Metagenomic evidence of the prevalence and distribution patterns of antimicrobial resistance genes in dairy agroecosystems

Antimicrobial resistance (AR) is a global problem with serious implications for public health. AR genes are frequently detected on animal farms but little is known about their origin and distribution patterns. We hypothesized that AR genes can transfer from animal feces to the environment via manure and to this end we characterized and compared the resistomes (collections of AR genes) of animal feces, manure, and soil samples collected from five dairy farms using a metagenomics approach. Resistomes constituted only up to 1% of the total gene content, but were variable by sector and also farm. Broadly, the identified AR genes were associated with18 antibiotic resistances classes across all samples; however, the most abundant genes were those encoding for multi-drug resistance (MDR) efflux systems (44.75%), followed by resistance to vancomycin (12.48%), tetracycline (10.52%), bacitracin (10.43%), beta-lactam resistance (7.12%) and MLS efflux pump (6.86%) antimicrobials. The AR gene profiles were variable between farms; farm 09 was categorized as a high risk farm as a greater proportion of AR genes were common to at least three sectors, suggesting possible transfer of organism(s)/horizontal transfer of AR genes. Taxonomic characterization of AR genes revealed that a majority of AR genes were associated with the phylum Proteobacteria. Nonetheless, there were several members of Bacteroidetes, particularly Bacteroides genus and several lineages from Firmicutes that carried similar AR genes in different sectors, suggesting a strong potential for horizontal transfer of AR genes between unrelated bacterial hosts in different sectors of the farms. Further studies are required to affirm the horizontal gene transfer mechanisms between microbiomes of different sectors in animal agroecosystems.

抗菌素耐药性（Antimicrobial Resistance, AR）是一道波及全球的公共卫生难题，其影响后果极为严峻。养殖场中频繁检出抗菌素耐药基因，但学界对其起源与分布模式仍知之甚少。我们提出假说：抗菌素耐药基因可通过粪便肥料从动物粪便传播至环境中。为此，我们采用宏基因组学（metagenomics）方法，对5座奶牛养殖场的动物粪便、粪便肥料以及土壤样本的耐药组（resistome，即抗菌素耐药基因集合）进行了表征与比较分析。
耐药组仅占总基因内容的1%以内，但在不同采样环节与养殖场间存在显著差异。总体而言，所有样本中检出的抗菌素耐药基因可归类为18类抗菌素耐药性类别；不过，丰度最高的基因为编码多重耐药（Multi-drug Resistance, MDR）外排系统的基因（占比44.75%），其次为针对万古霉素（vancomycin）、四环素（tetracycline）、杆菌肽（bacitracin）、β-内酰胺类（beta-lactam）耐药（7.12%）以及MLS外排泵（MLS efflux pump）类抗菌素的耐药基因。
不同养殖场的抗菌素耐药基因谱存在差异；09号养殖场被归类为高风险养殖场，因其有更大比例的耐药基因至少在3个采样环节中共同存在，这提示存在致病菌/抗菌素耐药基因水平转移的潜在可能。
对耐药基因的分类学表征显示，绝大多数耐药基因与变形菌门（Proteobacteria）相关。尽管如此，拟杆菌门（Bacteroidetes）的多个类群——尤其是拟杆菌属（Bacteroides）——以及厚壁菌门（Firmicutes）的多个演化支，在不同采样环节中均携带同类耐药基因，这表明在养殖场不同环节的非相关细菌宿主之间，抗菌素耐药基因存在极强的水平转移潜力。
未来仍需开展进一步研究，以证实农业动物生态系统（animal agroecosystems）中不同环节微生物组（microbiomes）之间的水平基因转移（horizontal gene transfer）机制。