Table_1_High Prevalence of Human-Associated Escherichia coli in Wetlands Located in Eastern France.xlsx

Escherichia coli that are present in the rivers are mostly brought by human and animal feces. Contamination occurs mostly through wastewater treatment plant (WWTP) outflows and field amendment with sewage sludge or manure. However, the survival of these isolates in river-associated wetlands remains unknown. Here, we assessed E. coli population structure in low-anthropized wetlands located along three floodplains to identify the major source of contamination of wetlands, whose functioning is different from the rivers. We retrieved 179 E. coli in water samples collected monthly from 19 sites located in eastern France over 1 year. Phylogroups B1 and B2 were dominant in the E. coli population, while phylogroup A was dominant in isolates resistant to third-generation cephalosporins, which harbored the extended-spectrum β-lactamase (ESBL) encoding genes blaCTX–M–15 and blaCTX–M–27 in half of the cases. The high proportion of isolates from human source can be attributed to WWTP outflows and the spread of sewage sludge. We analyzed the distribution of the isolates belonging to the most human-associated phylogroups (B2 and D) on a phylogenetic tree of the whole species and compared it with that of isolates retrieved from patients and from WWTP outflows. The distribution of the three E. coli populations was similar, suggesting the absence of a specific population in the environment. Our results suggest that a high proportion of E. coli isolates that reach and survive in low-anthropized environments such as wetlands are from human source. To the best of our knowledge, this is the first study assessing E. coli contamination and resistance genes in natural freshwater wetlands.

河流中存在的大肠杆菌（Escherichia coli）大多由人类与动物粪便带入，其污染途径主要为污水处理厂（WWTP）尾水排放，以及农田施用污水污泥或粪肥。然而，此类菌株在河流关联湿地中的存活情况仍不明晰。本研究针对法国东部三处洪泛区沿线的低人为干扰湿地展开分析，旨在解析其大肠杆菌种群结构，以明确湿地污染的主要来源——湿地的生态功能与河流存在显著差异。研究团队在为期1年的监测周期内，对法国东部19个采样点的水样进行月度采样，共分离得到179株大肠杆菌。大肠杆菌种群中以系统群（phylogroup）B1和B2占主导地位；而对第三代头孢菌素耐药的菌株则以系统群A占优，其中半数菌株携带编码超广谱β-内酰胺酶（ESBL）的基因blaCTX–M–15与blaCTX–M–27。分离菌株中源自人类源的比例较高，这可归因于污水处理厂尾水排放与污水污泥的扩散。我们基于大肠杆菌全物种系统发育树，分析了与人类关联度最高的系统群（B2和D）菌株的分布特征，并将其与临床患者及污水处理厂尾水分离菌株的分布进行对比。三类大肠杆菌种群的分布特征相似，表明环境中并未存在特异性种群。本研究结果显示，抵达并存活于低人为干扰环境（如湿地）的大肠杆菌菌株，有较高比例源自人类活动。据我们所知，这是首个针对天然淡水湿地中大肠杆菌污染及耐药基因展开的评估研究。