{
  "abstract": "Antimicrobial resistance (AMR) is a pressing global public health challenge. AMR is driven in part by the spread of antibiotic resistance genes (ARGs) through bacterial communities via mobile genetic elements. Influent wastewater is a promising sample type for monitoring AMR because it pools biological inputs shed by individuals across a population. However, untargeted sequencing approaches, such as metagenomic sequencing, often miss low-abundance targets such as clinically important ARGs. In this work, we develop a ligation-mediated PCR (LM-PCR) enrichment strategy that can directionally capture the genomic context surrounding an ARG using long-read sequencing. We applied this method to study the natural genomic context diversity of four clinically relevant ARGs (blaCTX-M, blaKPC, and blaOXA-48-like, and qnrS) across 13 wastewater treatment plants in Washington state, each sampled at two timepoints. Across all timepoints, LM-PCR identified distinct genomic context cluster families associated with each ARG, including seven for blaKPC, 11 for blaCTX-M, 24 for qnrS, and one for blaOXA-48-like. Notably, 11 of the 24 qnrS containing clusters were putatively novel, with no matches to existing sequences in public databases. Genomic contexts associated with blaCTX-M and blaKPC were comparatively conserved across clusters, whereas qnrS was associated with a more diverse set of genetic sequences. Together, these results demonstrate that LM-PCR can resolve low-abundance, ARG-associated genomic variation in complex wastewater samples and provide a scalable framework for tracking the dissemination of clinically relevant AMR determinants.",
  "abstract_shown": true,
  "affiliations": [
    "University of Washington"
  ],
  "article_type": "PUBLISHAHEADOFPRINT",
  "arxiv": null,
  "author_total": 15,
  "authors": [
    {
      "name": "M. E. O'Brien"
    },
    {
      "name": "B. Ahern"
    },
    {
      "name": "P. Brase"
    },
    {
      "name": "S. Kim"
    },
    {
      "name": "C. E. M. McCormack"
    },
    {
      "name": "D. Garcia"
    },
    {
      "name": "E. Keim"
    },
    {
      "name": "E. Dahl"
    },
    {
      "name": "M. Feck"
    },
    {
      "name": "K. Kauber"
    },
    {
      "name": "J. A. Marchand"
    },
    {
      "name": "R. S. Kantor"
    },
    {
      "name": "A. J. Pickering"
    },
    {
      "name": "B. McArdle"
    },
    {
      "affs": [
        0
      ],
      "name": "E. R. Fuhrmeister"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/e50ek2xs06r8z.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.09.26361541",
  "fulltext_url": "https://www.medrxiv.org/content/10.64898/2026.09.09.26361541v1.full",
  "id": "e50ek2xs06r8z",
  "issns": [],
  "landing_url": "https://www.medrxiv.org/content/10.64898/2026.09.09.26361541v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "medrxiv",
      "occupational and environmental health"
    ],
    [
      "openalex",
      "2310|Pharmaceutical and Antibiotic Environmental Impacts"
    ]
  ],
  "openalex": "W7212450518",
  "pdf_url": "https://www.medrxiv.org/content/10.64898/2026.09.09.26361541v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-09",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/e50ek2xs06r8z.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:30Z",
      "native_id": "10.64898/2026.09.09.26361541",
      "source": "medrxiv",
      "url": "https://www.medrxiv.org/content/10.64898/2026.09.09.26361541v1"
    }
  ],
  "subjects": [
    {
      "field": "medicine",
      "origin": "medrxiv:occupational and environmental health",
      "subfield": "epidemiology-public-health"
    }
  ],
  "title": "Resolving the Genomic Context of Clinically Relevant Antibiotic Resistance Genes in Wastewater with Ligation-Mediated PCR",
  "title_text": "Resolving the Genomic Context of Clinically Relevant Antibiotic Resistance Genes in Wastewater with Ligation-Mediated PCR",
  "type": "preprint",
  "updated_at": "2026-10-30T12:18:30Z",
  "url": "https://research.draconitic.com/paper/e50ek2xs06r8z",
  "venue": "medRxiv",
  "versions": []
}