{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,19]],"date-time":"2025-11-19T18:49:23Z","timestamp":1763578163482,"version":"3.45.0"},"reference-count":39,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2025,11,19]],"date-time":"2025-11-19T00:00:00Z","timestamp":1763510400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["INV-033578"],"award-info":[{"award-number":["INV-033578"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000877","name":"Rockefeller Foundation","doi-asserted-by":"publisher","award":["2021 HTH 018"],"award-info":[{"award-number":["2021 HTH 018"]}],"id":[{"id":"10.13039\/100000877","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    AMR is a growing concern in viral infections, where microbiome shifts contribute to resistance gene dissemination. While dengue and COVID-19, caused by ssRNA viruses, are not bacterial-driven, their resistome and microbial communities influence disease progression and AMR burden. This study analyzes the resistome and microbiome in 251 COVID-19 and 112 dengue patients using non-canonical metatranscriptomics. By mapping antimicrobial resistance genes (ARGs) and their transcriptionally active microbes (TAMs) hosts, we uncover greater ARG burden in COVID-19, particularly during mortality, with a diverse set of associated TAMs compared to dengue. MDR genes were prevalent, with beta-lactamase ARGs commonly detected in both infections. COVID-19 exhibited higher carbapenemase resistance genes (\n                    <jats:italic>NDM, OXA, VIM<\/jats:italic>\n                    ), while dengue was associated with TEM variants.\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    and\n                    <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n                    were dominant ARG hosts, with\n                    <jats:italic>Acinetobacter baumannii<\/jats:italic>\n                    in COVID-19 mortality and\n                    <jats:italic>Bacillus cereus<\/jats:italic>\n                    in severe dengue. These findings highlight resistome dynamics and emphasize the need for AMR surveillance in high-burden infections.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1013703","type":"journal-article","created":{"date-parts":[[2025,11,19]],"date-time":"2025-11-19T18:33:07Z","timestamp":1763577187000},"page":"e1013703","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Non-canonical Metatranscriptomic analysis of COVID-19 and Dengue reveals an expanded microbial and AMR landscape in COVID-19 mortality 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