Complete Genome Sequence of Helicobacter pylori Strain 29CaP Isolated from a Mexican Patient with Gastric Cancer.

Helicobacter pylori infection is a risk factor for the development of gastric cancer and other gastroduodenal diseases. We report here the complete genome sequence of H. pylori strain 29CaP, isolated from a Mexican patient with gastric cancer. The genomic data analysis revealed a cag-negative H. pylori strain that contains a prophage sequence.

GENOME ANNOUNCEMENT

Helicobacter pylori, a Gram-negative bacterium, infects half of the population worldwide (1, 2) and contributes to the development of diverse gastric diseases. Despite H. pylori infection being necessary but not sufficient for the development of diseases, infection with this bacterium is highly associated with gastric pathologies, including gastric cancer (3). Gastric cancer is a major cause of cancer death worldwide (4) and the third highest cause of cancer related to H. pylori infection in Mexico (5). However, circulating H. pylori strains in the Mexican population are poorly studied. Hence, there is a need for studies aimed at understanding H. pylori strains among the Mexican population.

We announce here the complete sequence genome of H. pylori strain 29CaP, isolated from a biopsy sample from a Mexican patient with advanced gastric adenocarcinoma. Total DNA sequencing was performed using three different technologies: PacBio RS, Illumina MiSeq 2000, and 454 Titanium. We obtained an average sequencing coverage of 135×. The quality control reads and de novo assembly were performed using the FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/), and SMRT (version 2.3)-MIRA assembler (version 3.4) tools, respectively. We closed the genome with a total assembly size of 1.6 Mb, with a G+C content of 38%.

Finally, we performed the genome annotation in GenBank using the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/). Overall, the annotation revealed a total of 1,615 genes, 117 pseudogenes, 36 tRNAs, 7 rRNAs, and 1 noncoding RNA (ncRNA). Additionally, sequence analysis of this strain showed the absence of the cag pathogenicity island, an s2i2m2 VacA genotype, and the presence of a complete prophage sequence of 31.7 kb. This genome and other sequenced genomes will be used for computational studies.

Nucleotide sequence accession number.

This whole-genome shotgun project has been deposited in GenBank under the accession number CP012907.