摘要

      抗生素耐药性是一种全球性的健康风险，但是动物农业对单个抗生素抗性等位基因的遗传背景和富集的影响仍不清楚。我们使用定量PCR和扩增测序，对美国实验室猪和中国三个地区猪场的44个微生物群中抗生素抗性、流动遗传因子和细菌发育相关基因进行了定量和测序。我们鉴定了高度丰富的抗性簇：共同产生的抗性组和移动遗传元件等位基因。例如，中国3个地区6类抗生素耐药基因的丰度与1类整合酶和is6100型转座子的丰度直接相关。这些抗性聚集基因可能在农场的微生物基因组中同域。抗性簇等位基因显著富集(高达1 - 10 %，与16SrRNA一样)，表明在这些群体中多药耐药细菌可能是普遍而不是例外。这种富集在很大程度上独立于系统发育成分；因此，许多细菌类群中可能存在抗性簇。此外，抗性簇含抗生素抗性基因，拥有抗生素抗性而与抗生素在农场上的特定用途无关。这些簇的选择可能是由于仅使用了含有抗性的大范围化学品。动物农业及其废物的规模，集群的丰富性和水平基因转移潜力，以及大量人口的附近，表明管理这种抗性库对于减少人类风险至关重要。

      Antibiotic resistance is a worldwide health risk, but the influence of animal agriculture on the genetic context and enrichment of individual antibiotic resistance alleles remains unclear. Using quantitative PCR followed by amplicon sequencing, we quantified and sequenced 44 genes related to antibiotic resistance, mobile genetic elements, and bacterial phylogeny in microbiomes from U.S. laboratory swine and from swine farms from three Chinese regions. We identified highly abundant resistance clusters: groups of resistance and mobile genetic element alleles that cooccur. For example, the abundance of genes conferring resistance to six classes of antibiotics together with class 1 integrase and the abundance of IS6100-type transposons in three Chinese regions are directly correlated. These resistance cluster genes likely colocalize in microbial genomes in the farms. Resistance cluster alleles were dramatically enriched (up to 1 to 10% as abundant as 16S rRNA) and indicate that multidrug-resistant bacteria are likely the norm rather than an exception in these communities. This enrichment largely occurred independently of phylogenetic composition; thus, resistance clusters are likely present in many bacterial taxa. Furthermore, resistance clusters contain resistance genes that confer resistance to antibiotics independently of their particular use on the farms. Selection for these clusters is likely due to the use of only a subset of the broad range of chemicals to which the clusters confer resistance. The scale of animal agriculture and its wastes, the enrichment and horizontal gene transfer potential of the clusters, and the vicinity of large human populations suggest that managing this resistance reservoir is important for minimizing human risk.

http://mbio.asm.org/content/7/2/e02214-15.short