Abstract
Helicobacter pylori-induced gastritis is a risk factor for developing gastric pathologies. Here, we report the complete genome sequence of a multidrug-resistant H. pylori strain isolated from a chronic gastritis patient in Mexico City, Mexico. Nonvirulent VacA and cag-pathogenicity island (PAI) genotypes were found, but the presence of a potential mobilizable plasmid carrying an IS605 element is of outstanding interest.
GENOME ANNOUNCEMENT
Helicobacter pylori infection produces chronic gastritis and increases the risk of peptic ulcer, gastric cancer, and mucosa-associated lymphoid tissue (MALT) lymphoma due to the bacterial interaction between its virulence factors and the cellular components of the host (1, 2). Whether the genome structure of the H. pylori strains isolated in Mexico is similar to that of the strains isolated worldwide or not remains unknown, as only one genome of H. pylori isolated in Mexico has been sequenced (3).
Here, we present the complete genome sequence of H. pylori strain 7C, which was isolated from a patient with chronic gastritis in Mexico City, Mexico. It is a multidrug-resistant strain, and, in a previous study, it was found to increase the apoptosis of the AGS human gastric epithelial cell line associated with the overexpression of cytosolic and membrane proteins of the bacterium (4). The genome was de novo assembled using a combination of PacBio RS, Roche 454, and Illumina MiSeq reads, with a total average coverage of 121×. Genome annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/). The H. pylori 7C chromosome is 1,624,441 bp in length, with a G+C content of 39%. It contains 1,553 genes, 83 pseudogenes, 36 tRNAs, 6 rRNAs, and 1 noncoding RNA (ncRNA). Additionally, a sequence analysis of this strain showed the absence of the cag pathogenicity island and s2i2m2 VacA genotype. Moreover, H. pylori 7C contains a 6,835-bp plasmid similar to other H. pylori plasmids previously reported in the NCBI genome database. This plasmid carries genes encoding 11 proteins that include a transposase of the IS605 insertion element, a replicase, mobilization gene (mobABD), and four hypothetical proteins. This genome and other sequenced genomes will be used for comparative genomics analyses.
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited in GenBank under the accession numbers CP012905 and CP012906.
ACKNOWLEDGMENTS
The present work was funded by CONACyT grants CB20070178787M, SALUD2009C01112588, and ICYTDF/150/2012. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
We gratefully acknowledge Victor M. Flores-López and Gabriela Guerrero for their helpful support in bioinformatics, Lucy González Villarroel for the genome annotation checkup, and Rosa Isabel Amieva-Fernández for the skillful microbiological technical support.
Footnotes
Citation Mucito-Varela E, Castillo-Rojas G, Cevallos MA, Lozano L, Merino E, López-Leal G, López-Vidal Y. 2016. Complete genome sequence of Helicobacter pylori strain 7C isolated from a Mexican patient with chronic gastritis. Genome Announc 4(1):e01503-15. doi:10.1128/genomeA.01503-15.
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