Helicobacter pylori Resistance in Latin American Populations Using Next Generation Sequencing Technology With Formalin-Fixed Paraffin-Embedded Samples: Initial Results of a 10-Nation Study

Introduction: Next-Generation Sequencing (NGS) has the potential to improve Helicobacter pylori (Hp) antibiotic resistance testing, making it more accessible and efficient across various sample types. This enhances patient care by enabling individual resistance testing prior to treatment. In resource-limited settings, population sampling offers insight into local Hp ecology and resistance patterns. We conduct an initial study in Latin America using NGS for Hp resistance in varied populations in 10 countries, and report preliminary results from 2 countries. Methods: Formalin-fixed paraffin-embedded samples were obtained from endoscopy biopsies. The NGS (PyloriARl; American Molecular Laboratories, Chicago, IL) identifies mutations or variances of the Hp DNA present in FFPE tissue. The platform permits simultaneous testing of 6 antibiotics based upon mutations for resistance: Clarithromycin (23S rRNA), Fluoroquinolones (gyrA), Metronidazole (rdxA), Amoxicillin (pbp1), tetracycline (16SrRMA), and Rifabutin (rpoB). Results: The initial phase examined 164 recent FFPE samples from a diverse group of patients in Chile. Successful analysis was performed on 149 samples (90.9%). The analysis revealed varying resistance rates to specific antibiotics. 38.4% did not show resistance to any antibiotic. Resistance to 1 antibiotic was found in 31.7% of the samples. The resistance rates were: Clarithromycin (CLR) 40.3%, fluoroquinolones (Lfx) 33.6%, metronidazole (MTZ) 34.2%, Amoxicillin (AMOX) 2.7%, Rifabutin (Rfb) 0.7% and tetracycline (TET) 0.0%. The combination of CLR and Lfx showed resistance in 19.5%, CLR and MTZ 14.6%, and Lfx and MTZ 12.8%. Notably, in Chile, antibiotic use requires a prescription. The results were inadequate from a second nation wherein FFPE samples were greater than 12 months old (Table 1). Conclusion: In the first phase of the 10-nation Latin America H. pylori antibiotic resistance study, high rates of resistance were observed for clarithromycin, fluoroquinolones, and metronidazole. Dual resistance with combinations of these antibiotics ranged 13-19.5%. Resistance to amoxicillin, tetracycline, and rifabutin were low. These results will help inform Ministry of Health Hp management guidelines in the region. Table 1. - Resistance Patterns Frequency (%) Frequency 95% CI Total Samples 164 Successful samples No 15 (9.1%) 5.6-14.7 Yes 149 (90.9%) 85.3-94.3 Clarithromycin 60 (40.3%) 32.6-48.4 Tetracycline 0 (0.0%) Fluoroquinolones 50 (33.6%) 26.4-41.6 Metronidazole 51 (34.2%) 27.0-42.26 Amoxicillin 4 (2.7%) 1,0-7.0 Rifabutin 1 (0.7%) 0.1-4.7 Resistant to (number of antibiotics) None 63 (38.4%) 25.2-40.2 One 52 (31.7%) 27.6-43.0 Two 34 (20.7%) 16.7-30.3 Three 14 ( 8.5%) 5.6-15.3 Four 1 ( 0.6%) 0.1-4.7 Clarithromycin + Fluoroquinolones 32 (19.5%) 15.6-28.9 Clarithromycin + Metronidazole 24 (14.6%) 11.0-23.0 Fluroquinolones + Metronidazole 21 (12.8%) 9.3-20.7 Clarithromycin + Fluroquinolones + MTZ 14 ( 8.5%) 5.6-15.3