Phattharaphon Wongphutorn1,4, Kittipan Samerpitak1, Narong Khuntikeo 2,4, Kookwan Sawadpanich3, Wongwarut Boonyanugomol5 and Chariya Chomvarin1,4*

1Department of Microbiology, 2Department of Surgery, 3Department of Medicine, Faculty of Medicine; Khon Kaen University, Khon Kaen, Thailand.
4Liver Fluke and Cholangiocarcinoma Research Center, Khon Kaen University,
5Mahidol University, AmnatChareon Campus, AmnatChareon, Thailand.


Helicobacter pylori is an important causative agent of gastrointestinal and hepatobiliary diseases.  The aim of this study was to investigate phylogenetic relationships among H. pylori strains from the oral cavities of healthy individuals, gastric biopsies from gastroduodenal (GI) patients and bile samples from hepatobiliary (HB) patients in the northeast of Thailand.  The DNA sequences of a portion of the vacuolating cytotoxin A gene (vacA) were investigated.  Phylogenetic trees were constructed using the neighbor-joining and maximum-likelihood methods.  The vacA sequences of H. pylori fell into four main groups on the trees.  Strains from healthy persons fell into two widely separated but well-supported groups, while most H. pylori vacA sequences from HB patients were distributed in another two groups.  In contrast, the H. pylori strains from GI patients were scattered across the tree, without a clear geographical pattern.  In conclusion, the sequence of vacA may be useful to classify the genetic relationship of H. pylori derived from different sources.

Keyword: H. pylori, vacuolating cytotoxin A gene, gastrointestinal diseases, hepatobiliary diseases and healthy persons.


Helicobacter pylori is a Gram-negative spiral-shaped bacterium, a causative agent of many gastrointestinal diseases such as dyspepsia, gastritis, peptic ulcer and gastro-esophageal reflux disease, which can lead to gastric adenocarcinoma1.  This pathogen has also been recognized as a type I carcinogen by the World Health Organization’s International Agency for Research on Cancer because it is associated with gastric mucosa-associated lymphoid tissue lymphoma and gastric adenocarcinoma2.

Helicobacter pylori was recently proposed to be associated with diseases outside the gastroduodenal tract, particularly the hepatobiliary duct system3.  Such diseases include cholangiocarcinoma (CCA), which is a primary cancer of the biliary epithelium and is highly endemic in Northeast Thailand4.  Several studies have demonstrated that the virulence genes in H. pylori, including the vacuolating cytotoxin gene A (vacA) and cytotoxin-associated gene A (cagA), may help to predict the association between H. pylori infection and clinical outcomes4,5.  However, cagA and other virulence genes (viz. babA, cagE and iceA) are present in only some strains of H. pylori, whereas vacA is present in all H. pylori strains6.

Vacuolating cytotoxin induces intracellular vacuoles, leading to epithelial damage of eukaryotic cells7 by suppressing epithelial proliferation, promoting apoptotic cell death8, inducing cytoskeletal changes8 and suppressing epithelial proliferation9.  Each allelic variant of vacA contains one of two classes of signal-region variant (s1 or s2) and one of two classes of middle region (m1 or m2) variant10.  Allelic variation among strains results in variation of vacuolating activity11.  The s1/m1 H. pylori strain displays a higher vacuolating activity than that does the s1/m2 strain and might be associated with gastritis and gastric adenocarcinoma. In contrast, the vacA s2/m2 strain is rarely associated with such diseases due to the absence of cytotoxic activity12.  Although, vacA genotype status might help predict the development of diseases, one report has suggested that genotype of vacA was not associated with the clinical outcome of peptic ulcer, duodenal ulcer and gastric cancer13.  Therefore, in this study, we test the idea that the vacA sequence can be used to distinguish among clinical sources of specimens.

