摘要

    几十年来全球城市化趋势已导致人们在室内花费越来越多的时间。因此，建筑物中，尤其是灰尘中的微生物暴露也在增加，并且与各种健康结果和抗生素抗性基因（ARG）相关。使用DNA测序可以最有效地筛选这些微生物，但是这种方法无法确定哪些微生物是可行的，也无法揭示其ARG是否可以真正传播到其他微生物。因此，我们进行了第一项研究，以：1）检查室内粉尘微生物群落中ARG传播的潜力，以及2）验证在可行的粉尘细菌中检测到的可移动ARG的存在。具体来说，我们整合了来自43个不同建筑物的166个尘埃基因组。组装，注释序列并筛选潜在的整合子，转座子，质粒和相关的ARG。使用培养，分离基因组和质粒测序进一步研究了相同的粉尘样品。在尘埃分离物基因组中检测到了潜在的ARGs，我们使用长时间阅读测序证实了它们在移动遗传元件上的位置。我们发现了183个ARG，其中52个具有潜在移动性（与推定的质粒，转座子或整合子相关）。一种与金黄色葡萄球菌有关的粉尘分离物被证明含有一种带有ARG的质粒，该质粒已通过基因组学检测并通过全基因组和质粒测序得到了证实。因此，这项研究强调了将栽培与宏基因组学相结合的能力，以评估可能移动的ARGs对公共卫生的风险。

    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