Towards understanding microbial degradation of chloroquine in large saltwater systems.

Circulating saltwater aquariums hosting marine animals contain a wide range of microorganisms, which have strong implications on promoting animal health. In this study, we investigated the degradation of chloroquine phosphate, an anti-parasitic bath pharmaceutical used in saltwater quarantine and exhibition systems, and attributed the reduction in drug concentration to microbial degradation of chloroquine associated with pipeline microbial communities. To advance our knowledge on chloroquine degradation in aquatic systems, we conducted microbial and chemical analyses on three tropical saltwater systems. Our findings show that aquarium microbiome composition is shaped by sampling location (i.e., tank water and pipeline; PERMANOVA R2 = 0.09992, p = 0.0134), chloroquine dosing (PERMANOVA R2 = 0.05700, p = 0.0030), and whether the aquarium is occupied by marine animals (PERMANOVA R2 = 0.07019, p = 0.0009). Several microbial taxa belonging to the phyla Actinobacteria, Bacteroidetes, Chloroflexi, and Proteobacteria, along with functional genes related to pathways such as phenylethylamine degradation and denitrification, appeared to have differential (relative) abundance between samples where chloroquine degradation was observed and those without degradation (Benjamini-Hochberg adjusted p-value <0.05). Together, these results provide practical mitigation options to prevent or delay the development of chloroquine-degrading microbial communities in saltwater aquariums. Our results further demonstrate the need to improve our understanding of the interactions between nitrogen availability and microbial activity in saltwater systems.

Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota.

BACKGROUND: While indoor microbiomes impact our health and well-being, much remains unknown about taxonomic and functional transitions that occur in human-derived microbial communities once they are transferred away from human hosts. Toothbrushes are a model to investigate the potential response of oral-derived microbiota to conditions of the built environment. Here, we characterize metagenomes of toothbrushes from 34 subjects to define the toothbrush microbiome and resistome and possible influential factors. RESULTS: Toothbrush microbiomes often comprised a dominant subset of human oral taxa and less abundant or site-specific environmental strains. Although toothbrushes contained lower taxonomic diversity than oral-associated counterparts (determined by comparison with the Human Microbiome Project), they had relatively broader antimicrobial resistance gene (ARG) profiles. Toothbrush resistomes were enriched with a variety of ARGs, notably those conferring multidrug efflux and putative resistance to triclosan, which were primarily attributable to versatile environmental taxa. Toothbrush microbial communities and resistomes correlated with a variety of factors linked to personal health, dental hygiene, and bathroom features. CONCLUSIONS: Selective pressures in the built environment may shape the dynamic mixture of human (primarily oral-associated) and environmental microbiota that encounter each other on toothbrushes. Harboring a microbial diversity and resistome distinct from human-associated counterparts suggests toothbrushes could potentially serve as a reservoir that may enable the transfer of ARGs. Video abstract.

Mobilizable antibiotic resistance genes are present in dust microbial communities.

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.