摘要

       有效的污水处理对于限制耐抗生素细菌的环境传播至关重要。然而，在许多低收入和中等收入国家，仍有很大一部分污水未经处理就被排放到受纳水体中。在很大程度上缺乏对未经处理的城市废物的这种排放如何影响环境抵抗力的深入了解。在这里，我们强调了未经控制的部分处理和/或未经处理的废水排放对细菌群落结构和从流经印度浦那市的穆塔河收集的沉积物的抵抗力的影响。使用鸟枪宏基因组学，我们发现了大量（n = 175）水平可转移的抗生素抗性基因 (ARG)，包括碳青霉烯酶，如 NDM、VIM、KPC、OXA-48 和 IMP 类型。与上游站点相比，城市内河流沉积物中总 ARG 的相对丰度高出 30 倍。 44 个 ARGs，包括对替加环素、OXA-58 和 GES 型碳青霉烯酶产生抗性的 tet(X) 基因，在城市沉积物中的含量明显更高，而两个 ARGs 在上游地点更常见。最近发现的移动粘菌素抗性基因mcr-1仅在上游样本之一中检测到，而在城市样本中未检测到。除了 ARGs 外，在城市样本中还发现了更高丰度的各种移动遗传元件，包括整合子相关整合酶和 ISCR 转座酶，以及一些杀生物剂/金属抗性基因。毒力毒素基因以及包含许多病原体的细菌属在此处更为丰富；不动杆菌属通常与多药耐药性和医院感染有关，占 16S rRNA 读数的 29%，据我们所知，这在任何其他深度测序的宏基因组中是无与伦比的。不动杆菌的丰度与 OXA-58 碳青霉烯酶基因之间存在很强的相关性。我们的研究表明，未经处理的城市垃圾不受控制地排放会导致环境中 ARGs 的丰度和多样性的整体增加，包括那些赋予对最后抗药性抗生素产生抗性的物质。

       Efficient sewage treatment is critical for limiting environmental transmission of antibiotic-resistant bacteria. In many low and middle income countries, however, large proportions of sewage are still released untreated into receiving water bodies. In-depth knowledge of how such discharges of untreated urban waste influences the environmental resistome is largely lacking. Here, we highlight the impact of uncontrolled discharge of partially treated and/or untreated wastewater on the structure of bacterial communities and resistome of sediments collected from Mutha river flowing through Pune city in India. Using shotgun metagenomics, we found a wide array (n = 175) of horizontally transferable antibiotic resistance genes (ARGs) including carbapenemases such as NDM, VIM, KPC, OXA-48 and IMP types. The relative abundance of total ARGs was 30-fold higher in river sediments within the city compared to upstream sites. Forty four ARGs, including the tet(X) gene conferring resistance to tigecycline, OXA-58 and GES type carbapenemases, were significantly more abundant in city sediments, while two ARGs were more common at upstream sites. The recently identified mobile colistin resistance gene mcr-1 was detected only in one of the upstream samples, but not in city samples. In addition to ARGs, higher abundances of various mobile genetic elements were found in city samples, including integron-associated integrases and ISCR transposases, as well as some biocide/metal resistance genes. Virulence toxin genes as well as bacterial genera comprising many pathogens were more abundant here; the genus Acinetobacter, which is often associated with multidrug resistance and nosocomial infections, comprised up to 29% of the 16S rRNA reads, which to our best knowledge is unmatched in any other deeply sequenced metagenome. There was a strong correlation between the abundance of Acinetobacter and the OXA-58 carbapenemase gene. Our study shows that uncontrolled discharge of untreated urban waste can contribute to an overall increase of the abundance and diversity of ARGs in the environment, including those conferring resistance to last-resort antibiotics.

https://www.sciencedirect.com/science/article/abs/pii/S0043135417306334