Assessment of target-enrichment library preparation and next-generation sequencing of paraffin-embedded gastric biopsies for H. pylori diagnosis and evaluation of virulome and resistome.

ABSTRACT: The diagnosis of Helicobacter pylori infection from gastric biopsies requires polymerase chain reaction or culture. However, culture is often unsuccessful due to the bacterial fragility and complex growth requirements. Next-generation sequencing (NGS), performed on primary clinical samples, offers a promising alternative for analysis of the bacterial resistome. In this study, we describe the adaptation of a target-enrichment library preparation and NGS workflow for use on formalin-fixed, paraffin-embedded (FFPE) gastric biopsies to investigate both the H. pylori resistome and virulome. In total, 30 FFPE gastric biopsy samples were analyzed, all derived from patients infected with H. pylori, the majority of whom presented with gastritis or epigastric pain. The Agilent SureSelect XT protocol

SUBMITTER: Gillet L 

PROVIDER: S-EPMC12615785 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature