摘要

高效的污水处理对于限制抗生素抗性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，仍有很大比例的污水未经处理就排放到接收水体中。关于这种未经处理的城市废物的排放如何影响环境抵抗力的深入知识很少。在这里，我们强调了部分处理和/或未处理废水的无控制排放对细菌群落结构和从流经印度浦那市的Mutha河收集的沉积物阻力的影响。利用散弹枪宏基因组学，我们发现了一系列广泛的( n = 175 )水平可转移的抗生素抗性基因( ARGs )，包括碳青霉烯酶，如NDM、VIM、KPC、OXA -48和IMP类型。全市河流沉积物中总ARGs的相对丰度是上游站点的30倍。44个ARGs，包括对替加环素、OXA - 58和GES型碳青霉烯酶具有抗性的Tet ( X)基因，在城市沉积物中明显更丰富，而两个ARGs在上游位点更常见。最近鉴定的可移动粘菌素抗性基因MCR -1仅在一个上游样品中检测到，而在城市样品中没有检测到。除ARGs外，在城市样品中还发现了更多的各种可移动遗传元件，包括整合子相关整合酶和ISCR转座子，以及一些杀生物剂/金属抗性基因。毒力毒素基因和多种病原菌的细菌属在这里比较丰富；通常与多药耐药和医院感染相关的真烟草占16S rRNA读数的29%，据我们所知，这在任何其他深测序的宏基因组中都是无与伦比的。不动杆菌的丰度与OXA -58碳青霉烯酶基因有很强的相关性。我们的研究表明，未经处理的城市废物的不加控制的排放可能有助于全面增加环境中精氨酸的丰度和多样性，包括那些对最后使用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 genusAcinetobacter, 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/pii/S0043135417306334