摘要

抗生素耐药性一直是全球公共卫生关注的问题。河湖系统是一个紧密相连的陆地生态系统，由于易受人类活动的影响，是抗生素耐药基因（ARGs）和耐药病原菌传播途径的储库。目前，对河湖系统ARGs的流行、转移风险和来源缺乏系统的认识。在本研究中，我们重点研究了连通的河湖系统（中国北方的抚河和白洋接受湖）沉积物中ARGs的高通量剖面和源-库关系。为此，我们收集了40个表层沉积物进行宏基因组鸟枪测序。本文综合分析了河流-湖泊系统沉积物中ARGs的剖面和共生特征，以及携带ARGs的可移动基因元件（MGEs）及其潜在的耐药性扩散风险。CrAssphage是最近发现的一种噬菌体，可用于跟踪人类粪便中ARGs的流行情况。同时，将一种新的快速期望最大化微生物源跟踪（FEAST）方法与线性判别分析效应大小法（LEfSe）相结合，定量分析了河流沉积物对受纳湖泊中ARGs的贡献。结果表明，河湖系统沉积物中含有丰富多样的ARGs（24种，510个亚型），包括mcr-1、tetX和碳青霉烯酶等新兴ARGs类型。网络分析表明，在同一类型和不同类型之间，ARGs存在非随机共现模式。重要的是，许多携带MGE的种群被认为共同含有一个或多个ARGs，导致白洋湖比世界上许多湖泊具有更高的耐药性风险的潜力。污染源跟踪表明，河湖系统沉积物中ARGs的普遍存在可以用人类粪便污染的程度来解释，而根据分摊来估计，来自抚河的负荷输送对白洋接收湖贡献了80%以上的ARGs。

Antimicrobial resistance has been a global public health concern. The river-lake systems are one of the tightly connected terrestrial ecosystems and, appear to be reservoirs of antibiotic resistant genes (ARGs) and dispersal routes of resistant pathogens because they are easily impacted by human activities. Currently, systematic knowledge on the prevalence, transfer risk and source of ARGs in river-lake systems is largely lacking. In this study, we focused on the high-throughput profiling and source-sink relationship disentangling of ARGs in the sediments of an interconnected river-lake system (Fuhe River and its receiving Lake Baiyang in northern China). To this end, 40 surface sediments were collected for metagenomic shotgun sequencing. The profile and co-occurrence of ARGs in the sediments of the river-lake system were comprehensively characterized, as well as the mobile genetic elements (MGEs) carrying ARGs and their potential resistome dissemination risk. CrAssphage, a recently-discovered bacteriophage, was used to track human fecal pollution on the prevalence of ARGs. Meanwhile, a novel fast expectation-maximization microbial source tracking (FEAST) method was combined with linear discriminant analysis effect size method (LEfSe) for quantitatively apportioning the contribution of river sediment to the presence of ARGs in the receiving lake. Results showed abundant and diverse ARGs (24 types consisting of 510 subtypes) were detected in the sediments of the river-lake system, including some emerging ARGs such as mcr-1, tetX and carbapenemases types. Network analysis suggested non-random co-occurrence patterns of ARGs within the same type and among different types. Importantly, a number of MGE-carrying contigs were identified with jointly containing one or more ARGs, resulting in higher resistome risk potential in Lake Baiyang than many worldwide lakes. Source tracking indicated the prevalence of ARGs in the sediments of the river-lake system might be largely explained by the extent of human fecal contamination, and apportionment estimates the load transport from Fuhe River contributed more than 80% of ARGs to the receiving Lake Baiyang.

https://www.sciencedirect.com/science/article/pii/S0160412019337845