Elucidating selection processes for antibiotic resisitance in sewage treatment plants using metagenomics
Elucidating selection processes for antibiotic resisitance in sewage treatment plants using metagenomics
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DOI：
10.1016/j.scitotenv.2016.06.228
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发表时间：
2016-12-01
影响因子：
9.8
通讯作者：
Larsson, D. G. Joakim
中科院分区：
文献类型：
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作者：
Bengtsson-Palme, Johan;Hammaren, Rickard;Larsson, D. G. Joakim
污水处理厂（STP）已多次被认为是耐药细菌出现和传播的热点。一个关键的问题仍然没有答案是，如果选择压力在STP内，残留的抗生素或其他共选择剂引起的，是足以具体促进耐药性。为了解决这个问题，我们采用了鸟枪宏基因组测序的样品从不同步骤的治疗过程中，在三个瑞典STP。同时，分析了所选抗生素、杀生物剂和金属的浓度。我们发现，四环素和环丙沙星在流入物中的浓度高于抗性选择的预测浓度，然而，没有一致的富集抗性基因的任何特定类别的抗生素在STP中，无论是杀生物剂和金属抗性基因。与人类粪便相比，细菌群落的最大变化已经发生在污水管道中，表现为从专性厌氧菌到兼性厌氧菌的强烈转变。通过处理过程，对抗生素，杀虫剂和金属的抗性基因没有减少到与粪便细菌相同的程度。OXA-48基因在剩余污泥和消化污泥中始终富集。我们发现这一点令人担忧，因为OXA-48在瑞典临床分离株中仍然很少见，它对碳青霉烯类抗生素（我们最重要的一类抗生素）具有耐药性。总之，宏基因组学分析没有为特定抗生素抗性选择提供明确的支持。然而，更强的选择力影响总的分类组成，并与抗性基因丰度，限制了解释。因此，有必要对相关种属内的耐药/非耐药菌株进行全面分析。(C)© 2016 Elsevier B. V.版权所有。
Sewage treatment plants (STPs) have repeatedly been suggested as hotspots for the emergence and dissemination of antibiotic-resistant bacteria. A critical question still unanswered is if selection pressures within STPs, caused by residual antibiotics or other co-selective agents, are sufficient to specifically promote resistance. To address this, we employed shotgun metagenomic sequencing of samples from different steps of the treatment process in three Swedish STPs. In parallel, concentrations of selected antibiotics, biocides and metals were analyzed. We found that concentrations of tetracycline and ciprofloxacin in the influent were above predicted concentrations for resistance selection, however, there was no consistent enrichment of resistance genes to any particular class of antibiotics in the STPs, neither for biocide and metal resistance genes. The most substantial change of the bacterial communities compared to human feces occurred already in the sewage pipes, manifested by a strong shift from obligate to facultative anaerobes. Through the treatment process, resistance genes against antibiotics, biocides and metals were not reduced to the same extent as fecal bacteria. The OXA-48 gene was consistently enriched in surplus and digested sludge. We find this worrying as OXA-48, still rare in Swedish clinical isolates, provides resistance to carbapenems, one of our most critically important classes of antibiotics. Taken together, metagenomics analyses did not provide clear support for specific antibiotic resistance selection. However, stronger selective forces affecting gross taxonomic composition, and with that resistance gene abundances, limit interpretability. Comprehensive analyses of resistant/non-resistant strains within relevant species are therefore warranted. (C) 2016 Elsevier B.V. All rights reserved.