Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo
Abstract Environmental surveillance of antibiotic resistance genes (ARGs) is critical for understanding and mitigating the spread of antimicrobial resistance. Current short-read-based ARG profiling methods are limited in their ability to provide detailed host information, which is indispensable for...
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| Format: | Article |
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Nature Portfolio
2025-02-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-57088-y |
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| author | Xi Chen Xiaole Yin Xiaoqing Xu Tong Zhang |
| author_facet | Xi Chen Xiaole Yin Xiaoqing Xu Tong Zhang |
| author_sort | Xi Chen |
| collection | DOAJ |
| description | Abstract Environmental surveillance of antibiotic resistance genes (ARGs) is critical for understanding and mitigating the spread of antimicrobial resistance. Current short-read-based ARG profiling methods are limited in their ability to provide detailed host information, which is indispensable for tracking the transmission and assessing the risk of ARGs. Here, we present Argo, a novel approach that leverages long-read overlapping to rapidly identify and quantify ARGs in complex environmental metagenomes at the species level. Argo significantly enhances the resolution of ARG detection by assigning taxonomic labels collectively to clusters of reads, rather than to individual reads. By benchmarking the performance in host identification using simulation, we confirm the advantage of long-read overlapping over existing metagenomic profiling strategies in terms of accuracy. Using sequenced mock communities with varying quality scores and read lengths, along with a global fecal dataset comprising 329 human and non-human primate samples, we demonstrate Argo’s capability to deliver comprehensive and species-resolved ARG profiles in real settings. |
| format | Article |
| id | doaj-art-96c31401c101410b91d0d308b6127747 |
| institution | DOAJ |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-96c31401c101410b91d0d308b61277472025-08-20T03:10:49ZengNature PortfolioNature Communications2041-17232025-02-0116111410.1038/s41467-025-57088-ySpecies-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with ArgoXi Chen0Xiaole Yin1Xiaoqing Xu2Tong Zhang3Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong KongAbstract Environmental surveillance of antibiotic resistance genes (ARGs) is critical for understanding and mitigating the spread of antimicrobial resistance. Current short-read-based ARG profiling methods are limited in their ability to provide detailed host information, which is indispensable for tracking the transmission and assessing the risk of ARGs. Here, we present Argo, a novel approach that leverages long-read overlapping to rapidly identify and quantify ARGs in complex environmental metagenomes at the species level. Argo significantly enhances the resolution of ARG detection by assigning taxonomic labels collectively to clusters of reads, rather than to individual reads. By benchmarking the performance in host identification using simulation, we confirm the advantage of long-read overlapping over existing metagenomic profiling strategies in terms of accuracy. Using sequenced mock communities with varying quality scores and read lengths, along with a global fecal dataset comprising 329 human and non-human primate samples, we demonstrate Argo’s capability to deliver comprehensive and species-resolved ARG profiles in real settings.https://doi.org/10.1038/s41467-025-57088-y |
| spellingShingle | Xi Chen Xiaole Yin Xiaoqing Xu Tong Zhang Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo Nature Communications |
| title | Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo |
| title_full | Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo |
| title_fullStr | Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo |
| title_full_unstemmed | Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo |
| title_short | Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo |
| title_sort | species resolved profiling of antibiotic resistance genes in complex metagenomes through long read overlapping with argo |
| url | https://doi.org/10.1038/s41467-025-57088-y |
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