The single nucleotide polymorphisms SNPs associated with multiple therapy resistance in Colombia.

The eradication of () using multiple therapies is used as a prevention strategy. However, its efficacy has been compromised by the emergence of single nucleotide polymorphisms in genes associated with resistance to multiple antibiotics. To estimate antibiotic resistance rates associated with mutations in genes in the high-cancer-risk population in Colombia, we included 166 whole genome sequences from a cohort of individuals with a high risk of gastric cancer. By using the reference strain ATCC 26695, we identified mutations in specific genes to evaluate resistance rates for different antibiotics: rRNA for clarithromycin, rRNA for tetracycline, for amoxicillin, for levofloxacin, and for metronidazole. The phylogenomic analysis was conducted using the core genome consisting of 1,594 genes of -ATCC 26695. Our findings revealed that the resistance rate of to clarithromycin was 3.62%, primarily associated with mutations A2143G and A2142G in the rRNA gene. For tetracycline, the resistance rate was 7.23%, with mutations A926G, A926T, and A928C observed in the rRNA gene. Amoxicillin resistance was found in 25.9% of cases, with observed mutations in the gene, including T556S, T593, R649K, R656P, and R656H. In the gene, mutations N87K, N87I, D91G, D91N, and D91Y were identified, resulting in a resistance rate of 12.04% to levofloxacin. The most common mutations in the gene associated with metronidazole resistance were a stop codon, and mutations at D59N and D59S, resulting in a resistance rate of 99.3%. The high resistance rate of to metronidazole indicated that this drug should be excluded from the eradication therapy. However, the resistance rates for tetracycline and clarithromycin did not exceed the established resistance threshold in Colombia. The increased resistance rate of to levofloxacin and amoxicillin may partially explain the observed therapeutic failures in Colombia. The phylogenomic tree showed that the isolate belongs to its own lineage (hspColombia). These findings offer valuable insights to enhance the characterization of treatment protocols for the specific lineage (hspColombia) at the local level.