{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T19:21:58Z","timestamp":1790882518133,"version":"4.1.0"},"reference-count":83,"publisher":"American Chemical Society (ACS)","issue":"23","license":[{"start":{"date-parts":[[2020,11,18]],"date-time":"2020-11-18T00:00:00Z","timestamp":1605657600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2020,11,18]],"date-time":"2020-11-18T00:00:00Z","timestamp":1605657600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2020,11,18]],"date-time":"2020-11-18T00:00:00Z","timestamp":1605657600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2017-68003-26498"],"award-info":[{"award-number":["2017-68003-26498"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1810886"],"award-info":[{"award-number":["1810886"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000089","name":"Office of International Science and Engineering","doi-asserted-by":"publisher","award":["1545756"],"award-info":[{"award-number":["1545756"]}],"id":[{"id":"10.13039\/100000089","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Comprehensive surveillance approaches are needed to assess sources, clinical relevance, and mobility of antibiotic resistance genes (ARGs) in watersheds. Here, we examined metrics derived from shotgun metagenomic sequencing and relationship to human fecal markers (HFMs; crAssphage, enterococci) and anthropogenic antibiotic resistance markers (AARMs; intI1, sul1) in three distinct Puerto Rican watersheds as a function of adjacent land use and wastewater treatment plant (WWTP) input 6 months after Hurricane Maria, a category V storm. Relative abundance and diversity of total ARGs increased markedly downstream of WWTP inputs, with ARGs unique to WWTP and WWTP-impacted river samples predominantly belonging to the aminoglycoside and \u03b2-lactam resistance classes. WWTP and other anthropogenic inputs were similarly associated with elevated resistome risk scores and mobility incidence (M%). Contig analysis indicated a wide variety of mobile \u03b2-lactam ARGs associated with pathogens downstream of WWTP discharge that were consistent with regional clinical concern, e.g., Klebsiella pneumoniae contigs containing KPC-2 within an ISKpn6-like transposase. HFMs and AARMs correlated strongly with the absolute abundance of total ARGs, but AARMs better predicted the majority of ARGs in general (85.4 versus &amp;lt;2%) and \u03b2-lactam ARGs in particular. This study reveals sensitive, quantitative, mobile, clinically relevant, and comprehensive targets for antibiotic resistance surveillance in watersheds.<\/jats:p>","DOI":"10.1021\/acs.est.0c05567","type":"journal-article","created":{"date-parts":[[2020,11,18]],"date-time":"2020-11-18T16:11:00Z","timestamp":1605715860000},"page":"15108-15119","source":"Crossref","is-referenced-by-count":50,"title":["Demonstrating\nan Integrated Antibiotic Resistance\nGene Surveillance Approach in Puerto Rican Watersheds Post-Hurricane\nMaria"],"prefix":"10.1021","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8752-6608","authenticated-orcid":true,"given":"Benjamin\nC.","family":"Davis","sequence":"first","affiliation":[{"name":"Virginia Tech , , , ,","place":["Blacksburg, Virginia, United States, 24060"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Virginia","family":"Riquelme","sequence":"additional","affiliation":[{"name":"Virginia Tech , , , ,","place":["Blacksburg, Virginia, United States, 24060"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Graciela","family":"Ramirez-Toro","sequence":"additional","affiliation":[{"name":"Inter American University , , , ,","place":["San Germa\u0301n, Puerto Rico, United States, 00683"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina","family":"Bandaragoda","sequence":"additional","affiliation":[{"name":"University of Washington , , , ,","place":["Seattle, Washington, United States, 98195"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1579-155X","authenticated-orcid":true,"given":"Emily","family":"Garner","sequence":"additional","affiliation":[{"name":"Virginia Tech , , , ,","place":["Blacksburg, Virginia, United States, 24060"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9325-4680","authenticated-orcid":true,"given":"William J.","family":"Rhoads","sequence":"additional","affiliation":[{"name":"Virginia Tech , , , ,","place":["Blacksburg, Virginia, United States, 24060"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2654-5132","authenticated-orcid":true,"given":"Peter","family":"Vikesland","sequence":"additional","affiliation":[{"name":"Virginia Tech , , , ,","place":["Blacksburg, Virginia, United States, 24060"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3191-6244","authenticated-orcid":true,"given":"Amy","family":"Pruden","sequence":"additional","affiliation":[{"name":"Virginia Tech , , , ,","place":["Blacksburg, Virginia, United States, 24060"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2020,11,18]]},"reference":[{"key":"2026081418152153300_cit1","first-page":"1","volume-title":"Global Action Plan on Antimicrobial Resistance","author":"World Health Organization (WHO)","year":"2015"},{"key":"2026081418152153300_cit2","doi-asserted-by":"publisher","first-page":"630","DOI":"10.1126\/science.aba3432","article-title":"Using Sewage for Surveillance of Antimicrobial Resistance","volume":"367","author":"Aarestrup","year":"2020","journal-title":"Science"},{"key":"2026081418152153300_cit3","volume-title":"Frontiers\n2017\ue5f8Emerging\nIssues of Environmental Concern","author":"Gaze","year":"2017"},{"key":"2026081418152153300_cit4","doi-asserted-by":"publisher","DOI":"10.1038\/nmicrobiol.2016.270","article-title":"Continental-Scale\nPollution of Estuaries with Antibiotic Resistance Genes","author":"Zhu","year":"2017","journal-title":"Nat. Microbiol."