Antibiotic Resistance of H. pylori in Central South China: Phenotype and Genotype Revealed by Short and Long Reads Based Whole Genome Sequencing

The antibiotic resistance rates of Helicobacter pylori (Hp) are increasing, and the resistant patterns are regional- and population-specific. Here, we elucidated the resistance pattern of Hp in central south China, compared short reads and long reads based whole genome sequencing to identify the genotypes. Resistance rates of 38.5%, 61.5%, 27.9%, and 13.5% against clarithromycin, metronidazole, levofloxacin, and amoxicillin, respectively, were detected. While no strain was resistant to tetracycline or furazolidone. Furthermore, the two copies of 23s rRNA of Hp, which was responsible for clarithromycin resistance were not the same in all strains tested, indicating their hybrid status, especially, three strains harboring the A2143R mutation. Nanopore sequencing showed good efficiency in elucidating single nucleotide variations in 23S rRNA and good diagnosis ability for clarithromycin resistance. However, this technology showed a limited ability in revealing small indels compared to short reads-based sequencing. In conclusion, our results provided evidence for an empirical first-line treatment for Hp eradication in clinical setting. Moreover, we presented that Nanopore sequencing is a potential tool in predicting clarithromycin resistance.