Screening and in silico characterization of prophages in Helicobacter pylori clinical strains

The increase of antibiotic resistance calls for alternatives to control Helicobacter pylori, a Gram-negative bacterium associated with various gastric diseases. Bacteriophages (phages) can be highly effective in the treatment of pathogenic bacteria. Here, we developed a method to identify prophages in H. pylori genomes aiming at their future use in therapy. A polymerase chain reaction (PCR)-based technique tested five primer pairs on 74 clinical H. pylori strains. After the PCR screening, 14 strains most likely to carry prophages were fully sequenced. After that, a more holistic approach was taken by studying the complete genome of the strains. This study allowed us to identify 12 intact prophage sequences, which were then characterized concerning their morphology, virulence, and antibiotic-resistance genes. To understand the variability of prophages, a phylogenetic analysis using the sequences of all H. pylori phages reported to date was performed. Overall, we increased the efficiency of identifying complete prophages to 54.1 %. Genes with homology to potential virulence factors were identified in some new prophages. Phylogenetic analysis revealed a close relationship among H. pylori-phages, although there are phages with different geographical origins. This study provides a deeper understanding of H. pylori-phages, providing valuable insights into their potential use in therapy.

Questions answered in this article: - What were the findings regarding the number of prophages identified in the H. pylori genomes? The study identified twelve new prophages in the genomes of Helicobacter pylori, with at least 10 out of the 14 sequenced strains containing at least one intact prophage, indicating a significant presence of these genetic elements in the clinical strains examined; -What percentage of H. pylori strains are compatible with the presence of prophage genes? The analysis of Helicobacter pylori genomes indicates that approximately 20% of strains are compatible with the presence of prophage genes; - What Polymerase Chain Reaction (PCR) techniques were employed to screen for prophages in H. pylori strains? The Polymerase Chain Reaction (PCR) techniques employed to screen for prophages in Helicobacter pylori strains included the use of four different primer sets targeting two regions of the integrase gene, the holin gene, and the insertion site region between specific genes. This approach aimed to enhance the detection of prophages in the clinical strains; What morphological characteristics are commonly associated with H. pylori prophages? H. pylori prophages are commonly associated with a podovirus-like morphology, as indicated by the results obtained with VIRFAM. This morphological characteristic aligns with most reported H. pylori prophages, which exhibit this specific structure; - What challenges exist in the genomic analysis and characterization of H. pylori prophages? The genomic analysis and characterization of Helicobacter pylori prophages face challenges such as the alarming rates of antibiotic resistance, which complicate treatment approaches and necessitate alternative strategies. Additionally, the variability in the genomic size and GC content among different H. pylori strains may pose difficulties in standardizing genomic analyses.