ORIGINAL RESEARCH article

Front. Microbiol.

Sec. Antimicrobials, Resistance and Chemotherapy

Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1604461

This article is part of the Research TopicMetagenomic Approach for Exploration of Antimicrobial Resistance in Uncultivated MicrobiotaView all 6 articles

ARGContextProfiler: Extracting and Scoring the Genomic Contexts of Antibiotic Resistance Genes using Assembly Graphs

Provisionally accepted
  • Virginia Tech, Blacksburg, United States

The final, formatted version of the article will be published soon.

Antibiotic resistance (AR) presents a global health challenge, necessitating an improved understanding of the ecology, evolution, and dissemination of antibiotic resistance genes (ARGs).Several tools, databases, and algorithms are now available to facilitate the identification of ARGs in metagenomic sequencing data; however, direct annotation of short-read data provides limited contextual information. Knowledge of whether an ARG is carried in the chromosome or on a specific mobile genetic element (MGE) is critical to understanding mobility, persistence, and potential for co-selection. Here we developed ARGContextProfiler, a pipeline designed to extract and visualize ARG genomic contexts. By leveraging the assembly graph for genomic neighborhood extraction and validating contexts through read mapping, ARGContextProfiler minimizes chimeric errors that are a common artifact of assembly outputs. Testing on real, synthetic, and semi-synthetic data, including long-read sequencing data from environmental samples, demonstrated that ARGContextProfiler offers superior accuracy, precision, and sensitivity compared to conventional assembly-based methods. ARGContextProfiler thus provides a powerful tool for uncovering the genomic context of ARGs in metagenomic sequencing data, which can be of value to both fundamental and applied research aimed at understanding and stemming the spread of AR. The source code of ARGContextProfiler is publicly available at GitHub.

Keywords: ARG, Assembly graph, Genomic context, pipeline, Antibiotc resistance

Received: 01 Apr 2025; Accepted: 28 Apr 2025.

Copyright: © 2025 Moumi, Ahmed, Brown, Pruden and Zhang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Nazifa Ahmed Moumi, Virginia Tech, Blacksburg, United States
Liqing Zhang, Virginia Tech, Blacksburg, United States

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