Routes of H. pylori transmission are oral-oral14, gastro-oral15 and fecal-oral16.  Saliva can be a reservoir of H. pylori, potentially infecting or reinfecting the stomach17.  It might be that the genotypes of H. pylori strains in saliva of healthy persons can be useful for mapping the geographical distribution of H. pylori strains associated with gastroduodenal (GI) and hepatobiliary (HB) diseases.  To explore this possibility, we sequenced portions of the vacA gene from specimens from healthy individuals and from patients with various gastroduodenal and hepatobiliary diseases.


Study subjects
Study subjects consisted of healthy persons, patients with GI diseases and patients with hepatobiliary diseases admitted to Srinagarind Hospital, Faculty of Medicine, Khon Kaen University, Thailand.  Approval for the study was obtained from the Human Ethics Committee of Khon Kaen University (approval nos. HE571489 and HE581271) and prior written informed consent was obtained from all participants.

Collection and processing of saliva samples
Thirty saliva samples were collected from healthy person using the method of Silva (2009), with slight modifications18.  Two ml of each saliva sample was added to 8 ml of Brucella broth (CRITERION™, USA) and incubated for 3 days at 37 °C with shaking under microaerobic atmosphere (5% O2, 10% CO2 and 85% N2).  After centrifugation at 13,000 rpm for 10 minutes at 4 °C, the pellet from each culture was used as a source of DNA for amplification of vacA by nested PCR.

Collection and processing of gastric biopsy and bile specimens
Gastric biopsies were performed on dyspeptic patients undergoing gastro-endoscopic examinations at the Endoscopy Unit, Srinagarind Hospital, Faculty of Medicine, Khon Kaen University.  Dyspeptic patients (GI) were characterized as having non-ulcer disease (NUD) (n = 20), peptic ulcer disease (PUD) (n = 3) or gastric cancer (GC) (n = 2).  Gastric samples from these patients were positive for the rapid urease test indicating H. pylori infection.  Bile samples, positive for H. pylori via PCR detection of ureA gene, were taken from patients with hepatobiliary disorders, namely, CCA (n = 20) and cholelithiasis (n = 9), at the Surgical Unit, Srinagarind Hospital, Faculty of Medicine, Khon Kaen University.  The sources of the clinical specimens are summarized in Table 1.

Table 1. Sources of samples used in this study

Source of samples
Number of samples
Sample code
Healthy persons (n=30)
·  Saliva samples
Gastroduodenal patients (n=25)
·  Non-ulcer disease (NUD)
·  Peptic ulcer diseases (PUD)
·  Gastric cancer (GC)
Hepatobiliary patients (n=30)
·   Cholangiocarcinoma (CCA)
·   Cholelithiasis
·    Other hepatobiliary diseases
Reference strains*
·  Japan
·  India
·  Kenya
·  USA
·  China
·  Italy
·  Western Africa

CP06826, AB190972, AB190973, AF071097, AB190965
GQ331975, GQ331980, GQ331984
AF191641, AF191642, AF191644
CP003474, AE000511


* = All reference strains taken from Genbank were isolated from GI patients

DNA extraction
DNA was extracted from pellets of saliva samples using a modified method based on the Puregene DNA Purification System (Gentra System, USA)19.  DNA was extracted from bile samples and biopsy specimens using the Gentra System DNA extraction and purification kit (Big Lake, MN, USA), respectively, as previously described4,20.

PCR amplification and DNA Sequencing
Amplification of a portion of the vacA gene from each sample was performed by nested PCR using primers and conditions as shown in Table 2.  The inner primers (forward: nt. 2673-2692, reverse: nt. 2929-2948; GenBank GQ331975) amplified a fragment of vacA encoding amino acid positions 892 to 979.  The region amplified does not include the s or the m region.  Nested PCR assay was performed in a total volume of 25 µl containing 500 ng of DNA template, 2 mM dNTPs (Amresco, Ohio, USA), 1X PCR buffer (10 mM Tris-HCl pH 8.3, 50 mM KCl, 0.1 mg/ml bovine serum albumin, 10 mM (NH4)2SO4, and 1.5 mM MgCl2) (RBC bioscience, Taipei, Taiwan), 0.5 U Taq polymerase (RBC Bioscience, Taipei, Taiwan), and 0.4 µM vacA primers.  Thermocycling was conducted in a C1000™ Thermal Cycler (BioRad, USA).  Amplicons were purified using spin column PCR clean up kit (DNA sequencing service; BIONEER, Korea) and sequenced using Sanger sequencing method (DNA sequencing service; BIONEER, Korea).  

