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The global crisis in antimicrobial resistance continues to grow. Estimating the risks of antibiotic resistance transmission across habitats is hindered by the lack of data on mobility and habitat‐specificity. Metagenomic samples of 6092 are analyzed to delineate the unique core resistomes from human feces and seven other habitats. This is found that most resistance genes (≈85%) are transmitted between external habitats and human feces. This suggests that human feces are broadly representative of the global resistome and are potentially a hub for accumulating and disseminating resistance genes. The analysis found that resistance genes with ancient horizontal gene transfer (HGT) events have a higher efficiency of transfer across habitats, suggesting that HGT may be the main driver for forming unique but partly shared resistomes in all habitats. Importantly, the human fecal resistome is historically different and influenced by HGT and age. The most important routes of cross‐transmission of resistance are from the atmosphere, buildings, and animals to humans. These habitats should receive more attention for future prevention of antimicrobial resistance. The study will disentangle transmission routes of resistance genes between humans and other habitats in a One Health framework and can identify strategies for controlling the ongoing dissemination and antibiotic resistance. [ABSTRACT FROM AUTHOR]

Chlorpyrifos is a widely used organophosphorus insecticide because of its high efficiency and overall effectiveness, and it is commonly detected in aquatic ecosystems. However, at present, the impact of chlorpyrifos on the aquatic micro-ecological environment is still poorly understood. Here, we established aquatic microcosm systems treated with 0.2 and 2.0 µg/L chlorpyrifos, and employed omics biotechnology, including metagenomics and 16S rRNA gene sequencing, to investigate the effect of chlorpyrifos on the composition and functional potential of the aquatic and zebrafish intestinal microbiomes after 7 d and 14 d chlorpyrifos treatment. After 14 d chlorpyrifos treatment, the aquatic microbial community was adversely affected in terms of its composition, structure, and stability, while its diversity showed only a slight impact. Most functions, especially capacities for environmental information processing and metabolism, were destroyed by chlorpyrifos treatment for 14 d. We observed that chlorpyrifos increased the number of risky antibiotic resistance genes and aggravated the growth of human pathogens. Although no clear effects on the structure of the zebrafish intestinal microbial community were observed, chlorpyrifos treatment did alter the metabolic capacity of the zebrafish. Our study highlights the ecological risk of chlorpyrifos to the aquatic environment and provides a theoretical basis for the rational use of pesticides in agricultural production. [Display omitted] • Chlorpyrifos disrupted aquatic microbial composition, structure, and stability. • Chlorpyrifos destroyed aquatic microbial functions. • Chlorpyrifos increeased risky ARGs and promoted human pathogens grow. • Chlorpyrifos altered the metabolic capacity of the zebrafish. [ABSTRACT FROM AUTHOR]

Antibiotic resistance genes (ARGs) and virulence factors (VFs) are critical threats to human health. Their abundance in aquatic ecosystems is maintained and enhanced via selection driven by environmental xenobiotics. However, their activity and expression in these environments under xenobiotic stress remains unknown. Here ARG and VF expression profiles were examined in aquatic microcosms under ciprofloxacin, glyphosate and sertraline hydrochloride treatment. Ciprofloxacin increased total expression of ARGs, particularly multidrug resistance genes. Total expression of ARGs and VFs decreased significantly under glyphosate and sertraline treatments. However, in opportunistic human pathogens, these agents increased expression of both ARGs and VFs. Xenobiotic pollutants, such as the compounds we tested here, have the potential to disrupt microbial ecology, promote resistance, and increase risk to human health. This study systematically evaluated the effects of environmental xenobiotics on transcription of ARGs and VFs, both of which have direct relevance to human health. Transcription of such genes has been overlooked in previous studies. [Display omitted] • ARGs and VFs were selectively expressed under different xenobiotic treatments. • Ciprofloxacin upregulated ARGs that confer resistance to wider range of antibiotics. • Glyphosate and sertraline hydrochloride induced ARGs and VFs expression in pathogens. • ARGs and VFs were co-expressed in the aquatic microbial community. • Changes of ARGs and VFs under xenobiotic treatments disrupted ecological functions. [ABSTRACT FROM AUTHOR]

