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Genomic Determinants of Antibiotic Resistance for Helicobacter Pylori Treatment: A Retrospective Phenotypic and Genotypic Observational Study Publisher



Martinezmartinez FJ ; Chineroms A ; Furio V ; Martinez F ; Furio V ; Comas I ; Yamaoka Y ; Dekker JP ; Megraud F ; Jauvain M ; Varon C ; Lehours P ; Jehanne Q ; Benejat L Show All Authors
Authors
  1. Martinezmartinez FJ
  2. Chineroms A
  3. Furio V
  4. Martinez F
  5. Furio V
  6. Comas I
  7. Yamaoka Y
  8. Dekker JP
  9. Megraud F
  10. Jauvain M
  11. Varon C
  12. Lehours P
  13. Jehanne Q
  14. Benejat L
  15. Ducournau A
  16. Romerogallo J
  17. Krishna U
  18. Peek Rm JR
  19. Piazuelo MB
  20. Wilson KT
  21. Loh JT
  22. Cover TL
  23. Vale FF
  24. Raaf N
  25. Aftab H
  26. Akada J
  27. Matsumoto T
  28. Haesebrouck F
  29. Bartelli TF
  30. Nunes DN
  31. Pelosof A
  32. Sztokfisz CZ
  33. Diasneto E
  34. Assumpcao PP
  35. Karagyozov P
  36. Tishkov I
  37. Goodman KJ
  38. Geary J
  39. Cromarty TJ
  40. Price NL
  41. Quilty D
  42. Corvalan AH
  43. Gonzalez R
  44. Riquelme A
  45. Garciacancino A
  46. Parrasepulveda C
  47. Castillo F
  48. Bravo MM
  49. Pazos A
  50. Bravo LE
  51. Fox JG
  52. Ramirezmayorga V
  53. Molinacastro S
  54. Duranbermudez S
  55. Camposnunez C
  56. Chavescervantes M
  57. Tshibangukabamba E
  58. Tumba GD
  59. Tshimpiwola A
  60. De Jesus Ngomakisoko P
  61. Tshibangu FM
  62. Mukanya AC
  63. Nkomba TK
  64. Cruz M
  65. Abreu JJ
  66. Secka O
  67. Link A
  68. Malfertheiner P
  69. Adinortey MB
  70. Bockarie AS
  71. Adinortey CA
  72. Ofori EG
  73. Sgouras DN
  74. Martinezgonzalez B
  75. Michopoulos S
  76. Georgopoulos S
  77. Hernandez E
  78. Dominguez RL
  79. Morgan DR
  80. Harardottir H
  81. Gunnarsdottir AI
  82. Gujonsson H
  83. Jonasson JG
  84. Bjornsson ES
  85. Ballal M
  86. Shetty V
  87. Miftahussurur M
  88. Sugihartono T
  89. Alfaray RI
  90. Waskito LA
  91. Fauzia KA
  92. Syam AF
  93. Maulahela H
  94. Malekzadeh R
  95. Peretz A
  96. Azrad M
  97. On A
  98. De Re V
  99. Zanussi S
  100. Cannizzaro R
  101. Canzonieri V
  102. Shimura T
  103. Tokunaga K
  104. Osaki T
  105. Kamiya S
  106. Jadallah K
  107. Matalka I
  108. Igissin NS
  109. Moldobaeva MS
  110. Rakhat A
  111. Choi IJ
  112. Kim JG
  113. Kim N
  114. Leja M
  115. Vangravs R
  116. Skenders G
  117. Rudule A
  118. Kikuste I
  119. Vanags A
  120. Rudzite D
  121. Kupcinskas J
  122. Kiudeliene E
  123. Kiudelis V
  124. Gedgaudas R
  125. Jonaitis P
  126. Kiudelis G
  127. Jonaitis L
  128. Skieceviciene J
  129. Vadivelu J
  130. Loke MF
  131. Vellasamy KM
  132. Herreragoepfert R
  133. Alonsolarraga JO
  134. Yee TT
