摘要

     近几十年来全球城市化的趋势导致人们在室内的时间越来越多。因此，暴露于建筑物中的微生物，特别是灰尘中的微生物也在增加，并与各种各样的健康问题和抗生素抗性基因（ARGs）息息有关。用DNA测序法对这些细菌进行了最有效的筛选，但这种方法不能确定哪些微生物是活的，也不能确定它们所携带的ARG是否真的能传播到其他微生物。因此，我们进行了第一项研究：1）检查ARG在室内灰尘微生物群落中传播的可能性，2）验证在活的灰尘细菌中能检测到移动ARG的存在。具体来说，我们整合了43个不同建筑的166个灰尘基因组。通过组装序列、注释，并筛选潜在的整合子，转座子，质粒和相关的ARGs。利用培养、分离基因组和质粒测序对同一粉尘样品进行了进一步研究。在粉尘分离的基因组中检测到潜在的ARG，我们通过长阅读测序确定了它们在可移动基因元件上的位置。我们发现了183个ARGs，其中52个具有潜在的可移动性（与假定的质粒、转座子或整合子相关）。一个与赤道葡萄球菌相关的粉尘分离物被证明含有一个携带ARG的质粒，该ARG通过宏基因组检测并通过全基因组和质粒测序得到证实。因此，这项研究强调了将培养与宏基因组学结合起来来评估可移动的ARG对公共健康造成的潜在的风险。

    The decades-long global trend of urbanization has led to a population that spends increasing amounts of time indoors. Exposure to microbes in buildings, and specifically in dust, is thus also increasing, and has been linked to various health outcomes and to antibiotic resistance genes (ARGs). These are most efficiently screened using DNA sequencing, but this method does not determine which microbes are viable, nor does it reveal whether their ARGs can actually disseminate to other microbes. We have thus performed the first study to: 1) examine the potential for ARG dissemination in indoor dust microbial communities, and 2) validate the presence of detected mobile ARGs in viable dust bacteria. Specifically, we integrated 166 dust metagenomes from 43 different buildings. Sequences were assembled, annotated, and screened for potential integrons, transposons, plasmids, and associated ARGs. The same dust samples were further investigated using cultivation and isolate genome and plasmid sequencing. Potential ARGs were detected in dust isolate genomes, and we confirmed their placement on mobile genetic elements using long-read sequencing. We found 183 ARGs, of which 52 were potentially mobile (associated with a putative plasmid, transposon or integron). One dust isolate related to Staphylococcus equorum proved to contain a plasmid carrying an ARG that was detected metagenomically and confirmed through whole genome and plasmid sequencing. This study thus highlights the power of combining cultivation with metagenomics to assess the risk of potentially mobile ARGs for public health.

     https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1008211