Characterization using ultra-deep sequencing of the intra-host distribution of the mutations associated with H. pylori antibiotic resistance

TL;DR

This study uses ultra-deep sequencing to show that Helicobacter pylori populations in the same person's stomach are genetically diverse, suggesting the need for multiple biopsies to accurately test antibiotic resistance.

Contribution

The study is the first to use in-house high-throughput sequencing on clinical H. pylori biopsies to reveal intra-host genetic heterogeneity.

Findings

Antral diversification is higher than fundic for rpoB and rdxA genes.

Fundic diversification is higher than antral for 23S rRNA, rdxA, and rpoB genes.

Minority variants in H. pylori justify taking at least two biopsies for accurate antibiotic resistance testing.

Abstract

Helicobacter pylori is a slow-growing, gram-negative strictly pathogenic bacterium, which colonizes the stomachs of half the global population and is responsible for gastritis, peptic ulcer and even adenocarcinoma, Treatment of choice for eradication is a combination of PPIs and multiple antibiotic therapy. Recently, therapeutic failures began to be attributable to increased antibiotic resistance due to mutations in identified genes (rpoB, 16S rRNA coding gene, gyrA, 23S rRNA coding gene, pbp1A, frxA, rdxA).

This study aimed to determine, using ultra-deep sequencing, the distribution of mutations in patient s hospitalized or undergoing screening for H. pylori.

Gastric biopsies were obtained from two different anatomical regions (antrum/fundus) in 18 patients’ samples from 1998 to 2021, in four French hospitals. Following automated extraction, DNA of H. pylori was amplified using multiplexed PCR, before sequencing on the Illumina iSeq100 platform.

Antral diversification of H. pylori populations is significantly greater than that at the fundic level for rpoB and rdxA. Fundic diversification of H. pylori populations is significantly greater than that at the antral level for the 23S rRNA coding, rdxA and rpoB genes (p < 0.05), with inter-individual variation.Conversely, the 16S rRNA, frxA, gyrA and pbp1A genes exhibited no significant variation (p > 0.05).

This first study using in-house high-throughput sequencing of H. pylori on clinical biopsies from the same patients reinforces the hypothesis that the bacterial population within the same host is heterogeneous. The presence of minority variants justifies the need for at least two biopsies to ensure robust testing of the H. pylori antibiotic susceptibility profile.

The online version contains supplementary material available at 10.1186/s12941-025-00840-5.

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