Novel clinically relevant antibiotic resistance genes associated with sewage sludge and industrial waste streams revealed by functional metagenomic screening.
Novel clinically relevant antibiotic resistance genes associated with sewage sludge and industrial waste streams revealed by functional metagenomic screening.
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DOI：
10.1016/j.envint.2019.105120
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发表时间：
2019-11
影响因子：
11.8
通讯作者：
Lihong Zhang;Lihong Zhang;L. Calvo-Bado;L. Calvo-Bado;Aimee K. Murray;G. Amos;G. Amos;P. Hawkey;E. Wellington;W. Gaze;W. Gaze
中科院分区：
文献类型：
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作者：
Lihong Zhang;Lihong Zhang;L. Calvo-Bado;L. Calvo-Bado;Aimee K. Murray;G. Amos;G. Amos;P. Hawkey;E. Wellington;W. Gaze;W. Gaze
越来越多的证据表明，人类活动可导致自然环境中细菌中抗菌素耐药基因(ARGs)的流行增加。许多环境研究已经使用下一代测序方法来对元基因组进行测序。然而，这种方法是有限的，因为它不能识别不同的未表征基因，也不能证明活性。环境元基因组中ARGs的特征对于理解抗药性的进化和传播是重要的，因为有几个临床上重要的抗药性基因起源于环境物种。本研究采用功能基因组学方法检测了城市污泥、污泥改良土壤、季铵盐类化合物对芦苇床沉积物影响较小的长期净化草地土壤中对超广谱β-内酰胺类抗生素和碳青霉烯类抗生素的抗性基因。在城市污泥、污泥改良土壤和氯仿污染土壤中检测到超广谱β-内酰胺酶和碳青霉烯酶基因，与临床重要的β-内酰胺酶基因有不同程度的同源性。对侧翼区域进行了测序，以确定潜在的寄主背景和遗传背景。在革兰氏阴性菌中发现了新的β-内酰胺酶基因，其中一个基因与插入序列ISPme1相邻，表明最近发生了动员事件和/或未来转移的可能性。污水污泥和富含季铵化合物(QAC)的工业废水似乎传播和/或选择了ESBL基因，而这些基因在长期净化的草原土壤中没有检测到。这项工作证实了自然环境是新的和可动员的抗性基因的储存库，这些基因可能对人类和动物的健康构成威胁。
A growing body of evidence indicates that anthropogenic activities can result in increased prevalence of antimicrobial resistance genes (ARGs) in bacteria in natural environments. Many environmental studies have used next-generation sequencing methods to sequence the metagenome. However, this approach is limited as it does not identify divergent uncharacterized genes or demonstrate activity. Characterization of ARGs in environmental metagenomes is important for understanding the evolution and dissemination of resistance, as there are several examples of clinically important resistance genes originating in environmental species. The current study employed a functional metagenomic approach to detect genes encoding resistance to extended spectrum β-lactams (ESBLs) and carbapenems in sewage sludge, sludge amended soil, quaternary ammonium compound (QAC) impacted reed bed sediment and less impacted long term curated grassland soil. ESBL and carbapenemase genes were detected in sewage sludge, sludge amended soils and QAC impacted soil with varying degrees of homology to clinically important β-lactamase genes. The flanking regions were sequenced to identify potential host background and genetic context. Novel β-lactamase genes were found in Gram negative bacteria, with one gene adjacent to an insertion sequence ISPme1, suggesting a recent mobilization event and/ the potential for future transfer. Sewage sludge and quaternary ammonium compound (QAC) rich industrial effluent appear to disseminate and/or select for ESBL genes which were not detected in long term curated grassland soils. This work confirms the natural environment as a reservoir of novel and mobilizable resistance genes, which may pose a threat to human and animal health.