High natural variability bacteria identification and typing: Helicobacter pylori analysis based on peptide mass fingerprinting.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) coupled to the original Biotyper database has a poor ability to identify Helicobacter pylori. Furthermore, the existing typing methods for H. pylori have no obvious correlation with the virulence and pathogenicity of H. pylori in East Asia. In this study, MALDI-TOF MS Biotyper system (MBS) was used to identify and type H. pylori. In addition, label-free and bioinformatics techniques were used to reveal the protein components of different types of H. pylori. A total of 56 H. pylori isolates were added to the original reference database. For the 92 H. pylori strains validated, the identification efficiency at the species level was improved from 3 (3.2%) to 82 (89.1%) strains. A new ribotyping method for H. pylori based on peptide mass fingerprinting was developed. For P1 and P2 type H. pylori, respectively, 7 specific peaks at m/z 4320, 5202, 5246, 5268, 6066, 6941, and 7128 and 2 specific peaks at m/z 5246 and 6941 were found. Between P1 and P2 type strains, 62 proteins were significantly different. A total of 206 proteins for H. pylori identification and typing were identified, of which 110 were located on the inner cell membrane and 103 were located in the cytoplasm. The major classifications of these proteins were ribosomal proteins (15.5%) and enzymes (29.6%). MBS is suitable for the identification and typing of variable bacteria such as H. pylori, particularly if further super reference spectra are constructed. BIOLOGICAL SIGNIFICANCE: Helicobacter pylori (H. pylori) possesses very high genetic variability. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) coupled to the original Biotyper system (MBS) has a poor ability to identify H. pylori isolated from China. The identification capabilities of MBS for highly variable bacterial species remain to be established. On the other side, Scholars of East Asia and Western dispute the theory that there are obvious correlations between cagA and gastric cancer. The existing typing methods for H. pylori based on cagA gene have no obvious correlation with the virulence and pathogenicity of H. pylori in East Asia. In light of this phenomenon of Asian enigma, we suppose that there are other genes beyond cagA that are correlated with the virulence of H. pylori. Here, we improved the original database using numerous H. pylori isolated from different countries and raised the identification capability of MBS from 3.2% to 89.1%. A new ribotyping method for H. pylori based on peptide mass fingerprinting was developed. Furthermore, the protein components of H. pylori identification and typing were revealed. These findings thus provide a new way for H. pylori identification, typing and the research of pathogenic mechanism.