Yin Xiaole, Li Liguan, Chen Xi, Liu Yang-Yu, Lam Tommy Tsan-Yuk, Topp Edward, Zhang Tong
Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China.
Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
Water Res. 2023 May 15;235:119875. doi: 10.1016/j.watres.2023.119875. Epub 2023 Mar 14.
The widely distributed antibiotic resistance genes (ARGs) were unevenly proliferated in various habitats. Great endeavors are needed to resolve the resistome features that can differentiate or connect different habitats. This study retrieved a broad spectrum of resistome profiles from 1723 metagenomes categorized into 13 habitats, encompassing industrial, urban, agricultural, and natural environments, and spanning most continents and oceans. The resistome features (ARG types, subtypes, indicator ARGs, and emerging mobilizable ARGs: mcr and tet(X)) in these habitats were benchmarked via a standardized workflow. We found that wastewater and wastewater treatment works were characterized to be reservoirs of more diverse genotypes of ARGs than any other habitats including human and livestock fecal samples, while fecal samples were with higher ARG abundance. Bacterial taxonomy composition was significantly correlated with resistome composition across most habitats. Moreover, the source-sink connectivities were disentangled by developing the resistome-based microbial attribution prediction model. Environmental surveys with standardized bioinformatic workflow proposed in this study will help comprehensively understand the transfer of ARGs in the environment, thus prioritizing the critical environments with high risks for intervention to tackle the problem of ARGs.
广泛分布的抗生素抗性基因（ARGs）在不同生境中呈不均衡增殖。需要付出巨大努力来解析能够区分或联系不同生境的抗性组特征。本研究从1723个宏基因组中获取了广谱的抗性组图谱，这些宏基因组被分为13种生境，涵盖工业、城市、农业和自然环境，涉及大部分大洲和海洋。通过标准化流程对这些生境中的抗性组特征（ARG类型、亚型、指示性ARGs以及新兴可移动ARGs：mcr和tet(X)）进行了基准测试。我们发现，与包括人类和牲畜粪便样本在内的任何其他生境相比，废水和污水处理厂的特征是具有更多样化基因型的ARGs储存库，而粪便样本的ARG丰度更高。在大多数生境中，细菌分类组成与抗性组组成显著相关。此外，通过开发基于抗性组的微生物溯源预测模型，理清了源-汇连通性。本研究提出的采用标准化生物信息学流程的环境调查将有助于全面了解ARGs在环境中的转移，从而确定具有高风险的关键环境进行优先干预，以解决ARGs问题。
