Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes
Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes
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DOI：
10.1128/aac.01324-19
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发表时间：
2020-01-01
影响因子：
4.9
通讯作者：
Wright, Gerard D.
中科院分区：
文献类型：
--
作者：
Guitor, Allison K.;Raphenya, Amogelang R.;Wright, Gerard D.
鉴定编码抗生素抗性元件的核苷酸序列并确定其与抗生素抗性的关联对于改善抗生素抗性的监测和监测趋势至关重要。目前在各种环境中研究抗生素耐药性的方法依赖于广泛的深度测序或费力地培养挑剔的生物体，这两种方法都是非常耗时的操作。需要一种准确且灵敏的方法来鉴定复杂宏基因组样品中的稀有和常见抗性元件。参考综合抗生素耐药性数据库中的序列，我们设计了一组37，826个探针，以特异性靶向临床相关细菌中与抗生素耐药性相关的2，000多个核苷酸序列。在由多重耐药细菌产生的DNA文库上测试该探针组以选择性地捕获耐药基因，与鸟枪测序相比，在更大的覆盖长度下可重复地产生更高数量的靶上读段。我们还从人类肠道微生物组样本中确定了其他耐药基因序列，这些序列单独测序无法检测到。我们捕获耐药基因组的方法能够在不同环境中灵敏地检测基因，其中编码抗生素耐药性的基因占宏基因组的不到0.1%。
Identification of the nucleotide sequences encoding antibiotic resistance elements and determination of their association with antibiotic resistance are critical to improve surveillance and monitor trends in antibiotic resistance. Current methods to study antibiotic resistance in various environments rely on extensive deep sequencing or laborious culturing of fastidious organisms, both of which are heavily time-consuming operations. An accurate and sensitive method to identify both rare and common resistance elements in complex metagenomic samples is needed. Referencing the sequences in the Comprehensive Antibiotic Resistance Database, we designed a set of 37,826 probes to specifically target over 2,000 nucleotide sequences associated with antibiotic resistance in clinically relevant bacteria. Testing of this probe set on DNA libraries generated from multidrug-resistant bacteria to selectively capture resistance genes reproducibly produced higher numbers of reads on target at a greater length of coverage than shotgun sequencing. We also identified additional resistance gene sequences from human gut microbiome samples that sequencing alone was not able to detect. Our method to capture the resistome enables a sensitive means of gene detection in diverse environments where genes encoding antibiotic resistance represent less than 0.1% of the metagenome.