, JW;Hochhut, B;Waldor, MK
通讯作者：
Waldor, MK
影响因子：
5.2
作者：
Baquero F;Tedim AP;Coque TM
通讯作者：
Coque TM
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：
4.4
作者：
Gow, Sheryl P.;Waldner, Cheryl L.;Boerlin, Patrick
通讯作者：
Boerlin, Patrick