Activated sludge comprises diverse bacteria, fungi, and other microorganisms, featuring a rich repertoire of genes involved in antibiotic resistance, pollutant degradation, and elemental cycling. In this regard, hybrid assembly technology can revolutionize metagenomics by detecting greater gene diversity in environmental samples. Nonetheless, the optimal utilization and comparability of genomic information between hybrid assembly and short- or long-read technology remain unclear. To address this gap, we compared the performance of the hybrid assembly, short- and long-read technologies, abundance and diversity of annotated genes, and taxonomic diversity by analysing 46, 161, and 45 activated sludge metagenomic datasets, respectively. The results revealed that hybrid assembly technology exhibited the best performance, generating the most contiguous and longest contigs but with a lower proportion of high-quality metagenome-assembled genomes than short-read technology. Compared with short- or long-read technologies, hybrid assembly technology can detect a greater diversity of microbiota and antibiotic resistance genes, as well as a wider range of potential hosts. However, this approach may yield lower gene abundance and pathogen detection. Our study revealed the specific advantages and disadvantages of hybrid assembly and short- and long-read applications in wastewater treatment plants, and our approach could serve as a blueprint to be extended to terrestrial environments. [Display omitted] • Higher-diversity microbiota was detected in the hybrid assembly. • Greater pathogen detection in short-read reads. • Long-read detection of increased gene abundance. • Hybrid assembly harbored a wider range of potential gene hosts. [ABSTRACT FROM AUTHOR]

As the most abundant organisms on Earth, phages play a key role in the evolution of bacterial antibiotic resistance. Although previous studies have demonstrated the molecular mechanisms of horizontal gene transfer mediated by mobile genetic elements, our understanding of the intertwined relationships between antibiotic resistance genes (ARGs) and phages is limited. In this study, we analysed 2781 metagenomic samples to reveal the composition and species interactions of phage communities in different habitats as well as their capacity to carry ARGs with health risks. The composition of phage communities varies in different habitats and mainly depends on environmental conditions. Terrestrial habitats display more complex and robust interactions between phages than aquatic and human-associated habitats, resulting in the highest biodiversity of phages. Several types of phages in certain taxa (4.95–7.67%, mainly belonging to Caudoviricetes) have the capacity to carry specific ARGs and display a high potential risk to human health, especially in human-associated habitats. Overall, our results provide insights into the assembly mechanisms of phage communities and their effects on the dissemination of antibiotic resistance. [Display omitted] • The composition of phage communities varies in different habitats. • Terrestrial-inhabiting phage communities display complex and robust interactions. • Caudoviricetes have the capacity to carry specific antibiotic resistance genes. • Caudoviricetes display a high potential risk to human health. [ABSTRACT FROM AUTHOR]

• Non-antibiotic antimicrobial agents influence antibiotic resistance in freshwater. • Silver nanoparticles inhibited the expression of antibiotic resistance genes. • Silver nanoparticles inhibited the expression of virulence factors. • Azoxystrobin increased the expression profiles of both ARGs and VFs. • The expressed antibiotic resistance genes were mostly classified into multidrug. The emergence and transmission of antibiotic resistance genes (ARGs) and virulence factors (VFs) pose health risks to the ecosystem and humans. Understanding how non-antibiotic antimicrobial agents drive the expression of ARGs and VFs in freshwater ecosystems, however, remains large challenges. Here, we employed freshwater microcosms and performed metatranscriptomic analysis to investigate the expression profiles of ARGs and VFs in response to pollutants of non-antibiotic antimicrobial agents, including silver nanoparticles (AgNPs) and azoxystrobin. Results showed that AgNPs significantly inhibited the total expression of ARGs and VFs and decreased the number of pathogenic microorganisms expressing these genes. Azoxystrobin increased the total expression of ARGs and VFs, as well as the number of pathogens expressing VFs, but concomitantly reduced the number of pathogens expressing ARGs. Two tested pollutants dramatically changed the expression profiles of ARGs and VFs, with distinct patterns: AgNPs displayed a negative effect, while azoxystrobin showed a positive effect on their expression profiles. Our findings provided a systematical insight to demonstrate that non-antibiotic antimicrobial agents with different mechanisms of action showed various effects on ARGs and VFs, and therefore represented different ecological risks. [Display omitted] [ABSTRACT FROM AUTHOR]