Complete Genome Sequence of Helicobacter pylori Strain 3192, Isolated from a Chinese Patient with Chronic Nonatrophic Gastritis

ABSTRACT

Here, we present the complete genome sequence of Helicobacter pylori 3192, isolated from a patient diagnosed with nonatrophic gastritis in China. The genome is 1.6 Mbp long and encompasses 1,566 genes, including cagA and vacA genes.

ANNOUNCEMENT

Helicobacter pylori is closely related with many digestive system diseases, including chronic active gastritis, gastroduodenal ulcer, gastric mucosa-associated lymphoid tissue lymphoma, and gastric cancer (1). The H. pylori biofilm can significantly improve antibiotic resistance, which poses a challenge to the treatment of infected humans (2). Among 10 H. pylori strains, strain 3192 could form more biofilms at the gas-liquid interface in Brucella broth medium (Qingdao Hope Bio-technology Co., Ltd., China) containing 2% Gibco fetal serum (3). Here, we report the complete genome sequence of H. pylori 3192 under the World Medical Association (WMA) Declaration of Helsinki (https://www.wma.net/policies-post/wma-declaration-of-helsinki-ethical-principles-for-medical-research-involving-human-subjects/).

H. pylori 3192 was isolated from a patient with chronic nonatrophic gastritis in China and cultured on Columbia blood agar plates containing 5% sterile defibrinated sheep blood for 48 to 72 h at 37°C under microaerobic conditions. After a single colony picked from a plate grew in Brucella broth containing 2% fetal serum for 48 to 72h, its genomic DNA was extracted by a modified phenol-chloroform method (4). Genomic DNA was sequenced using the Next Ultra DNA library prep kit for Illumina (New England BioLabs [NEB], USA) on the Illumina Novaseq 6000 platform generating 150-bp paired-end reads and the SQK-LSK109 sequencing kit protocol (Oxford Nanopore Technologies, Oxford, UK) on the Nanopore PromethION platform. For Illumina sequencing, 7,181,160 raw reads (~654.9× coverage) were trimmed with sickle v1.33 (5) by removing low-quality bases at both ends of the sequence and the sequences with joints, a low average quality of bases, multiple Ns, or a short length. A total of 7,120,712 clean reads were generated. For Oxford Nanopore sequencing, GUPPY v5.0.16 (6) (https://staff.aist.go.jp/yutaka.ueno/guppy/) was used for base calling, 158,531 raw reads (~1,073.1× coverage) were quality controlled with NanoPlot v1.15.0 (7) (a threshold quality [Q] value of ≥7), and 150,516 clean reads were generated with an average length of 199,77 bp and an N₅₀ value of 21,632 bp.

The de novo genome was assembled by Unicycler v0.4.9 (8) and optimized by arrow v2.3.2 (9) to generate one single circular contig that was 1,637,585 bp long and had GC content of 38.72%; the genome coverage was 604.0×. NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v5.3 (10) was used to annotate the genome. It predicted a total of 1,566 genes with 1,453 protein-coding sequences, 2 complete sets of rRNAs (5S, 16S, and 23S rRNAs), 36 tRNAs, and 3 noncoding RNAs (ncRNAs). The types of vacA and cagA genes were further analyzed by PCR and MEGAX v10.1.8 (11) separately, and PCR primers and software parameters were same as those of Yamazaki’s research (12). The genome contains the major virulence factor Western-type cagA (3,518 bp), S1a/m2 type vacA (3,911 bp), babA (2,225 bp), and sabA (1,946 bp) (12, 13). Default parameters were used for all software unless otherwise specified.

Data availability.

The sequence read files and the genome sequences of H. pylori strain 3192 have been deposited in the GenBank database with the accession number CP086760. The raw data were deposited in the Sequence Read Archive (SRA) with the accession number SRR18740288 and SRR18210285.