摘要
      饮用水源中的抗生素耐药性基因（ARGs）表明，可能存在危害人类健康的耐药性微生物。然而，对原位存在特定ARGs的解释在很大程度上是未知的，特别是它们的流行是如何受到当地微生物生态学、分类群组装和全群落基因转移的影响的。在这里，我们对太浦河流域的耐药性和细菌群落进行了表征，太浦河是全球特大城市上海的一个重要饮用水库。总的来说，随着河流向下游流向水库，ARG丰度显著降低（P<0.01），而水传播细菌作为温度和溶解氧条件的函数而聚集（|βNRI|>2.0 = 4.22）。基因组内ARGs的细菌宿主在整个流域保持在相同水平（每百万次读取60～70个基因组拷贝）。其中，假定的耐药病原体（如伯克霍尔德菌科）携带ARGs的混合物，表现出高传播概率（转移计数 = 126，P＜0.001），尤其是在微生物群落占优势的分类群中。这些假定的抗性病原体的密度在3.0到4.0之间 × 106细胞/L，与环境因素相比，受抗性和微生物组装结构的影响更明显（SEM，std coeffβ = 0.62 vs.0.12）。这项工作表明，微生物组装和抗性病原体在受纳水中抗性体的预防和传播中发挥着主要作用，这在制定减少集水区原位ARGs和抗性菌株的控制策略时值得更多关注。
Abstract
Antibiotic resistance genes (ARGs) in drinking water sources suggest the possible presence of resistant microorganisms that jeopardize human health. However, explanations for the presence of specific ARGs in situ are largely unknown, especially how their prevalence is affected by local microbial ecology, taxa assembly and community-wide gene transfer. Here, we characterized resistomes and bacterial communities in the Taipu River catchment, which feeds a key drinking water reservoir to a global megacity, Shanghai. Overall, ARG abundances decreased significantly as the river flowed downstream towards the reservoir (P < 0.01), whereas the waterborne bacteria assembled deterministically (|βNRI| > 2.0) as a function of temperature and dissolved oxygen conditions with the assembly-dominant taxa (e.g. Ilumatobacteraceae and Cyanobiaceae) defining local resistomes (P < 0.01, Cohen's D = 4.22). Bacterial hosts of intragenomic ARGs stayed at the same level across the catchment (60 ∼ 70 genome copies per million reads). Among them, the putative resistant pathogens (e.g. Burkholderiaceae) carried mixtures of ARGs that exhibited high transmission probability (transfer counts = 126, P < 0.001), especially with the microbial assembly-dominant taxa. These putative resistant pathogens had densities ranging form 3.0 to 4.0 × 106 cell/L, which was more pronouncedly affected by resistome and microbial assembly structures than environmental factors (SEM, std-coeff β = 0.62 vs. 0.12). This work shows that microbial assembly and resistant pathogens play predominant roles in prevelance and dissemination of resistomes in receiving water, which deserves greater attention in devisng control strategies for reducing in-situ ARGs and resistant strains in a catchment.

https://www.sciencedirect.com/science/article/abs/pii/S0043135422013045