Culture-free Helicobacter pylori genomics reveals within-host virulence heterogeneity and antibiotic resistance
Helicobacter pylori (Hp) infects over 40% of the world population and causes most cases of gastric cancer worldwide, yet fundamental questions about its within-host genetic diversity remain unresolved. Decades of work on Hp genomics depends on culturing clinical isolates, which can distort within-host genetic heterogeneity that informs Hp virulence and antimicrobial resistance. Culture-free alternatives have been limited by the extremely low Hp abundance in gastric tissue (usually 10^-3 to 10^-7 of total genomic DNA), making direct metagenomics prohibitively expensive and existing enrichment strategies insufficient for whole-genome recovery. Here we develop ultra-sensitive Hp sequencing (uHp-seq) for reconstructing Hp genomes directly from gastric biopsies. uHp-seq achieves a thousand-fold Hp DNA enrichment and recovers near-complete genomes across samples spanning orders of magnitude in Hp abundance. Notably, individual hosts may harbor multiple co-existing Hp strains or cagA EPIYA variants with different oncogenic potential. Resistance-associated variants for six commonly used antibiotics are resolved with greater accuracy than PCR-based and probe-based commercial panels. Applied to minimally invasive gastric string samples, uHp-seq delivers reliable resistance profiles without endoscopy, opening a path to genome-guided Hp eradication.
Authors
- Mi Ni (ORCID: https://orcid.org/0000-0002-8930-6887)
- Wendy A. Szymczak (ORCID: https://orcid.org/0000-0002-0747-1169)
- Amy D. Klion (ORCID: https://orcid.org/0000-0002-4986-5326)
- Jessica R. Bass (ORCID: https://orcid.org/0000-0002-5776-1690)
- Hao Chen (ORCID: https://orcid.org/0000-0003-0393-723X)
- ZHANG Yanchun
- Emmanuel Dias‐Neto (ORCID: https://orcid.org/0000-0001-5670-8559)
- Richard M. Peek (ORCID: https://orcid.org/0000-0002-4836-5960)
- Edward A. Mead (ORCID: https://orcid.org/0000-0002-4588-8096)
- Panchajanya Deshpande
- Wanjin Qiao (ORCID: https://orcid.org/0000-0002-5708-516X)
- Gang Fang (ORCID: https://orcid.org/0000-0002-2462-9124)
- Constanza Camargo
- Rachel Brody (ORCID: https://orcid.org/0000-0001-9280-517X)
- Judith Romero–Gallo (ORCID: https://orcid.org/0000-0002-6023-7793)
- Alejandro H. Corvalán (ORCID: https://orcid.org/0000-0001-5492-3853)
- Xuesong Zhang
- Martin J Blaser (ORCID: https://orcid.org/0000-0003-2447-2443)
- Yu Fan
- Yujie Liu
- Difei Wang
Institutions
- Rutgers, The State University of New Jersey (US)
- National Institutes of Health (US)
- Albert Einstein College of Medicine (US)
- Pontificia Universidad Católica de Chile (CL)
- Vanderbilt University (US)
- National Institute of Allergy and Infectious Diseases (US)
- Rutgers Cancer Institute (US)
- Division of Cancer Epidemiology and Genetics (US)
- Vanderbilt University Medical Center (US)
- Icahn School of Medicine at Mount Sinai (US)
Publication Details
- Journal
- medRxiv
- Published
- 2026-10-26
- DOI
- https://doi.org/10.64898/2026.10.23.26365955
- Primary Topic
- Helicobacter pylori-related gastroenterology studies
- Type
- preprint