Recent “omics” advances in Helicobacter pylori

Abstract

The development of high-throughput whole genome sequencing (WGS) technologies is changing the face of microbiology, facilitating the comparison of large numbers of genomes from different lineages of a same organism. Our aim was to review the main advances on Helicobacter pylori "omics" and to understand how this is improving our knowledge of the biology, diversity and pathogenesis of H. pylori. Since the first H. pylori isolate was sequenced in 1997, 510 genomes have been deposited in the NCBI archive, providing a basis for improved understanding of the epidemiology and evolution of this important pathogen. This review focuses on works published between April 2015 and March 2016. Helicobacter "omics" is already making an impact and is a growing research field. Ultimately these advances will be translated into a routine clinical laboratory setting in order to improve public health.

Genomics of Helicobacter pylori

“…The ultimate aim for many researchers considering H. pylori genomics is the development of new therapies . Accordingly, Chaput et al .…”

“…The ultimate aim for many researchers considering H. pylori genomics is the development of new therapies. 23 Accordingly, Chaput et al 24 studied an isogenic mutant of the amiA gene encoding a N-acetylmuramoyl-l-alanyl amidase, showing the mutant was impaired in colonizing mouse stomach. Thus, these authors suggested AmiA is a valid target for the development of new antibiotics.…”

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

“…The multilocus sequence typing (MLST), in which seven housekeeping genes (atpA, efp, mutY, ppa, trpC, ureA, and yphC) are sequenced and compared, has shown H. pylori populations to be highly structured into clusters of related lineages. 5,6 According to Bayesian cluster of the seven housekeeping genes, there are currently seven H. pylori populations, hpAfrica1, hpAfrica2, hpNEAfrica, hpSahul, hpAsia2, hpEurope, and hpEastAsia. [7][8][9] This structured population provided strong evidence of ancient ancestry in Africa and of co evolution with the human host since then.…”

Biomarker Characterization and Prediction of Virulence and Antibiotic Resistance from Helicobacter pylori Next Generation Sequencing Data

“…These new approaches enable several limitations of the previously referred to methods to be overcome and allow for a wider perspective on H. pylori biomarkers, pathogenicity and evolution. The importance and potential of whole genome data on bacterial pathogen evolution, virulence and pathogenicity has been acknowledged for over two decades [224] and we now have the technologies to get the best possible out of such data [225]. Presently (as of January 2022), a total of 2251 H. pylori genomes are recorded in the Pathosystem Resource Integration Center (PATRIC) database [226], reflecting the commitment of the scientific community to this technology (Figure 3).…”