摘要

在过去十年中，由于下一代测序的发展，微生物学家已经从检测单一抗生素抗性基因（ARG）转向检测样品中所有已知的抗性基因。这提供了关于细菌总群中ARG的变化和相对丰度的大量数据。但是，为了在治疗或患者风险方面使用这些数据，必须在背景微生物群的背景下对其进行分析。使用定量PCR ARG芯片和16S rRNA扩增子测序，我们试图使用基因组工具来鉴定存在于健康成人粪便样品中的ARG和细菌。在检测到的42个ARG中，有12个适用于ARG的ResCon1类：cfxA，cphA，bacA，sul3，aadE，blaTEM，aphA1，aphA3，aph（2'） - Id，aacA / aphd，catA1和vanC。因此，我们将这12个基因描述为该人粪便微生物组的核心抗体组，并将剩余的30个ARG描述为粪便微生物群内的微生物群体的描述符。主要的门类和属与之前在健康人粪便样品中丰度最高的一致。检测到的大多数ARG与特定细菌分类群的存在相关，这些细菌分类群通过微生物群分析得到确认。我们承认在有限的样本范围内数据的局限性。然而，结合qPCR和微生物群分析的原理显示有助于确定ARG与特定分类群的关联。

Within the past decade, microbiologists have moved from detecting single antibiotic resistance genes (ARGs) to detecting all known resistance genes within a sample due to advances in next generation sequencing. This has provided a wealth of data on the variation and relative abundances of ARGs present in a total bacterial population. However, to use these data in terms of therapy or risk to patients, they must be analyzed in the context of the background microbiome. Using a quantitative PCR ARG chip and 16S rRNA amplicon sequencing, we have sought to identify the ARGs and bacteria present in a fecal sample of a healthy adult using genomic tools. Of the 42 ARGs detected, 12 fitted into the ResCon1 category of ARGs: cfxA, cphA, bacA, sul3, aadE, blaTEM, aphA1, aphA3, aph(2′)-Id, aacA/aphd, catA1, and vanC. Therefore, we describe these 12 genes as the core resistome of this person's fecal microbiome and the remaining 30 ARGs as descriptors of the microbial population within the fecal microbiome. The dominant phyla and genera agree with those previously detected in the greatest abundances in fecal samples of healthy humans. The majority of the ARGs detected were associated with the presence of specific bacterial taxa, which were confirmed using microbiome analysis. We acknowledge the limitations of the data in the context of the limited sample set. However, the principle of combining qPCR and microbiome analysis was shown to be helpful to identify the association of the ARGs with specific taxa.

https://www.liebertpub.com/doi/abs/10.1089/mdr.2017.0199