摘要

虽然在临床环境中观察到病原体对抗生素耐药性增加的最急剧影响，但是越来越清楚，抗性基因播散的进化和传播动力学是一个生态问题。事实上，在过去的一个世纪中，食用动物，人类和环境中抗生素的稳定使用和滥用为富集每种相关微生物群中的抗性基因型提供了实质性的选择性压力。过度依赖基于文化的方法（临床抗性研究的标准）大大低估了这些抗性基因（或“抗体组”）的储存。为了解决这个问题，我们最近开发了高通量的宏基因组功能选择，辅助下一代测序，以表征由健康成人和儿童以及不同土壤的微生物群编码的抗体组。通过将这些分析与16S扩增子测序和深度鸟枪测序相结合，我们模拟了不同时间和生境中各种人为干扰对微生物群落及其抵抗体的传播和进化动态的影响。我们从这些不同微生物群落中的特定分类群中鉴定出的数百种抗性基因与主要人类病原体中发现的抗性基因相同，表明这些微生物之间最近的遗传交换。我们还发现了数千个功能验证的抗性基因，这些基因在遗传上是新颖的，但侧翼是涉及水平基因转移的基因，包括转座酶和整合酶。总之，这些发现突出显示了来自不同环境的微生物编码的大量抗生素抗体组，其可用于与病原体交换，并有可能严重加剧临床抗性问题。

While the most acute effects of increasing antibiotic resistance in pathogens are observed in clinical settings, it is becoming increasingly clear that the evolution and transmission dynamics of resistance gene dissemination is an ecological problem. Indeed, steady use and abuse of antibiotics over the past century in food animals, humans, and the environment has provided substantial selective pressure for enrichment of resistance genotypes in each of their associated microbiomes. An over-reliance on culture-based methods, the standard in the study of clinical resistance, has vastly underestimated these reservoirs of resistance genes (or ‘resistomes’). To address this issue, we have recently developed high-throughput metagenomic functional selections, aided by next-generation sequencing, to characterize resistomes encoded by the microbiota of healthy human adults and children as well as diverse soils. By combining these analyses with 16S amplicon sequencing and deep shotgun sequencing, we model the impact of various anthropogenic perturbations on the transmission and evolutionary dynamics of microbial communities and their resistomes across time and habitats. Hundreds of resistance genes we identify from specific taxa in these different microbial communities are identical to resistance genes found in major human pathogens, indicating recent genetic exchange between these microbes. We also find thousands of functionally validated resistance genes which are genetically novel, but flanked by genes involved in horizontal gene transfer, including transposases and integrases. Together, these findings highlight the substantial antibiotic resistome encoded by microbes from diverse environments, which is available for exchange with pathogens, with the potential to severely exacerbate the problems with clinical resistance.

http://www.fasebj.org/doi/abs/10.1096/fasebj.31.1_supplement.404.1