Molecular methods for typing of Helicobacter pylori and their applications

Abstract

Microbial typing is a useful tool in clinical epidemiology for defining the source and route of infection, for studying the persistence and reinfection rates, clonal selection in the host and bacterial evolution. Phenotypic methods such as biotyping, serotyping and hemagglutinin typing have little discriminatory power compared to genotypic methods concerning the typing of Helicobacter pylori. Therefore great efforts have been made to establish useful molecular typing methods. In this context, the most frequently used genotypic methods are described based on our own experience and the literature: (1) restriction endonuclease analysis, (2) endonuclease analysis using pulsed-field gel electrophoresis, (3) ribotyping, (4) polymerase chain reaction (using either random primers or repetitive DNA sequence primers), and (5) polymerase chain reaction-restriction fragment length polymorphism analysis of e.g. the urease genes. Furthermore, reproducibility, discriminatory power, ease of performance and interpretation, cost and toxic procedures of each method are assessed. To date no direct comparison of all the molecular typing methods described has been performed in the same study with the same H. pylori strains. However, PCR analysis of the urease gene directly on suspensions of H. pylori or gastric biopsy material seems to be useful for routine use and applicable in specific epidemiological situations.

CRISPR-like sequences in Helicobacter pylori and application in genotyping

“…This might be due to the low number of spacers detected in the tested isolates in this work. However, the reproducibility of RAPD is poor and the method lacks validated interpretation criteria for inter-laboratory comparison [ 18 , 45 ]. CRISPR-virulence typing is more reliable for long-term global epidemiology and evolutionary studies and the CRISPR locus databank is excellent for inter-laboratory interpretation and inter-laboratory reproducibility.…”

“…In studies of H. pylori , biotyping, serotyping and hemagglutinin typing, have been reported to possess low discriminatory power index (DI) compared to genotyping such as RAPD [ 14 ], pulse field gel electrophoresis (PFGE) [ 15 ], restriction fragment length polymorphism-PCR (RFLP-PCR) [ 16 ], and repetitive extragenic palindromic PCR fingerprinting (REP-PCR) [ 17 ]. PFGE is not widely used for H. pylori because inter-patient variation is rare in the fingerprints obtained [ 18 ]. The DI of PFGE is between 0.24 and 0.88 whereas RAPD analysis reveals excellent DI (between 0.99 and 1).…”

The co-evolved Helicobacter pylori and gastric cancer: trinity of bacterial virulence, host susceptibility and lifestyle

“…This 'old fashioned medical detective work' impressed the Nobel Assembly of the Karolinska Institute, to move away from basic research [1,2] and to reward the research that proposes a much controversial bacterial organism as a dangerous pathogen. It was a long-standing dogma in the medical science that stress and lifestyle factors lead to gastritis and peptic ulcer disease.…”

Evaluation of Protocol Using Gene Capture and PCR for Detection of Helicobacter pylori DNA in Feces

“…Publication of the complete genome sequence of H. pylori (21) and advances in molecular genotyping methods make possible the genotypic analysis of H. pylori DNA isolates within individuals, families, and communities (2). Studies suggest that transmission within families occurs most readily between siblings of similar ages (6) and is uncommon between couples (18).…”