Genomic characterization of a Helicobacter pylori isolate from a patient with gastric cancer in China

Helicobacter pylori, a Gram-negative bacterium that colonizes in the human stomach, has been widely recognized as a pathogenic bacteria related to the pathogenesis of gastritis, ulcers, and carcinoma [1‐3]. The high genetic variability of H. pylori drives its dramatic ability to adapt to the gastric niche [4‐9]. However, although many studies have been performed, its mechanisms are still not well elucidated.

With the rapid development of the next generation sequencing technology and reduced costs, it has become possible to perform large scale genome sequencing procedures to obtain ample information about biological population structure and disease markers. Over the past few years, increasingly more H. pylori strains from different geographic regions, ethnicities, and diseases have been sequenced [10‐12], and at least 50 genome sequences are currently available in public databases.

In a previous study, we published genome sequences of three strains recovered from patients with ulcers and atrophic gastritis in Heilongjiang province [13]. It is well known that H. pylori strains isolated from different geographic areas show dramatic genomic diversity [14]. Thus, at the genomic level, comparative analysis among strains with different clinical manifestations should initially eliminate such interference. Comparative genomic sequencing analysis of strains isolated from single patients could be a reliable way to eliminate such interference [15‐17]. However, it is usually difficult to follow a patient and obtain strains isolated from various unpredictable manifestations.

In this study, we reported a draft genome sequence of strain HLJ039 that was isolated from a patient with gastric cancer in Heilongjiang province. After integration with the other three genomes from the same area, initial comparative genomic analysis was performed to investigate the genetic features of gastric cancer isolates.

This research was approved by the meeting of ethics committee of national institute for communicable disease control and prevention, China CDC, according to Chinese ethics laws and regulations. NO:ICDC-2013001.

We ultimately obtained 42 contigs with a total length of 1,611,192 bp and predicted 1,687 CDS within the draft genome of strain HLJ039. Additional information is included in the sequencing reports of HLJ039 (Additional file 2). The G + C content was 38.72%. The subsystem distribution and general information about the potential functional distribution of HLJ039 are shown in Figure 1. Compared to the additional three HLJ genomes, HLJ039 has 10 different regions (DRs). Detailed information about these fragments is shown in Table 1. The locations of these DRs are labeled in the whole genome (Figure 2). Approximately half of these sequences encoded hypothetical proteins. Most of the DR sequences encoded proteins involved in DNA methylase and a restriction modification enzyme. Notably, a unique 547-bp fragment (DR9) sharing 93% identity with a hypothetical protein of Helicobacter cinaedi ATCC BAA-847 was found that had never been present in any other H. pylori strains previously, which indicated a possible horizontal gene transfer between H. pylori and H. cinaedi. DR9, located in scaffold 5, inserts into a 1,371-bp gene encoding type III restriction endonuclease, which is responsible for adenine-specific DNA methylase modifications.

All of the above findings highlight the important role of DNA restriction modification systems in H. pylori genomic recombination. A total of 29,259 core SNPs were found among the 54 analyzed genome sequences. Based on a core genome SNP analysis of 54H. pylori strains distributed in various worldwide regions, a phylogenetic tree was generated to show the HLJ039 subtype. All strains were classified into different groups defined by earlier studies according to multilocus sequence typing [24, 25]. Figure 3 shows that HLJ039 was defined as belonging to the hspEAsia subgroup, which belonged to the hpEastAsia group.

Note: Different regions (DRs) refers to coding sequence insertion and deletion in HLJ039 compared to the other three genomes.

The incidence of gastric carcinoma in East Asian countries is quite high [18, 19]. To explore the potential pathogenic mechanisms that may contribute to this phenomenon, more East Asian H. pylori strains must first be sequenced. The strains selected for sequencing should be representative and eliminate geographic variation. Our future directions will focus on large-scale genomic sequencing of different clinical isolates from areas with a high incidence of gastric cancer. More detailed analyses involved in DNA methylation as well as restriction and modification systems would be the most attractive directions for studies of H. pylori-induced gastric cancer.

Additional data supporting the results reported here are included within the additional files.