  135. Htet K
  136. Matsuhisa T
  137. Shrestha PK
  138. Ansari S
  139. Abiodun O
  140. Jemilohun C
  141. Akande KO
  142. Oluabiodun O
  143. Magaji FA
  144. Omotoso A
  145. Okonkwo U
  146. Osuagwu CC
  147. Owoseni OO
  148. Castaneda C
  149. Castillo M
  150. Velapatino B
  151. Gilman RH
  152. Krzyzek P
  153. Gosciniak G
  154. Pawelka D
  155. Koronaglowniak I
  156. Cichozlach H
  157. Oleastro M
  158. Figueiredo C
  159. Machado JC
  160. Ferreira RM
  161. Bordin DS
  162. Livzan MA
  163. Tsukanov VV
  164. Tan P
  165. Yeoh KG
  166. Zhu F
  167. Ally R
  168. Haas R
  169. Fischer W
  170. Montes M
  171. Fernandezreyes M
  172. Tamayo E
  173. Lizasoain J
  174. Bujanda L
  175. Lario S
  176. Ramirezlazaro MJ
  177. Calvet X
  178. Brunetmas E
  179. Domperarnal MJ
  180. Garciamateo S
  181. Abadbaroja D
  182. Delgadoguillena P
  183. Moreira L
  184. Botargues J
  185. Perezmartinez I
  186. Barreiroalonso E
  187. Flores V
  188. Gisbert JP
  189. Muro EA
  190. Linares P
  191. Alcoba L
  192. Martin V
  193. Engstrand L
  194. Enroth H
  195. Keller PM
  196. Wagner K
  197. Pohl D
  198. Lee YC
  199. Liou JM
  200. Wu MS
  201. Kocazeybek B
  202. Saribas S
  203. Tasci I
  204. Demiryas S
  205. Kepil N
  206. Quiel L
  207. Villagra M
  208. Norton M
  209. Johnson D
  210. Huang RJ
  211. Hwang JH
  212. Szymczak W
  213. Jacobs Wr JR
  214. In H
  215. Bollag R
  216. Lopez A
  217. Kruse EJ
  218. White J
  219. Lane C
  220. Gao Y
  221. Gold BD
  222. Cruzcorrea M
  223. Gonzalezpons M
  224. Rodriguez LM
  225. Tuan VP
  226. Quy Dung HD
  227. Binh TT
  228. Huyen Trang TT
  229. Van Khien V
  230. Katsura Y
  231. Gonzalezhormazabal P
  232. Tarazonasantos E
  233. Zamudio R
  234. Marinoramirez L
  235. Backert S
  236. Naumann M
  237. Smet A
  238. Berg DE
  239. Yahara K
  240. Blaser MJ
  241. Vincze T
  242. Morgan RD
  243. Roberts RJ
  244. Torres J
  245. Torres RC
  246. Noureen M
  247. Cherry JL
  248. Osada N
  249. Fukuyo M
  250. Arita M
  251. Sandovalmotta S
  252. Agostini RB
  253. Ghirotto S
  254. Munozramirez ZY
  255. Falush D
  256. Thorell K
  257. Uchiyama I
  258. Kobayashi I
  259. Wang D
  260. Hicks B
  261. Yeager M
  262. Hutchinson A
  263. Teshome K
  264. Jones K
  265. Luo W
  266. Goldstein AM
  267. Hu N
  268. Taylor PR
  269. Song M
  270. Yu K
  271. Zhu B
  272. Abnet CC
  273. Rabkin CS
  274. Camargo MC
  275. Yamaoka Y
  276. Dekker JP
  277. Megraud F
  278. Benejat L
  279. Giese A
  280. Camargo MC
  281. Comas I
  282. Lehours P

Source: The Lancet Microbe Published:2026


Abstract

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. © 2025 The Author(s).
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