背景
抗生素耐药性使常见的细菌感染无法治愈。野生动物可以在环境（例如水系统）中掺入并分散抗生素抗性细菌，而细菌又可以作为人类病原体抗性基因的储存库。人为活动可能会导致细菌抗性循环在自然环境中传播，包括通过释放人类废物，这是因为污水处理只能部分去除抗药性细菌。但是，目前支持这些效果的经验数据有限。在这里，我们使用大量RNA测序（元转录组学）来评估具有水生习性的鸟类肠道微生物组中功能可行的抗性基因在不同位置的多样性和表达水平。

结果
我们从澳大利亚南极的企鹅到澳大利亚的污水处理厂的鸭子中，发现了各地鸟类的抗生素抗性基因。比较分析表明，在废水处理厂饲养的鸟类携带的抗性基因负担最大，包括通常与多重耐药性质粒相关的基因，如aac（6）-Ib-cr基因。抗性基因负担的差异也反映了鸟类生态，分类学和微生物功能的各个方面。值得注意的是，以鸭子喂养的鸭子比通常在更多原始水域捕食的转石，长嘴鳄和企鹅携带更高的抗性基因丰度和多样性。

结论
这些转录组数据表明，即使经过处理，人类废物也可能导致抗生素抗性基因向野外传播。不同鸟类谱系中微生物组功能的差异也可能在野生鸟类携带的抗生素耐药性负担中起作用。总而言之，我们揭示了解释抗性基因的分布及其在人类与野生生物之间的交换途径的复杂因素，并表明元转录组学是访问整个微生物群落中功能性抗性基因的有价值的工具。

Background
Antibiotic resistance is rendering common bacterial infections untreatable. Wildlife can incorporate and disperse antibiotic-resistant bacteria in the environment, such as water systems, which in turn serve as reservoirs of resistance genes for human pathogens. Anthropogenic activity may contribute to the spread of bacterial resistance cycling through natural environments, including through the release of human waste, as sewage treatment only partially removes antibiotic-resistant bacteria. However, empirical data supporting these effects are currently limited. Here we used bulk RNA-sequencing (meta-transcriptomics) to assess the diversity and expression levels of functionally viable resistance genes in the gut microbiome of birds with aquatic habits in diverse locations.

Results
We found antibiotic resistance genes in birds from all localities, from penguins in Antarctica to ducks in a wastewater treatment plant in Australia. Comparative analysis revealed that birds feeding at the wastewater treatment plant carried the greatest resistance gene burden, including genes typically associated with multidrug resistance plasmids as the aac(6)-Ib-cr gene. Differences in resistance gene burden also reflected aspects of bird ecology, taxonomy, and microbial function. Notably, ducks, which feed by dabbling, carried a higher abundance and diversity of resistance genes than turnstones, avocets, and penguins, which usually prey on more pristine waters.

Conclusions
These transcriptome data suggest that human waste, even if it undergoes treatment, might contribute to the spread of antibiotic resistance genes to the wild. Differences in microbiome functioning across different bird lineages may also play a role in the antibiotic resistance burden carried by wild birds. In summary, we reveal the complex factors explaining the distribution of resistance genes and their exchange routes between humans and wildlife, and show that meta-transcriptomics is a valuable tool to access functional resistance genes in whole microbial communities.

https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-019-0649-1