City-scale monitoring of antibiotic resistance genes by digital PCR and metagenomics.

IF 6.2 2区 环境科学与生态学 Q1 GENETICS & HEREDITY Environmental Microbiome Pub Date : 2024-03-15 DOI:10.1186/s40793-024-00557-6
Lucia Maestre-Carballa, Vicente Navarro-López, Manuel Martinez-Garcia
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Abstract

Background: Anthropogenic activities significantly contribute to the dissemination of antibiotic resistance genes (ARGs), posing a substantial threat to humankind. The development of methods that allow robust ARG surveillance is a long-standing challenge. Here, we use city-scale monitoring of ARGs by using two of the most promising cutting-edge technologies, digital PCR (dPCR) and metagenomics.

Methods: ARG hot-spots were sampled from the urban water and wastewater distribution systems. Metagenomics was used to provide a broad view of ARG relative abundance and richness in the prokaryotic and viral fractions. From the city-core ARGs in all samples, the worldwide dispersed sul2 and tetW conferring resistance to sulfonamide and tetracycline, respectively, were monitored by dPCR and metagenomics.

Results: The largest relative overall ARG abundance and richness were detected in the hospital wastewater and the WWTP inlet (up to ≈6,000 ARGs/Gb metagenome) with a large fraction of unclassified resistant bacteria. The abundance of ARGs in DNA and RNA contigs classified as viruses was notably lower, demonstrating a reduction of up to three orders of magnitude compared to contigs associated to prokaryotes. By metagenomics and dPCR, a similar abundance tendency of sul2 and tetW was obtained, with higher abundances in hospital wastewater and WWTP input (≈125-225 ARGs/Gb metagenome). dPCR absolute abundances were between 6,000 and 18,600 copies per ng of sewage DNA (≈105-7 copies/mL) and 6.8 copies/mL in seawater near the WWTP discharging point.

Conclusions: dPCR was more sensitive and accurate, while metagenomics provided broader coverage of ARG detection. While desirable, a reliable correlation of dPCR absolute abundance units into metagenomic relative abundance units was not obtained here (r2 < 0.4) suggesting methodological factors that introduce variability. Evolutionary pressure does not significantly select the targeted ARGs in natural aquatic environments.

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通过数字 PCR 和元基因组学监测城市规模的抗生素耐药基因。
背景:人类活动极大地助长了抗生素耐药基因(ARG)的传播,对人类构成了巨大威胁。开发可对 ARG 进行有力监测的方法是一项长期挑战。在此,我们利用数字 PCR(dPCR)和元基因组学这两种最有前途的前沿技术,对 ARGs 进行城市规模的监测:方法:从城市供水和污水处理系统中采集 ARG 热点样本。方法:从城市供水和污水输配系统中采集了ARG热点地区的样本,并利用元基因组学对原核生物和病毒部分的ARG相对丰度和丰富度进行了广泛的研究。从所有样本中的城市核心 ARGs 中,通过 dPCR 和元基因组学监测了分散在世界各地的分别赋予磺胺和四环素抗性的 sul2 和 tetW:结果:在医院废水和污水处理厂进水口中检测到的 ARGs 相对总丰度和丰富度最高(高达 ≈6,000 ARGs/Gb 元基因组),其中有大量未分类的耐药菌。被归类为病毒的 DNA 和 RNA 等位基因中的 ARGs 丰度明显较低,与原核生物相关的等位基因相比减少了三个数量级。通过元基因组学和 dPCR,发现 sul2 和 tetW 的丰度趋势相似,但在医院废水和污水处理厂输入物中的丰度更高(≈125-225 ARGs/Gb元基因组)。dPCR 的绝对丰度为每 ng 污水 DNA 6,000 至 18,600 个拷贝(≈105-7 个拷贝/毫升),而在污水处理厂排放点附近的海水中为 6.8 个拷贝/毫升。dPCR绝对丰度单位与元基因组相对丰度单位之间没有可靠的相关性(r2
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来源期刊
Environmental Microbiome
Environmental Microbiome Immunology and Microbiology-Microbiology
CiteScore
7.40
自引率
2.50%
发文量
55
审稿时长
13 weeks
期刊介绍: Microorganisms, omnipresent across Earth's diverse environments, play a crucial role in adapting to external changes, influencing Earth's systems and cycles, and contributing significantly to agricultural practices. Through applied microbiology, they offer solutions to various everyday needs. Environmental Microbiome recognizes the universal presence and significance of microorganisms, inviting submissions that explore the diverse facets of environmental and applied microbiological research.
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