Draft genome sequence of a Helicobacter pylori strain isolated from a patient with diffuse gastritis from a region of high cancer risk in Colombia
Gutiérrez Escobar, Andrés J. | 2016
Helicobacter pylori is a Gram-negative microaerophilic bacterium. It has been estimated that it colonizes half of the human
population (1, 2). The prevalence of the infection correlates with the
socioeconomic status of the populations studied, more frequently
affecting developing rather than developed countries (3). The infection is associated with the development of chronic gastritis, gastric
ulcer, and stomach cancer (4), although in most cases the infection
persistsin the gastric mucosa without affecting the individual’s health
(5). In this communication, we present the genome sequence of the
strain Col2025. This strain was isolated from a 36-year-old man diagnosed with diffuse antral gastritis from Tibaná, Boyacá, a region
with high gastric cancer risk in Colombia (6). Interestingly, neither
CagA phosphorylation nor interleukin 8 (IL-8) secretion was detected when the strain Col2025 was cultured with AGS cells.
To obtain a genome sequence, 1 g of DNA was fragmented
by Covaris, and the fragments were repaired by attaching an A
to the 3= end. Illumina adaptors were ligated to the fragments
and selected for sizes between 400 and 500 bp. The size-selected
fragments were amplified by PCR and the final products validated in an Agilent Bioanalyzer. The short reads were assembled
using SOAPdenovo (7). Finally, the sequences were annotated in
GenBank using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) according to the submission guidelines (http://www.ncbi.nlm.nih.gov/genbank/genomesubmit.html).
Overall, this whole-genome shotgun sequencing revealed the following data: scaffolds, 54; contigs, 73; N50, 60,455; L50, 9; genome
size, 1.64; GC content, 38.9%; proteins, 1,451; rRNAs, 3; tRNAs,
36; genes, 1,543; pseudogenes, 52. This genome and others sequenced using strains isolated in Colombia (8, 9) will be the basis
for evolutionary computational studies.
Nucleotide sequence accession number. This whole-genome
shotgun project has been deposited in DDBJ/ENA/GenBank under the accession no.