Genomic determinants of antibiotic resistance for Helicobacter pylori treatment: a retrospective phenotypic and genotypic observational study
Number of Authors: 2722026 (English)In: The Lancet Microbe, ISSN 2666-5247, Vol. 7, no 1, article id 101217Article in journal (Refereed) Published
Abstract [en]
Background: Rising antimicrobial resistance of Helicobacter pylori is a public health challenge. Genomic-based susceptibility testing allows for the identification of resistance-associated mutations, complementing conventional diagnostics and advancing towards pathogen-based personalised therapies. Our study aimed to identify genes and mutations involved in antimicrobial resistance in H pylori and evaluate the extent to which these markers can be used as predictors of phenotypic resistance against clarithromycin and levofloxacin.
Methods: In this retrospective phenotypic and genotypic observational study, we included 1011 H pylori whole-genome sequences and strains of known geographical origin from the H pylori Genome Project (Hp GP) collection. We performed phenotypic clarithromycin and levofloxacin susceptibility testing on a subset of 419 Hp GP strains using Etest at a centralised laboratory. A genomic analysis was conducted to identify 23S rRNA and gyrA variants and build a curated catalogue of mutations associated with resistance to clarithromycin (ie, 23S rRNA 2142A→G, 2142A→C, and 2143A→G) and levofloxacin (ie, gyrA A88V or A88P, N87K or N87I, and D91G, D91N, or D91Y). Genotype–phenotype concordance was assessed to estimate sensitivity and specificity, and the curated catalogue of resistance-associated mutations was applied to the complete Hp GP set. Region-specific prevalence of resistance-associated mutations was calculated for a combined dataset including the Hp GP genomes and 768 whole-genome sequences retrieved from the US National Center for Biotechnology Information Sequence Read Archive repository. Associations between resistance genotypes, H pylori subpopulations, and minimum inhibitory concentrations (MICs) were tested.
Findings: Clarithromycin-resistant and levofloxacin-resistant Hp GP strains were estimated with a sensitivity and specificity of 100%, with all confidence intervals ranging from 96% to 100%. The combined analysis (n=1779) found the highest prevalence of clarithromycin resistance in the western Pacific region (173 [51·2%] of 338 in southeast Asia and 75 [29·8%] of 252 in eastern Asia), north African region (seven [38·9%] of 18), and western Asian region (12 [31·6%] of 38), whereas the highest prevalence of levofloxacin resistance was found in south Asia (14 [51·85%] of 27), Central America (48 [38·7%] of 124), eastern Europe (four [36·4%] of 11), and southern Africa (three [33·3%] of nine). Similarly, 23S rRNA and gyrA genotypes are variable across H pylori subpopulations. MIC values changed depending on the specific mutation in 23S rRNA (mean clarithromycin MIC 24·61 mg/L [95% CI 12·27–36·96] for 2143A→G and 142·25 mg/L [95% CI 77·88–206·61] for 2142A→G) and gyrA (mean levofloxacin MIC 9·66 mg/L [95% CI 6·75–12·56] for mutations on codon 91, and 27·97 mg/L [95% CI 25·82–30·11] for mutations on codon 87).
Interpretation: Mutations in specific genes are reliable indicators to clarithromycin and levofloxacin resistance in H pylori, making them useful markers for the development of diagnostic assays and molecular monitoring. Our results suggest that using clarithromycin and levofloxacin empirically, without previous susceptibility testing, is unsuitable in all geographical regions covered by this study.
Funding: Intramural Research Program of the US National Cancer Institute, the European Research Council, and the Spanish Ministry of Science and Innovation.
