Resistome, virulome, anti-defense mechanisms, and prophages in Helicobacter pylori strains in Asia

Background: Helicobacter pylori, an important human gastrointestinal bacterium, exhibits rising antibiotic resistance, posing a huge challenge to disease management. Despite their key roles in disease progression, limited information on H. pylori antibiotic resistance patterns and key virulence factors is available in Asia. Material and methods: We pulled out all publicly available complete genome sequences (191 strains of H. pylori) from Asia and analyzed them through the comprehensive antibiotic resistance database (CARD) to identify antibiotic resistance patterns and key responsible genes. The virulence factors database (VFDB), phage search tool with enhanced translation (PHASTEST), prokaryotic antiviral defence locator (PADLOC), and Defense Finder were used for the identification of virulence factors, prophage sequences, clustered regularly interspaced short palindromic repeats (CRISPR) arrays, and defense mechanisms respectively. Result and conclusion: We observed 858 antibiotic resistance genes (ARGs), which belong to eight drug classes, with maximum genes showing penicillin-binding protein mutations (27.39 %) that confer resistance to beta-lactam antibiotics, and glycopeptide resistance gene clusters, vanT (22.26 %) for Vancomycin resistance. The hp1181, a part of major facilitator superfamily (MFS) efflux pump family, was observed in 189 genomes. The 191 H. pylori genomes harbor 20,626 virulence factors (VFs) that belong to the adherence, effector delivery system, motility, exotoxin, immune modulation and stress survival. The cagA and vacA, major virulence factors, are represented in 85.86 % and 42.41 % of genomes, respectively. Out of six major defense systems, restriction-modification was predominantly found in all genomes as determined by the DefenseFinder tool. Twenty-eight genomes carried CRISPR arrays, whereas 22 contained prophage elements with 25 VF genes and no antibiotic resistance genes. Of 22 prophages, 12 may follow a temperate, and 9 may follow a lytic life cycle. Our analysis demonstrated a high prevalence of antibiotic resistance and large numbers of virulence factors in H. pylori strains from Asia. Understanding these will be crucial for better management of patients suffering from H. pylori-associated diseases.