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Recently, therapeutic failures began to be attributable to increased antibiotic resistance due to mutations in identified genes\n (rpoB<\/jats:italic>\n , 16S rRNA coding gene,\n gyrA<\/jats:italic>\n , 23S rRNA coding gene,\n pbp1A<\/jats:italic>\n ,\n frxA<\/jats:italic>\n ,\n rdxA)<\/jats:italic>\n .\n <\/jats:p>\n <\/jats:sec>\n \n Objectives<\/jats:title>\n \n This study aimed to determine, using ultra-deep sequencing, the distribution of mutations in patient s hospitalized or undergoing screening for\n H. pylori<\/jats:italic>\n .\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n Gastric biopsies were obtained from two different anatomical regions (antrum\/fundus) in 18 patients\u2019 samples from 1998 to 2021, in four French hospitals. Following automated extraction, DNA of\n H. pylori<\/jats:italic>\n was amplified using multiplexed PCR, before sequencing on the Illumina iSeq100 platform.\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n Antral diversification of\n H. pylori<\/jats:italic>\n populations is significantly greater than that at the fundic level for\n rpoB<\/jats:italic>\n and\n rdxA<\/jats:italic>\n . Fundic diversification of\n H. pylori<\/jats:italic>\n populations is significantly greater than that at the antral level for the 23S rRNA coding,\n rdxA<\/jats:italic>\n and\n rpoB<\/jats:italic>\n genes (\n p<\/jats:italic>\n \u2009<\u20090.05), with inter-individual variation.Conversely, the 16S rRNA, frxA,\n gyrA<\/jats:italic>\n and pbp1A genes exhibited no significant variation (\n p<\/jats:italic>\n > 0.05).\n <\/jats:p>\n <\/jats:sec>\n \n Discussion<\/jats:title>\n \n This first study using in-house high-throughput sequencing of\n H. pylori<\/jats:italic>\n 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\n H. pylori<\/jats:italic>\n antibiotic susceptibility profile.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.1186\/s12941-025-00840-5","type":"journal-article","created":{"date-parts":[[2026,1,22]],"date-time":"2026-01-22T18:45:36Z","timestamp":1769107536000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Characterization using ultra-deep sequencing of the intra-host distribution of the mutations associated with H. pylori antibiotic resistance"],"prefix":"10.1186","volume":"25","author":[{"given":"Laura","family":"Chaufour","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra","family":"Herve","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Birama","family":"Ndiaye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucie","family":"Karayan-Tapon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M\u00e9d\u00e9ric","family":"Briand","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fr\u00e9d\u00e9rique","family":"Lartigue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christophe","family":"Burucoa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maxime","family":"Pichon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,1,22]]},"reference":[{"key":"840_CR1","doi-asserted-by":"publisher","first-page":"104135","DOI":"10.1016\/j.meegid.2019.104135","volume":"78","author":"A Hanafiah","year":"2020","unstructured":"Hanafiah A, Lopes BS. 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