Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins

Abstract

Helicobacter pylori genetic diversity is known to be influenced by mobile genomic elements. Here we focused on prophages, the least characterized mobile elements of H. pylori. We present the full genomic sequences, insertion sites and phylogenetic analysis of 28 prophages found in H. pylori isolates from patients of distinct disease types, ranging from gastritis to gastric cancer, and geographic origins, covering most continents. The genome sizes of these prophages range from 22.6–33.0 Kbp, consisting of 27–39 open reading frames. A 36.6% GC was found in prophages in contrast to 39% in H. pylori genome. Remarkably a conserved integration site was found in over 50% of the cases. Nearly 40% of the prophages harbored insertion sequences (IS) previously described in H. pylori. Tandem repeats were frequently found in the intergenic region between the prophage at the 3′ end and the bacterial gene. Furthermore, prophage genomes present a robust phylogeographic pattern, revealing four distinct clusters: one African, one Asian and two European prophage populations. Evidence of recombination was detected within the genome of some prophages, resulting in genome mosaics composed by different populations, which may yield additional H. pylori phenotypes.

Molecular characterization of carbapenem-resistant Klebsiella pneumoniae isolates with focus on antimicrobial resistance

“…To understand genetic diversity, mobile genetic elements of 24 prophages are identified in seven CRKP genomes, with sizes ranging from 8.4 kb to 49.3 kb ( Figure 1 ). According to the criterion that the length of an intact prophage should be more than 20 kb 22 . Prophages detected in most strains (except for 2036D) are complete with a size of at least 20.2 kb with an average GC percentage of 52.7%.…”

Population genetic structure of Helicobacter pylori strains from Portuguese‐speaking countries

“…18,38 The ancestry's proportions of Portuguesespeaking countries presented a higher proportion of AE2. Interestingly, a similar segregation of European population was found using a phage sequence typing based on prophage sequences of H. pylori.…”

“…Interestingly, a similar segregation of European population was found using a phage sequence typing based on prophage sequences of H. pylori. 18,38 The ancestry's proportions of Portuguesespeaking countries presented a higher proportion of AE2. This was similarly found for Spain, France, Italy, and Middle East (sequences retrieved from H. pylori pubMLST, Figure 4).…”

Genomics of Helicobacter pylori

“…This particular point was also studied by Vale et al in 28 strains of different phylogeographic origins. 11 The strains harbored large prophages ranging from 22.6 to 30.0 Kbp, and the prophage insertion site was preserved in half of the cases (with similarities depending on the geographic origin of the strains). The authors highlight the presence of insertion sequences in these prophages and of tandem repeated sequences at the 3′ end of the insertion site.…”