Table 2. Primer sequences and PCR condition for detection of H. pylori

Specific for Primer sequence (5’>>>3’) Product size (bp) PCR condition

(H. pylori)

OF-GCATGATTTTGGCACCATTG 429 95 °C 30 s, 54 °C 30 s,

72 °C 45 s (35 cycles)

IF-GCATGATTTTGGCACCATTG 276 95 °C 30 s, 62 °C 30 s,

72 °C 45 s (35 cycles)

vacA s1/s224 F-ATGGAAATACAACAAACACAC 259/286 94 °C 60 s, 58 °C 60 s, 72 °C 60 s (35 cycles)
vacA m1/m224 F-CAATCTGTCCAATCAAGCGAG 567/642 94 °C 60 s, 55 °C 60 s, 72 °C 60 s (35 cycles)

Phylogenetic analysis
The vacA sequences from all samples, including sixteen reference sequences of H. pylori vacA from GenBank (Table 1), were aligned using the MAFFT program (  The aligned sequences were adjusted and edited using BioEdit v.  Phylogenetic analyses were conducted in MEGA software version 7.021.  The phylogenetic trees were constructed and compared using the neighbor-joining and maximum-likelihood methods with 1,000 bootstrap replicates.  The Kimura 2-parameter model with Gamma distribution was used as the best model (the model giving the best log-likelihood value.


The phylogenetic trees (Figs. 1 and 2) revealed that most sequences from Thai samples fell into distinct clades and were generally also distinct from sequences from other countries.  The alignment of 101 partial sequences of the vacA gene was 276 bp in length, and translated to 88 amino acids (Fig. 3).

Fig. 1. Neighbor joining tree with 1,000 bootstraps from a dataset of partial vacA gene sequences.  Numbers on the branches are bootstrap values (%).  Disease conditions are represented by NUD; nonpeptic ulcer diseases, PUD; peptic ulcer diseases and CCA; cholangiocarcinoma

Fig. 2. Maximum likelihood tree with 1,000 bootstraps from a dataset of partial vacA gene sequences.  Numbers on the branches are bootstrap values (%).  Disease conditions are represented by NUD; nonpeptic ulcer diseases, PUD; peptic ulcer diseases and CCA; cholangiocarcinoma

Fig. 3. Differences among the source-groups of H. pylori strains in an 88-amino acid portion translated from the vacA gene sequence.  H. pylori PG225 is the reference strain from the NCBI database (GQ331975).  Abbreviation of amino acids represented by A, Alanine; C, Cysteine; D, Aspartic acid; E, Glutamic acid; G, Glycine; H, Histidine; I, Isoleucine; K, Lysine; L, Leucine; N, Asparagine; Q, Glutamine; R, Arginine; S, Serine; T, Threonine; V, Valine

The neighbor-joining tree (Fig. 1) placed the thirty sequences from healthy Thai people into two very distinct groups with high bootstrap support: group 1 (82% support) consisted of 23 sequences and group 4 (97% support) included 6 sequences.  Sequences from Thai hepatobiliary patients mostly fell into two groups, group 2 consisting of 10 sequences from CCA patients together with 5 sequences from Thai gall-stone patients (58% bootstrap support), and group 3 consisting of 8 sequences from CCA patients and 1 sequence from patients with other hepatobiliary diseases (98% support).  In contrast, most vacA sequences from Thai GI patients were not close to those from healthy individuals or HB patients, but were scattered across the tree and often among vacA sequences of GI patients from various countries.  Similarly, H. pylori sequences from saliva samples of healthy persons, gastric biopsies of gastrointestinal tract patients (GI) and bile samples of hepatobiliary patients were grouped in the maximum likelihood tree (Fig. 2) in a manner consistent with the neighbor joining tree.  Bootstrap values differed slightly between the trees and the 4 groups, while still strongly supported, fell in somewhat different parts of the two trees.

