Whole-genome sequencing of Helicobacter pylori isolates from Native American gastric biopsy specimens

ABSTRACT Helicobacter pylori infection has been linked to gastrointestinal diseases including gastric cancer. High rates of H. pylori infection and gastric cancer have been reported in indigenous populations within the United States. We report whole-genome sequencing of three H. pylori isolates originating from Native American patients presenting with gastric disease.

gastric infections and is linked to gastric cancer (1)(2)(3).Indigenous communities in the United States have elevated rates of infection and gastric cancer.Members of the Navajo Nation have rates of infection ranging between 56% and 70% (4, 5) and gastric cancer rates three to four times higher than non-Hispanic white populations (6).Navajo patients with gastric symptoms had a gastric biopsy during endoscopy and H. pylori culturing or PCR was performed.H. pylori was present in ~23% of these biopsy samples (7).We describe whole-genome sequencing of three H. pylori isolates from these patients.
Patients were enrolled by informed consent (Navajo Nation IRB #NNR16.263).Gastric pinch biopsy samples were collected during a routine scheduled patient endoscopy.Samples were ground in sterile phosphate-buffered saline, inoculated onto Columbia Agar plates containing 5% defibrinated sheep blood and H. pylori selective supplement (Dent), and incubated for 72 h at 37°C under microaerophilic conditions (5% O 2 , 10% CO 2 , and 85% N 2 ).Minimum inhibitory concentrations (MICs) for clarithromycin and metronidazole were determined with ETESTs (bioMérieux) by inoculating 100 µL of a 3 McFarland equivalent isolate suspension onto Mueller-Hinton II plates with 5% defibrinated sheep blood and incubating at 37°C for 4 days under microaerophilic conditions.
Genome assembly information is presented in Table 1.The three isolates are putatively genotyped as cagA − and vacA type s2i2m2.A SNP phylogeny (Fig. 1) indicates that the isolates are closely related to isolates originating from Indigenous or Mestizo individuals presenting with gastritis in Mexico (25,26).ETESTS indicate some isolates are resistant to clarithromycin and metronidazole (Table 1).  1 were identified within the 23S rRNA gene for all three isolates, but specific mutations listed within the CARD were not identified.e Genomic data queried against features associated with metronidazole resistance in H. pylori in the Comprehensive Antimicrobial Resistance Database.An antibiotic efflux pump gene was identified in all three genomes.Mutations were identified within frxA and rdxA in all three genomes; specific mutations listed within the CARD are in bold text.

FIG 1
FIG 1 Core genome SNP phylogeny (midpoint rooted) of 186 publicly available H. pylori genomes and three newly sequenced H. pylori genomes.Colors indicate the continent of origin for the H. pylori isolates included in the tree.The blue box highlights the three newly sequenced isolates (408F, 412F, and 427F) and closely related isolates.The three newly sequenced isolates are closely related to isolates collected from Indigenous or Mestizo individuals presenting with gastritis in Mexico.

TABLE 1
Genome assembly metrics and accession numbers A Reverse reads trimmed to 228 nucleotides due to sequencing quality.b Resistance breakpoint for clarithromycin-EUCAST v13.1.c Resistance breakbpoint for metronidazole-EUCAST v13.1.d Genomic data queried against features associated with clarithromycin resistance in H. pylori in the Comprehensive Antimicrobial Resistance Database.The mutations in Table