The structure and diversity of human, animal and environmental resistomes.
The structure and diversity of human, animal and environmental resistomes.
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DOI：
10.1186/s40168-016-0199-5
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发表时间：
2016-10-07
期刊：
影响因子：
15.5
通讯作者：
Larsson DG
中科院分区：
文献类型：
--
作者：
Pal C;Bengtsson-Palme J;Kristiansson E;Larsson DG
抗生素耐药基因（ARG）广泛存在，但仅在病原体中存在时才会引起问题。抗生素耐药性的选择和传播经常发生的环境可能以水平可转移的ARG的高丰度和多样性为特征。然而，包括人类和动物在内的大多数类型的环境缺乏关于精氨酸的大规模定量数据，关于抗潜在共选择剂（如杀生物剂和金属）的抗性基因的数据也是如此。这种缺乏妨碍了对风险环境的有效识别。我们提供了来自人类（n = 350）、动物（n = 145）和外部环境（n = 369）的864个宏基因组的抗性基因、移动的遗传元件（MGE）和细菌分类组成的全面表征，所有宏基因组均使用Illumina技术进行深度测序。环境类型在抗性谱和细菌群落组成方面表现出明显的差异。人类和动物微生物群落的特点是有限的分类多样性和低丰度和多样性的杀生物剂/金属抗性基因和MGE，但相对较高丰度的ARG。与此相反，外部环境表现出一贯高的分类多样性，这反过来又与高多样性的杀生物剂/金属抗性基因和MGE。水、沉积物和土壤中的已知ARGs一般相对丰度较低，种类较少，而废水/污泥与人类肠道相当。ARG相对丰度和/或多样性最大的环境，包括编码对最后抗生素耐药性的基因，是那些受到工业抗生素污染的环境和来自北京烟雾事件的有限一组深度测序的空气样本。我们的研究将空气和有害生物污染的环境确定为未充分调查的传播途径和抗生素耐药性的储存库。外部环境的高度分类和遗传多样性支持了这样一种假设，即这些环境也形成了未知抗性基因的巨大来源，并有可能在未来转移到病原体中。本文的在线版本（doi：10.1186/s40168-016-0199-5）包含补充材料，可供授权用户使用。
Antibiotic resistance genes (ARGs) are widespread but cause problems only when present in pathogens. Environments where selection and transmission of antibiotic resistance frequently take place are likely to be characterized by high abundance and diversity of horizontally transferable ARGs. Large-scale quantitative data on ARGs is, however, lacking for most types of environments, including humans and animals, as is data on resistance genes to potential co-selective agents, such as biocides and metals. This paucity prevents efficient identification of risk environments. We provide a comprehensive characterization of resistance genes, mobile genetic elements (MGEs) and bacterial taxonomic compositions for 864 metagenomes from humans (n = 350), animals (n = 145) and external environments (n = 369), all deeply sequenced using Illumina technology. Environment types showed clear differences in both resistance profiles and bacterial community compositions. Human and animal microbial communities were characterized by limited taxonomic diversity and low abundance and diversity of biocide/metal resistance genes and MGEs but a relatively high abundance of ARGs. In contrast, external environments showed consistently high taxonomic diversity which in turn was linked to high diversity of both biocide/metal resistance genes and MGEs. Water, sediment and soil generally carried low relative abundance and few varieties of known ARGs, whereas wastewater/sludge was on par with the human gut. The environments with the largest relative abundance and/or diversity of ARGs, including genes encoding resistance to last resort antibiotics, were those subjected to industrial antibiotic pollution and a limited set of deeply sequenced air samples from a Beijing smog event. Our study identifies air and antibiotic-polluted environments as under-investigated transmission routes and reservoirs for antibiotic resistance. The high taxonomic and genetic diversity of external environments supports the hypothesis that these also form vast sources of unknown resistance genes, with potential to be transferred to pathogens in the future. The online version of this article (doi:10.1186/s40168-016-0199-5) contains supplementary material, which is available to authorized users.
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影响因子：
10.4
作者：
Chapin A;Rule A;Gibson K;Buckley T;Schwab K
通讯作者：
Schwab K
影响因子：
10.4
作者：
Ashbolt NJ;Amézquita A;Backhaus T;Borriello P;Brandt KK;Collignon P;Coors A;Finley R;Gaze WH;Heberer T;Lawrence JR;Larsson DG;McEwen SA;Ryan JJ;Schönfeld J;Silley P;Snape JR;Van den Eede C;Topp E
通讯作者：
Topp E
影响因子：
11.8
作者：
Cheng, Zhen;Luo, Lina;Hao, Jiming
通讯作者：
Hao, Jiming
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