Abstract
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.
Highlights
Antibiotic resistance is a public health priority worldwide, to the point where the World Health Organization has forecasted an entry into a post-antibiotic era within the current century [1]
Of potential microbial hosts in these environments, we focused on Staphylococcus, resulting in a parallel phenotypic characterization, genome, and plasmid sequencing in cultivable isolates that carry mobile genetic elements (MGE) and potentially mobile ARGs
Our results suggest that mobile ARG detected using metagenomics but not confirmed through cultivation and molecular biology approach, cannot constitute systematically a health risk and that further investigation with different complementary approaches, namely cultivation and molecular biology are needed to assess the actual real risk associated to the detection of ARG and mobile ARG in a public environment
Summary
Antibiotic resistance is a public health priority worldwide, to the point where the World Health Organization has forecasted an entry into a post-antibiotic era within the current century [1]. Antibiotics are intensively used from agriculture to medicine and have become widespread in the environment, enriching resistance factors in areas as diverse as hospitals, cattle stool, wastewater treatment plants, and drinking water [2,3,4]. In some settings, such as healthcare environments, the presence of antimicrobial resistant organisms is a direct risk to human health, either due to frank pathogens or organisms that become opportunistic in immunocompromised patients [5, 6]. While the effects related to the presence of these ARGs have been closely studied in hospitals [28,29,30,31,32,33,34], little information is available regarding the prevalence or transmissibility of ARGs in public spaces and individual households
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