Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology,Environmental Science & Technology

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Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology
Environmental Science & Technology ( IF 10.8 ) Pub Date : 2023-03-13 , DOI: 10.1021/acs.est.2c09739
Qin Qi ₁ , Timothy M Ghaly ₁ , Anahit Penesyan _{1,

2} , Vaheesan Rajabal _{1,

2} , Jeremy Ac Stacey ₁ , Sasha G Tetu _{1,

2} , Michael R Gillings _{1,

2}

Affiliation

Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbor class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction (PCR)) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multigene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts toward hotspots of class 1 integron-mediated dissemination of AMR.

中文翻译：

用单细胞融合-聚合酶链反应技术发现城市沿海水生环境中 1 类整合子的细菌宿主

水平基因转移 (HGT) 是细菌进化的关键驱动因素，通过跨类群遗传物质的传递。1 类整合子是与人为污染密切相关的遗传元件，并有助于通过 HGT 传播抗菌素耐药性 (AMR) 基因。尽管它们对人类健康具有重要意义，但仍缺乏可靠的、无需培养的监测技术来识别含有 1 类整合子的未开垦环境类群。我们开发了一种改良版的 epicPCR（乳液、配对分离和串联聚合酶链反应 (PCR)），它将从单个细菌细胞扩增的 1 类整合子与乳化水滴中相同细胞的分类学标记物联系起来。使用这种单细胞基因组方法和纳米孔测序，我们成功地将主要包含 AMR 基因的 1 类整合子基因盒阵列分配给受污染影响的沿海水样中的宿主。我们的工作展示了 epicPCR 在靶向变量、多基因目标位点方面的首次应用。我们还确定了根杆菌属作为 1 类整合子的新宿主。这些发现确立了 epicPCR 作为将分类群与环境细菌群落中的 1 类整合子联系起来的有力工具，并提供了将缓解工作导向 1 类整合子介导的 AMR 传播热点的潜力。

更新日期：2023-03-13

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