{
  "abstract": "Background: The inability to quantitatively distinguish endogenous within-host evolution (mutation, homologous recombination, and heterologous recombination) from superinfection as the origin of intrahost Helicobacter pylori genetic diversity remains a critical bottleneck constraining precision therapeutics.\n\nMethods: We developed a novel gene-based sequence difference ratio (SDR) framework utilizing single-nucleotide polymorphism counts and percentile-derived regional reference ranges to quantitatively classify the origins of mixed infections, including homologous and heterologous recombination (interspecies horizontal gene transfer). A dual-hospital cohort (34 patients, 114 flagellar isolates; 28 patients, 152 housekeeping isolates) was enrolled after excluding those with recent antibiotic or acid-suppressant exposure. Isolates were recovered using a patented single-colony culture system (US 18/278,425; EP 21927415.6) to eliminate conventional streaking bias. The model was validated using phylogenetic analysis, hierarchical clustering, and geographical divergence assessment.\n\nResults: The SDR framework achieved the first dedicated quantitative classification of five distinct H. pylori mixed infection mechanisms: mutation, homologous recombination, heterologous recombination, combined mutation–homologous recombination, and superinfection. Flagellar gene profiling identified a 51.5% mixed infection rate (17/33), with mutations as the dominant pattern (82.4%, 14/17); recombination involved the conserved flagellar genes flgE and flaA . Housekeeping gene analysis yielded a 14.8% superinfection rate (4/27), including the first documented triple-strain case; recombination involved the conserved housekeeping genes atpA and yphC . Strain H42 exhibited heterologous recombination in trpC (SDR 23.89–25.66%), providing the first nucleotide-resolution evidence of cross-species genetic exchange. Convergent mutations in fliD and mutY indicated niche-specific selective pressure. SDR thresholds were strongly correlated with evolutionary distance.\n\nConclusion: We report the first validated quantitative framework for distinguishing intrahost microbial evolution (mutation, homologous recombination, and heterologous recombination) from superinfection in H. pylori . These findings challenge the long-standing single-strain therapeutic paradigm, and this scalable approach lays a universal foundation for the precise management of infectious diseases.",
  "abstract_shown": true,
  "affiliations": [
    "Health Science Center, Ningbo University",
    "Laboratory of Helicobacter Pylori Section, Professional Committee of Clinical Microbiology, Chinese Society for Microbiology, Ningbo University",
    "Department of Gastrology, Ninghai First Hospital"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Haiying Gu"
    },
    {
      "affs": [
        2
      ],
      "name": "Zhouhong Shi"
    },
    {
      "affs": [
        2
      ],
      "name": "Weiqin Chen"
    },
    {
      "affs": [
        2
      ],
      "name": "Weiwei Ye"
    },
    {
      "affs": [
        2
      ],
      "name": "Cheng Zhang"
    },
    {
      "affs": [
        1
      ],
      "name": "Airu Li"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/7pcbsb0tb1hnd.bib",
  "cited_by": 0,
  "doi": "10.3389/fmicb.2026.1948969",
  "fulltext_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13718763/?tool=EBI",
  "id": "7pcbsb0tb1hnd",
  "issns": [
    "1664-302X"
  ],
  "landing_url": "https://www.frontiersin.org/articles/10.3389/fmicb.2026.1948969/full",
  "language": "eng",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Original Research"
    ],
    [
      "openalex",
      "2746|Helicobacter pylori-related gastroenterology studies"
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  "openalex": "W7220655912",
  "pdf_url": "https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2026.1948969/pdf",
  "pmcid": "PMC13718763",
  "pmid": "42960244",
  "published": "2026-10-06",
  "publisher": "Frontiers Media SA",
  "ris": "https://research.draconitic.com/paper/7pcbsb0tb1hnd.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:12Z",
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      "url": "https://www.frontiersin.org/articles/10.3389/fmicb.2026.1948969/full"
    },
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    {
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  "subjects": [
    {
      "field": "medicine",
      "origin": "openalex:2746|Helicobacter pylori-related gastroenterology studies",
      "subfield": "surgery"
    }
  ],
  "title": "A validated sequence difference ratio framework distinguishes intrahost evolution from superinfection in Helicobacter pylori mixed infections",
  "title_text": "A validated sequence difference ratio framework distinguishes intrahost evolution from superinfection in Helicobacter pylori mixed infections",
  "type": "peer-reviewed",
  "updated_at": "2026-11-02T12:22:43Z",
  "url": "https://research.draconitic.com/paper/7pcbsb0tb1hnd",
  "venue": "Frontiers in Microbiology",
  "versions": []
}