摘要

       长达数十年的全球城市化趋势导致人们在室内度过越来越多的时间。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，并且与各种健康结果和抗生素抗性基因 (ARG) 相关。使用 DNA 测序最有效地筛选这些，但这种方法不能确定哪些微生物是可行的，也不能揭示它们的 ARG 是否真的可以传播给其他微生物。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，以及 2) 验证在活灰尘细菌中检测到的移动 ARG 的存在。具体来说，我们整合了来自 43 座不同建筑物的 166 个灰尘宏基因组。序列被组装、注释和筛选潜在的整合子、转座子、质粒和相关的 ARG。使用培养和分离基因组和质粒测序进一步研究了相同的灰尘样品。在粉尘分离基因组中检测到潜在的 ARG，我们使用长读长测序确认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 个具有潜在的移动性（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相关的灰尘分离物被证明含有携带 ARG 的质粒，该质粒通过宏基因组学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相结合以评估潜在移动 ARG 对公共卫生的风险的能力。

       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