Comparative Analysis of the Full Genome of Helicobacter pylori Isolate Sahul64 Identifies Genes of High Divergence

Abstract

cIsolates of Helicobacter pylori can be classified phylogeographically. High genetic diversity and rapid microevolution are a hallmark of H. pylori genomes, a phenomenon that is proposed to play a functional role in persistence and colonization of diverse human populations. To provide further genomic evidence in the lineage of H. pylori and to further characterize diverse strains of this pathogen in different human populations, we report the finished genome sequence of Sahul64, an H. pylori strain isolated from an indigenous Australian. Our analysis identified genes that were highly divergent compared to the 38 publically available genomes, which include genes involved in the biosynthesis and modification of lipopolysaccharide, putative prophage genes, restriction modification components, and hypothetical genes. Furthermore, the virulence-associated vacA locus is a pseudogene and the cag pathogenicity island (cagPAI) is not present. However, the genome does contain a gene cluster associated with pathogenicity, including dupA. Our analysis found that with the addition of Sahul64 to the 38 genomes, the core genome content of H. pylori is reduced by approximately 14% (ϳ170 genes) and the pan-genome has expanded from 2,070 to 2,238 genes. We have identified three putative horizontally acquired regions, including one that is likely to have been acquired from the closely related Helicobacter cetorum prior to speciation. Our results suggest that Sahul64, with the absence of cagPAI, highly divergent cell envelope proteins, and a predicted nontransportable VacA protein, could be more highly adapted to ancient indigenous Australian people but with lower virulence potential compared to other sequenced and cagPAI-positive H. pylori strains.

Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission

“…Such variation in size is due to inherent differences in (i) methodology (some used microarray and others used different gene prediction and ortholog clustering algorithms), (ii) the use of strict vs relaxed core genome definitions, and (iii) sample size/diversity (some were limited to only a few isolates or an individual strain lineage). Nonetheless, taken together these studies show C. difficile displays ultra-low levels of genome conservation, a trait rarely seen in bacteria and lower than other bacterial species considered to have high levels of genetic variability such as Campylobacter jejuni (59.2%), Helicobacter pylori (58.5%), Streptococcus pneumoniae (46.5%), and E. coli (~40.0%; Welch et al, 2002; Hiller et al, 2007; Lu et al, 2013; Vernikos et al, 2015). …”

Genetic variants of Helicobacter pylori type IV secretion system components CagL and CagI and their association with clinical outcomes

“…Using WGS, we and others detected potential mutations throughout the H. pylori genome and identified variants when sequence changes were present [20, 24, 25]. Here, we used WGS technology to detect novel variants in uncharacterized cag PAI genes associated with H. pylori pathogenicity.…”

Genotyping of the Helicobacter pylori isolates of raw milk and traditional dairy products

“…Yahaghi et al (2014) 9 revealed that cagA (57.62%), vacA s1a (37.28%) and vacA m1a (30.50 %) had the highest prevalence among the H. pylori strains of vegetables. High prevalence of vacA genotypes among the clinical isolates and cases of gastrointestinal disorders have been reported from Iran, 22 United States, 23 Australia, 24 United Kingdom 25 and China. 26 Adjacent connotation of vacA genotypes with production of interleukin 8 (IL-8) and cytotoxins, adhesion to gastric epithelial cells, occurrence of inflammation, vacuolization, necrosis and apoptosis of epithelial cells has been reported in previously published data.…”