Draft Genome Sequences of 29 Helicobacter pylori Strains Isolated from Colombia

Here, we present the draft genome sequences of 29 Colombian Helicobacter pylori strains. These strains were isolated in Bogotá, Colombia, from patients diagnosed with chronic gastritis. The genomic characterization of these strains will provide more information on the genetic composition of H. pylori strains from Colombia.

H elicobacter pylori is a Gram-negative, pathogenic bacterium capable of colonizing and persisting in the human stomach. The infection is considered the most frequent chronic bacterial infection worldwide (1)(2)(3), reaching prevalence rates of up to 80% in Colombia (4).
This report announces the genome sequences of 29 H. pylori strains isolated between 2009 and 2010 from patients residing in Bogotá, Colombia. The patients who signed informed consent were 48 years old on average (range, 18 to 79 years); from the histology results, 65.5% were diagnosed with chronic nonatrophic gastritis and 34.5% with chronic atrophic gastritis. The strains were recovered from gastric biopsy samples, and those were cultivated on BBL Brucella agar (Becton, Dickinson) supplemented with 7% horse blood, 0.4% IsoVitalex (BD, USA), and 0.2% Dent selective supplement (Oxoid, UK) under microaerophilic conditions (11% CO 2 ) at 37°C for 4 to 7 days. The strains were preserved in 20% glycerol and stored until required for DNA extraction. They were recovered by culture every time. After that, total DNA was extracted using a DNeasy blood and tissue kit (Qiagen, Hilden, Germany) following the manufacturer's instructions. Fluorometric assay DNA quantification was performed using a Qubit 2.0 fluorometer and the Qubit double-stranded DNA (dsDNA) high-sensitivity (HS) assay kit (Life Technologies, Carlsbad, CA, USA). To verify that the DNA obtained was from H. pylori, a conventional PCR technique for the vacA gene was carried out. The primers and protocols previously described by Atherton et al. (5) were used.
Genomic DNA was sequenced using the MiSeq platform (Illumina, San Diego, CA); DNA libraries were prepared using a Nextera XT DNA library preparation kit (Illumina), followed by 2 Â 300-bp paired-end sequencing resulting in 80Â coverage. The lowquality sequences were removed with the software package Trimmomatic v0.39 (6). The reads were used for de novo genome assembly with SPAdes v13.3 (7). Assembly statistics for analyzed strains are provided in Table 1. The sequences were annotated using the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP) (8). Default parameters were used for all software tools unless otherwise specified.
The data reported here provide information on the genetic population structure of Colombian H. pylori. This information will help future functional comparative genomic studies that will greatly enhance the understanding of H. pylori infection dynamics in the Latin American region.
Data availability. This whole-genome shotgun project has been deposited in GenBank under accession number PRJNA656306. The accession numbers for the genomes are provided in Table 1.

ACKNOWLEDGMENTS
We thank the entities that financially supported the development of this work. and projects UIDB/04138/2020 and UIDP/04138/2020; these funds partially supported this work. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.