Long-Read- and Short-Read-Based Whole-Genome Sequencing Reveals the Antibiotic Resistance Pattern of Helicobacter pylori

• DOI: 10.1128/spectrum.04522-22
• Publication Date: 2023-04-17T14:01:44Z
• Authors: Limiao Hu; Xi Zeng; Qi Ai; Caijuan Liu; Xiaotuan Zhang; Yajun Chen; Logen Liu; Guo-Qing Li
• Keywords: single nucleotide variation; antibiotic resistance; Nanopore sequencing; Helicobacter pylori; Nucleotides; Furazolidone; Drug Resistance, Microbial; Levofloxacin; Microbial Sensitivity Tests; Tetracycline; Microbiology; QR1-502; 3. Good health; Helicobacter Infections; Anti-Bacterial Agents; RNA, Ribosomal, 23S; whole-genome sequencing; Clarithromycin; Metronidazole; Drug Resistance, Bacterial; Humans; Research Article

The rates of antibiotic resistance Helicobacter pylori are increasing, and the patterns region population specific. Here, we elucidated pattern H. in a single center China compared short-read- long-read-based whole-genome sequencing for identifying genotypes. Resistance 38.5%, 61.5%, 27.9%, 13.5% against clarithromycin, metronidazole, levofloxacin, amoxicillin were determined, respectively, while no strain was resistant to tetracycline or furazolidone. Single nucleotide variations (SNVs) 23S rRNA GyrA/B genes revealed by Illumina short-read showed good diagnostic abilities clarithromycin levofloxacin resistance, respectively. Nanopore long-read also efficiency elucidating SNVs gene and, thus, ability detect resistance. two technologies displayed consistency discovering shared 76% detected gene. Taking Sanger as gold standard, slightly higher accuracy than sequencing. There copies genome pylori, found that not same at least 26% strains tested, indicating their heterozygous status. Especially, three harboring 2143G/A status gene, which is most important site found. In conclusion, our results provide evidence an empirical first-line treatment eradication clinical settings. Moreover, show potential tool predicting