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<p>Frequently touched surfaces in indoor public environments may serve as reservoirs for potentially pathogenic microorganisms and antimicrobial resistance genes (ARGs), yet their microbial composition and functional potential remain insufficiently characterized. We performed paired DNA- and RNA-based metagenomic profiling of 25 high-contact surfaces across four functional areas of a hotel lobby in Arizona, USA, to differentiate total microbial communities from their transcriptionally enriched fraction. Bacterial taxa dominated all samples, with comparatively minor contributions from microbial eukaryotes (primarily fungi and protozoa) and viruses. DNA-based metagenomics revealed a diverse repertoire of resistance determinants, including genes conferring resistance to antibiotics, metals, biocides, and multidrug efflux systems. Although only a subset of these resistance determinants exhibited detectable transcriptional enrichment, the cDNA-derived microbial community showed lower alpha diversity and distinct compositional clustering relative to the DNA-derived community. Hotspot analysis identified elevator buttons, reception counters, and shared seating areas as sites with elevated microbial abundance and a higher prevalence of transcriptionally enriched potentially pathogenic taxa. Respiratory-associated, enteric, and vector-associated taxa were more highly represented in the cDNA-derived dataset, whereas electronic devices and other high-contact surfaces exhibited greater transcriptional enrichment among potentially pathogenic taxa. Co-occurrence network analysis revealed structured associations between specific bacterial taxa and ARG classes. Collectively, our findings demonstrate that although indoor public surfaces harbor a diverse resistome, only a limited fraction exhibited detectable transcriptional enrichment. Integrating metagenomic and metatranscriptomic approaches provides a more comprehensive characterization of microbial composition and transcriptional representation in built environments and may help inform evidence-based hygiene strategies for shared public settings.</p>

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Integrated DNA- and RNA-based characterization of microbial and resistome communities in a hotel lobby

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年8月4日

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  • Jose A. Freixas-Coutin,
  • Jin Seo,
  • Shweta Malik,
  • Carolyn Buckley,
  • Sophie Upson,
  • Stephanie Cooper,
  • Jonathan D. Sexton,
  • Kelly A. Reynolds

摘要

Frequently touched surfaces in indoor public environments may serve as reservoirs for potentially pathogenic microorganisms and antimicrobial resistance genes (ARGs), yet their microbial composition and functional potential remain insufficiently characterized. We performed paired DNA- and RNA-based metagenomic profiling of 25 high-contact surfaces across four functional areas of a hotel lobby in Arizona, USA, to differentiate total microbial communities from their transcriptionally enriched fraction. Bacterial taxa dominated all samples, with comparatively minor contributions from microbial eukaryotes (primarily fungi and protozoa) and viruses. DNA-based metagenomics revealed a diverse repertoire of resistance determinants, including genes conferring resistance to antibiotics, metals, biocides, and multidrug efflux systems. Although only a subset of these resistance determinants exhibited detectable transcriptional enrichment, the cDNA-derived microbial community showed lower alpha diversity and distinct compositional clustering relative to the DNA-derived community. Hotspot analysis identified elevator buttons, reception counters, and shared seating areas as sites with elevated microbial abundance and a higher prevalence of transcriptionally enriched potentially pathogenic taxa. Respiratory-associated, enteric, and vector-associated taxa were more highly represented in the cDNA-derived dataset, whereas electronic devices and other high-contact surfaces exhibited greater transcriptional enrichment among potentially pathogenic taxa. Co-occurrence network analysis revealed structured associations between specific bacterial taxa and ARG classes. Collectively, our findings demonstrate that although indoor public surfaces harbor a diverse resistome, only a limited fraction exhibited detectable transcriptional enrichment. Integrating metagenomic and metatranscriptomic approaches provides a more comprehensive characterization of microbial composition and transcriptional representation in built environments and may help inform evidence-based hygiene strategies for shared public settings.