Computational protocol: Complete Genome Sequences of Two Helicobacter pylori Strains from a Canadian Arctic Aboriginal Community

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Protocol publication

[…] Helicobacter pylori is a genetically diverse gastric pathogen that chronically infects billions of people worldwide (), including many residents of indigenous Arctic communities (). Different sets of genotypes tend to predominate in different geographic regions or with different ethnic groups. Although strains from diverse peoples, including South American Amerindians, have been sequenced, no Arctic strains have been sequenced to date. Here, we report the complete genome sequences of two H. pylori strains from Aklavik, Northwest Territories, a Canadian Aboriginal community (~600 residents; 93% of Inuvialuit or Gwich’in ethnicity) with a high prevalence of severe H. pylori-associated gastritis ().Preliminary random amplified polymorphic DNA (RAPD) fingerprinting () placed 52 of 57 isolates into just six distinct groups, a homogeneity typical of isolated communities (). Multilocus sequencing typing (MLST) () identified four RAPD groups and the five unique strains (43 isolates) as Amerind (more related to Amazonian than even East Asian strains). The other two RAPD groups exhibited European and hybrid Amerind/European MLSTs (4 and 10 isolates, respectively).We completely sequenced (454 FLX with PCR-capillary to fill all gaps) (, ) two representative strains: Aklavik86, from the most abundant RAPD/MLST group (17 members), and Aklavik117, a unique RAPD/MLST Amerind type, distinguished by an ftsZ-linked IS606 fragment PCR marker, which is common in Peruvian Amerind strains but rare in Aklavik (although present in Alaskan Native) strains and absent from non-Amerind H. pylori () (D. Kersulyte and D. E. Berg, unpublished data). Each strain contains a typical H. pylori chromosome size (1.5 kb or 1.6 kb) and two unrelated plasmids (<3 kb and 12.1 kb or 18.8 kb). BLASTn analyses of sequential 1-kb chromosomal segments confirmed that these two strains are of the Amerind type genome-wide.PCR tests showed that Aklavik86 and Aklavik117 lack cag pathogenicity islands, as do all Aklavik Amerind strains, whereas most South American Amerind strains contain these islands (). Aklavik117 does contain two TnPZ virulence-associated transposons, (), one type I (fragmented) and one type II (intact), whereas Aklavik86 lacked TnPZs. Only two insertion sequence (IS) elements were present, IS607 in Aklavik117 and IS605 (deletion mutant) in Aklavik86, and no prophages were present in these two genomes.Two Aklavik86 features merit special mention: (i) iron-dependent urease genes (previously observed only in helicobacters from carnivores [, , ]), next to cheW, as in Helicobacter acinonychis and Helicobacter cetorum, and (ii) an unprecedented ~140 rearrangements in its chromosome (identified using Mauve software) relative to Aklavik117 and all other sequenced H. pylori strains. This contrasts with ≤10 such rearrangements between most other H. pylori strain pairs (, ). Follow-up PCR tests for six Aklavik86-specific rearrangements identified each in most of the Aklavik Amerind strains. In contrast, no rearrangements were found in Aklavik117 or in one of the Amerind or one European RAPD group of Aklavik strains (11 and 10 isolates, respectively), or in any of 80 other strains variously from Peru, Europe, or Asia.Aklavik86’s extraordinary iron-dependent urease genes and many chromosomal rearrangements suggest that it might represent a novel lineage, possibly derived from a jump many millennia ago from some ancient animal host. More generally, these findings should stimulate analyses of H. pylori population structure and evolution in human health and disease, especially in Arctic Aboriginal communities. […]

Pipeline specifications

Software tools BLASTN, Mauve
Databases RAPD
Application Nucleotide sequence alignment
Organisms Helicobacter pylori
Chemicals Iron