},{"key":"2026081418152153300_cit5","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1016\/j.envint.2017.10.016","article-title":"Review of Antibiotic\nResistance in China and Its Environment","volume":"110","author":"Qiao","year":"2018","journal-title":"Environ.\nInt."},{"key":"2026081418152153300_cit6","doi-asserted-by":"publisher","first-page":"1379","DOI":"10.1016\/j.chemosphere.2014.02.040","article-title":"Occurrence of Antibiotics\nand Antibiotic Resistance Genes in a Sewage Treatment Plant and Its\nEffluent-Receiving River","volume":"119","author":"Xu","year":"2015","journal-title":"Chemosphere"},{"key":"2026081418152153300_cit7","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1016\/j.vetmic.2014.02.017","article-title":"Functional\nMetagenomic Analysis Reveals Rivers Are a Reservoir for Diverse Antibiotic\nResistance Genes","volume":"171","author":"Amos","year":"2014","journal-title":"Vet. Microbiol."},{"key":"2026081418152153300_cit8","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1016\/j.tim.2013.11.001","article-title":"The Role\nof Aquatic Ecosystems as\nReservoirs of Antibiotic Resistance","volume":"22","author":"Marti","year":"2014","journal-title":"Trends\nMicrobiol."},{"key":"2026081418152153300_cit9","doi-asserted-by":"publisher","first-page":"11541","DOI":"10.1021\/es302657r","article-title":"Correlation\nbetween Upstream Human\nActivities and Riverine Antibiotic Resistance Genes","volume":"46","author":"Pruden","year":"2012","journal-title":"Environ. Sci. 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Technol."},{"key":"2026081418152153300_cit12","volume-title":"Geospatial Distribution of Antimicrobial\nResistance Genes in US Rivers and Streams","author":"Garland","year":"2019"},{"key":"2026081418152153300_cit13","doi-asserted-by":"publisher","first-page":"732","DOI":"10.1016\/j.scitotenv.2019.03.242","article-title":"Advancements\nin Mitigating Interference in Quantitative Polymerase Chain Reaction\n(QPCR) for Microbial Water Quality Monitoring","volume":"671","author":"Nappier","year":"2019","journal-title":"Sci. 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Microbiol."},{"key":"2026081418152153300_cit17","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1021\/acs.estlett.8b00329","article-title":"Elevated Levels\nof Pathogenic Indicator Bacteria and Antibiotic Resistance Genes after\nHurricane Harvey\u2019s Flooding in Houston","volume":"5","author":"Yu","year":"2018","journal-title":"Environ. Sci. Technol. Lett."},{"key":"2026081418152153300_cit18","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-07992-3","article-title":"Fecal Pollution\nCan Explain Antibiotic Resistance Gene Abundances in Anthropogenically\nImpacted Environments","author":"Karkman","year":"2019","journal-title":"Nat. Commun."},{"key":"2026081418152153300_cit19","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.1089\/ees.2017.0520","article-title":"An Environmental Science and Engineering\nFramework for Combating Antimicrobial Resistance","volume":"35","author":"Pruden","year":"2018","journal-title":"Environ. Eng. 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Microbiol."},{"key":"2026081418152153300_cit31","doi-asserted-by":"publisher","first-page":"2427","DOI":"10.1016\/j.watres.2006.04.017","article-title":"Effect of River Landscape\non the Sediment Concentrations of Antibiotics and Corresponding Antibiotic\nResistance Genes (ARG)","volume":"40","author":"Pei","year":"2006","journal-title":"Water Res."},{"key":"2026081418152153300_cit32","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1111\/j.1574-6968.2007.00992.x","article-title":"Quantification\nof Class 1 Integron Abundance in Natural Environments Using Real-Time\nQuantitative PCR","volume":"278","author":"Hardwick","year":"2008","journal-title":"FEMS Microbiol. Lett."},{"key":"2026081418152153300_cit33","doi-asserted-by":"publisher","first-page":"9146","DOI":"10.1021\/acs.est.7b02703","article-title":"Quantitative CrAssphage PCR Assays\nfor Human Fecal\nPollution Measurement","author":"Stachler","year":"2017","journal-title":"Environ. Sci. Technol."},{"key":"2026081418152153300_cit34","unstructured":"EPA\n          . Method\n1611: Enterococci in Water by TaqMan Quantitative Polymerase Chain\nReaction (QPCR) Assay. 2012."},{"key":"2026081418152153300_cit35","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0162442","article-title":"MetaStorm: A Public Resource for Customizable Metagenomics Annotation","volume":"11","author":"Arango-Argoty","year":"2016","journal-title":"PLoS One"},{"key":"2026081418152153300_cit36","doi-asserted-by":"publisher","first-page":"3348","DOI":"10.1128\/AAC.00419-13","article-title":"The Comprehensive\nAntibiotic Resistance Database","volume":"57","author":"McArthur","year":"2013","journal-title":"Antimicrob.\nAgents Chemother."},{"key":"2026081418152153300_cit37","doi-asserted-by":"publisher","first-page":"D57","DOI":"10.1093\/nar\/gkp938","article-title":"ACLAME: A CLAssification of Mobile\nGenetic Elements, Update 2010","volume":"38","author":"Leplae","year":"2010","journal-title":"Nucleic Acids\nRes."},{"key":"2026081418152153300_cit38","doi-asserted-by":"publisher","first-page":"612","DOI":"10.1038\/nature13377","article-title":"Bacterial\nPhylogeny Structures Soil\nResistomes across Habitats","volume":"509","author":"Forsberg","year":"2014","journal-title":"Nature"},{"key":"2026081418152153300_cit39","doi-asserted-by":"publisher","first-page":"5069","DOI":"10.1128\/AEM.03006-05","article-title":"Greengenes, a Chimera-Checked 16S\nRRNA Gene Database and Workbench Compatible with ARB","volume":"72","author":"Larsen","year":"2006","journal-title":"Appl. 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