Place, publisher, year, edition, pages
Elsevier, 2026. Vol. 7, no 1, article id 101217
National Category
Microbiology in the Medical Area Infectious Medicine
Research subject
Infection Biology
Identifiers
URN: urn:nbn:se:his:diva-26147DOI: 10.1016/j.lanmic.2025.101217ISI: 001675331400001PubMedID: 41453373Scopus ID: 2-s2.0-105028095936OAI: oai:DiVA.org:his-26147DiVA, id: diva2:2035868
Funder
EU, European Research Council
Note
CC BY 4.0
© 2025 The Author(s)
Correspondence Address: I. Comas; Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, 46020, Spain; email: icomas@ibv.csic.es
Our special thanks are extended to all the individuals who were the hosts of the HpGP strain collection, who represent the human populations that bear the burden of H pylori-associated disease, and whose biological samples serve to advance research aimed at reducing this disease burden. The HpGP was mainly supported by the Intramural Research Program from the US National Cancer Institute at the National Institutes of Health (NIH). This work was supported in part by the intramural research programmes of the US National Library of Medicine, the US National Institute on Minority Health and Health Disparities, and the division of Intramural Research, US National Institute of Allergy and Infectious Diseases, NIH. FFV is funded by Fundação para a Ciência e a Tecnologia (FCT) through project grants (project PTDC/BTM-TEC/3238/2020 and CPCA-IAC/AV/478719/2022) that partially supported this work, alongside national funds from FCT projects UIDB/04138/2020, UIDP/04138/2020, and UIDB/04046/2020 (https://doi.org/10.54499/UIDB/04046/2020). The collaborating centres for sample collection received grant support from the US NIH (P01CA116087,R01CA077955,R01DK058587, and P30DK058404 toRMP; P01CA028842 and R01CA190612 to KTW; P01CA028842, R01CA190612, K07CA125588, R03CA167773, and P30CA068485 to DRM; K08CA252635 toRJH;K22CA226395 to MG-P; andU54GM133807 to MC-C), the German Federal Ministry of Education and Research (BMBF-0315905D, ERA-NET PathoGenoMics to PM), the French Association pour la Recherche Contre le Cancer (8412 to FM), the French Institut National du Cancer (07/3D1616/IABC-23–12/NC-NG and 2014–152 to FM), the Canceropole Grand Sud-Ouest (2010–08-canceropole GSO-Universite Bordeaux 2 to FM), the Japanese Ministry of Education, Culture, Sports, Science, and Technology (21H00346 221S0002, 22H02871, and 23K24133 to YY), the Japanese Adopting Sustainable Partnerships for Innovative Research Ecosystem (ASPIRE; 23jf0126006h0001 to YY), the National Fund for Innovation and Development of Science and Technology from the Ministry of Higher Education Science and Technology of the Dominican Republic (2012–2013–2A1–65 and 2015–3A1–182 to MC), the National Cancer Center of South Korea (2210630, IJC), ArcticNet (RES0010178 to KJG), the Network of Centres of Excellence of Canada, the Canadian Institutes for Health Research (MOP115031 to KJG),Alberta Innovates Health Solutions (201201159 toKJG), the University of Malaya-Ministry of Higher Education (UM.C/625/1/HIR/MOHE/CHAN-02 to JV), the Ministry of Science and Technology of Vietnam, the Kyrgyz State Medical Academy, the Italian Ministry of Health for Institutional Research, the Chilean National Fund for Health Research and Development (FONIS A19/0188, FONDECYT 1230504, and ANID-FONDAP 152220002 to AR; CONICYT-FONDAP 15130011 and FONDECYT 1231773 to AHC), the Chilean Cancer Prevention and Control Center, the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP; 2014/26847–0, 2018/14267–2, 2018/ 02972–3 to ED-N), the Departamento de Ciência e Tecnologia (DECIT), Ministry of Health, Brazil (PRONON, SIPAR 2500⋅035–167/2015–23 to ED-N), the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, 314344/2020–9 to ET-S), the Universidad de Costa Rica (742-B9–310 and 742–90912–19 to VR-M), LABGIPAT (SD-B), the Hospital Clínica Bíblica (CC-N), the Greek Ministry of Culture and Education (InfeNeutra Project, NSRF 2007–2013, MIS450598, DNS), the National Strategic Reference Framework Operational Program “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014–2020, MIS5002486, DNS), the Hellenic Publishing Helicobacter pylori Study Group (2012–2016, BM-G), the Hellenic Society of Gastroenterology (National Multicenter Laboratory Surveillance Studies, 2018–2019, BM-G), Articles 10 www.thelancet.com/microbe Vol 7 January 2026 the Ministry of Science and Technology, Executive Yuan, Taiwan (109–2314-B-002–096; MOST 111–2314-B-002–012; and MOST 109–2314-B-002–090-MY3 to J-ML and M-SW), the National Research Foundation of Singapore, the Singapore Ministry of Health’s National Medical Research Council (Open Fund-Large Collaborative Grant, MOH[1]OFLCG18May-0003), the University of Puerto Rico Comprehensive Cancer Center, the Fondo Nacional de Desarrollo Científico y Tecnológico (196–2015-FONDECYT to CC), Universidad Científica del Sur, the Instituto Nacional de Enfermedades Neoplásicas (INEN, Peru), the European Research Council (ERC): H2020-ERC-COG/0800; Ministerio Español de Ciencia e Innovación: PID2022–137607OB-I00 and PRE2020–094308, and Prometeo Programme Generalitat Valenciana CIPROM2023 MICROGLOCAL received by IC, the RyC grant RYC2021-031461-I funded by MCIN/AEI/10⋅13039/501100011033 and by the “European Union Next GenerationEU/PRTR” received by ACO. ACO and IC are part of the CSIC’s Global Health Platform (PTI Salud Global).
2026-02-052026-02-052026-02-10Bibliographically approved