Metagenomic co-assembly uncovers mobile antibiotic resistance genes in airborne microbiomes

Antibiotic resistance poses a major global threat to health and ecosystems. Genes that confer resistance and can move between microbes, known as mobile antibiotic resistance genes, are especially concerning, as they can spread into disease-causing bacteria. While many pathways for gene dispersal are known, airborne transport remains poorly understood due to the difficulty of collecting and analyzing low-biomass air samples. Here we sampled air during clear weather and Middle Eastern dust storms and applied a genomic method called co-assembly, which merges multiple datasets to improve gene detection. This approach enhanced gene recovery and revealed resistance genes against clinically important antibiotics, including aminoglycosides, beta-lactams, fosfomycin, glycopeptides, quinolones, and tetracyclines. However, most resistance genes were not clearly linked to mobile elements, reflecting the complexity of airborne microbial communities. Our findings suggest the potential for long-range airborne spread of antibiotic resistance and underscore the need for continued atmospheric monitoring and strategies to mitigate environmental dissemination. Co-assembling air metagenomes improves genome reconstruction and mobile genetic detection of antibiotic-resistant genes, according to genetic analysis of air samples under both dust-storm and clear conditions in Israel.