In this study, we also determined the alleles of vacA (s and m) present in the bile samples of hepatobiliary patients which are nearly all of were s1 and m1 (data not shown).  Therefore, these alleles can’t be used to identify the different clinical origins of samples.

Translated amino acid sequences were compared among the four groups of H. pylori (indicated in Fig. 1 and 2) and found to differ at many positions (Fig. 3).


Our study is the first investigation on the genetic diversity and relationships of vacA gene sequences of H. pylori from different sources; saliva from healthy persons, gastric biopsies from gastrointestinal tract patients (GI) and bile samples from hepatobiliary patients (CCA and cholelithiasis) in Thailand  Partial vacA gene sequences from healthy persons were obviously very different from those of HB patients.  H. pylori strains from saliva samples of healthy persons fell into two well-supported but widely separated clades (clades 1 and 4).  Strains isolated from HB patients, especially those with CCA, mostly also fell into distinct clades (clades 2 and 3).  These results indicate that particular genotypes of vacA may occur in strains of H. pylori specific to particular sources (disease status of the host and geography).  This applied strongly to strains from CCA patients: this disease is highly endemic in Thailand.  Interestingly, most H. pylori strains from GI tracts of Thai patients were distributed among other strains of GI patients from different countries, but not among the strains from healthy persons or HB patients.  It seems that most H. pylori strains in saliva of healthy persons in Northeast Thailand may not be derived from the strains isolated from GI and HB patients. The partial vacA gene sequence developed in this study has the potential to distinguish among H. pylori strains from different origins and sources.  In this study, genetic diversity and relationships of H. pylori from different sources were determined using neighbor-joining and maximum-likelihood methods.  Results from the two methods were in broad agreement, suggesting we were close to the true phylogenetic tree.  An advantage of the neighbor-joining method is more computational efficiency and speed than maximum-likelihood method, making it suitable for analysis of large data sets.  However, this method is unsuitable if very divergent sequences are included22.  The maximum-likelihood (ML) approach is character-based and is now widely used owing to the development of increasingly realistic and explicit models of sequence evolution.  However, likelihood calculations and tree searches under the likelihood criterion are computationally demanding, making this approach very slow, especially if many sequences are included in the alignment22.  Researchers can choose the method that best suits their data24.

Differences were apparent between the four clades of sequences at both the DNA and the amino acid level.  Presumably, this is a consequence of adaptation to different environmental sources, hosts and geography13,23.  However, the relationship between vacA diversity, origin, and disease state in the host should be further investigated.

In conclusion, these findings support that the partial vacA sequence may be useful as a marker to distinguish H. pylori from difference sources, such as from healthy persons or patients with gastrointestinal and hepatobiliary disease, and as a marker to investigate genetic relationships among the strains isolated from different sources.


This study was supported by the Higher Education Research Promotion and National Research University Project of Thailand, Office of the Higher Education Commission, through the Center of Excellence in Specific Health Problems in Greater Mekong Sub-region cluster (SHeP-GMS), Khon Kaen University to Chariya Chomvarin et al.  The authors thank the Liver Fluke and Cholangiocarcinoma Research Center for a scholarship.  We would like to acknowledge Prof. David Blair, Publication Clinic, Khon Kaen University for editing the manuscript via Publication Clinic, Khon Kaen University, Thailand.


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