Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes
Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes
复制标题
DOI：
10.1038/ismej.2015.59
复制
发表时间：
2015-11-01
期刊：
影响因子：
11
通讯作者：
Zhang, Tong
中科院分区：
文献类型：
--
作者：
Li, Bing;Yang, Ying;Zhang, Tong
采用宏基因组学方法和网络分析方法，对10个典型环境中50个样品的抗生素耐药基因（ARG）的广谱谱及其共现模式进行了研究。共检测到18种ARG亚型260种，每拷贝16 S-rRNA基因ARG丰度范围为5.4 × 10（-6）~ 2.2 × 10（-1）拷贝。环境中的汞总丰度趋势与人类活动对这些环境的影响程度相吻合。从受影响较小的环境到受影响严重的环境，总的ARG丰度增加了三个数量级，即从3.2 × 10（-3）到3.1 × 10（0）拷贝ARG每拷贝16 S-rRNA基因。丰富的ARG与氨基糖苷类、杆菌肽、β-内酰胺类、氯霉素、大环内酯类-林可酰胺类-链阳性菌素、喹诺酮类、磺胺类和四环素相关，与人用或兽药/促进剂中广泛使用的抗生素一致。万古霉素耐药基因在不同环境中的广泛存在和丰度变化趋势可能暗示了万古霉素耐药基因的传播是由于万古霉素使用产生的选择压力。同时富集的12个ARG类型的成年鸡的粪便表明，在这个生产系统中的多种ARG的共选择。非度量多维尺度分析表明，属于同一环境的样品一般具有相似的ARG组成。基于网络分析所揭示的共现模式，提出以tetM和氨基糖苷类耐药蛋白作为ARG网络的枢纽，通过幂函数定量估计其他23种共现ARG亚型的丰度。
A metagenomic approach and network analysis was used to investigate the wide-spectrum profiles of antibiotic resistance genes (ARGs) and their co-occurrence patterns in 50 samples from 10 typical environments. In total, 260 ARG subtypes belonging to 18 ARG types were detected with an abundance range of 5.4 x 10(-6)-2.2 x 10(-1) copy of ARG per copy of 16S-rRNA gene. The trend of the total ARG abundances in environments matched well with the levels of anthropogenic impacts on these environments. From the less impacted environments to the seriously impacted environments, the total ARG abundances increased up to three orders of magnitude, that is, from 3.2 x 10(-3) to 3.1 x 10(0) copy of ARG per copy of 16S-rRNA gene. The abundant ARGs were associated with aminoglycoside, bacitracin, beta-lactam, chloramphenicol, macrolide-lincosamide-streptogramin, quinolone, sulphonamide and tetracycline, in agreement with the antibiotics extensively used in human medicine or veterinary medicine/promoters. The widespread occurrences and abundance variation trend of vancomycin resistance genes in different environments might imply the spread of vancomycin resistance genes because of the selective pressure resulting from vancomycin use. The simultaneous enrichment of 12 ARG types in adult chicken faeces suggests the coselection of multiple ARGs in this production system. Non-metric multidimensional scaling analysis revealed that samples belonging to the same environment generally possessed similar ARG compositions. Based on the co-occurrence pattern revealed by network analysis, tetM and aminoglycoside resistance protein, the hubs of the ARG network, are proposed to be indicators to quantitatively estimate the abundance of 23 other co-occurring ARG subtypes by power functions.