Global Helicobacter pylori Genome Sequencing

We sampled 149 previously undescribed H. pylori isolates from 12 countries in America, from Canada in the North to Argentina in the South and from the Iberian Peninsula (Spain and Portugal) (Supplementary Table 1). These isolates were augmented with 105 published [10 , 12 (link)] genomes from samples isolated from three Latin American countries to give a total of 254 genomes. Study sites contributed samples from urban areas of mixed ancestry as well as Indigenous communities (Supplementary Table 1). Study site technicians isolated H. pylori strains from gastric biopsies of patients or research participants in a selective blood agar media under a microaerobic atmosphere and extracted DNA using the DNeasy Mini Kit (Qiagen, Hilden Germany). Purified DNA from clinical H. pylori isolates was sent from the study sites and following quality control, libraries were prepared using Illumina^® TruSeq^® Nano kit (San Diego, CA, USA) aiming for an insert size of 900 bp. Libraries were sequenced on the MiSeq platform using v3 chemistry, 2*300 bp paired end reads generating a coverage of on average 256-fold (22.3 min to 1063.3 max) (Supplementary Table 2).