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ORIGINAL RESEARCH article

Front. Microbiol.

Sec. Antimicrobials, Resistance and Chemotherapy

Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1461293

This article is part of the Research Topic Critical Assessment of Massive Data Analysis (CAMDA) Annual Conference 2023 View all 6 articles

Topological data analysis captures Horizontal Gene Transfer in Antimicrobial Resistance gene families among clinically relevant bacteria

Provisionally accepted
Shaday Guerrero-Flores Shaday Guerrero-Flores 1Haydeé Contreras-Peruyero Haydeé Contreras-Peruyero 1Jose Ibarra Jose Ibarra 2Jose Abel Lovaco-Flores Jose Abel Lovaco-Flores 3Francisco Nieto Francisco Nieto 1Fernando Fontove-Herrera Fernando Fontove-Herrera 2Nelly Selem-Mojica Nelly Selem-Mojica 1*
  • 1 Center of Mathematical Sciences, National Autonomous University of Mexico, Morelia, Mexico
  • 2 C3-Idea, Guanajuato, Mexico
  • 3 Unidad Irapuato (CINVESTAV), Irapuato, Guanajuato, Mexico

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

    Antibiotic resistance, projected to cause 10 million deaths annually by 2050, remains a critical health threat. Hospitals drive multidrug resistance via horizontal gene transfer. The Critical Assessment of Massive Data Analysis 2023 challenge presents resistance markers from 146 Johns Hopkins bacterial isolates, aiming to analyze resistomes without metadata or genomic sequences. Persistent homology, a topological data analysis method, effectively captures processes beyond vertical inheritance. A 1-hole is a topological feature representing a loop or gap in data, where relationships form a circular structure rather than a linear one. Unlike vertical inheritance, which lacks topological 1-holes, horizontal gene transfer generates distinct patterns.Since antimicrobial resistance genes often spread via horizontal gene transfer, we simulated vertical and horizontal inheritance in bacterial resistomes. The number of 1-holes from simulations and a documented horizontal gene transfer case were analyzed using persistence barcodes. In a simulated population of binary sequences, we observed that, on average, two 1-holes form for every group of three genomes undergoing horizontal gene transfer. Using a presence-absence gene table, we confirmed 1-holes in a documented case of horizontal gene transfer between two bacterial genera in a Pittsburgh hospital. Notably, the Critical Assessment of Massive Data Analysis resistomes of Klebsiella and Escherichia exhibit 1-holes, while Enterobacter shows none.Lastly, we provide a mathematical example of a non-tree-like space with no 1-holes. Persistent homology provides a framework for uncovering complex clinical patterns, offering an alternative to understanding resistance mobility using presence-absence data, which could be obtained through methods beyond genomic sequencing. GitHub: github.com/shadayguerrero/TDA Horizontal Genes Transfer .

    Keywords: Antimicrobial resistance (AMR), Persistence barcode, horizontal gene transfer (HGT), topological data analysis, Persistent homology

    Received: 08 Jul 2024; Accepted: 28 Mar 2025.

    Copyright: © 2025 Guerrero-Flores, Contreras-Peruyero, Ibarra, Lovaco-Flores, Nieto, Fontove-Herrera and Selem-Mojica. 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: Nelly Selem-Mojica, Center of Mathematical Sciences, National Autonomous University of Mexico, Morelia, Mexico

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

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