title: Effectiveness of enterobacterial repetitive intergenic consensus PCR and random amplified polymorphic DNA fingerprinting for Helicobacter pylori strain differentiation.
abstract: We compared the robustness and discriminatory power of the enterobacterial repetitive intergenic consensus (ERIC) and random amplified polymorphic DNA (RAPD) fingerprinting methods for detecting cases of mixed Helicobacter pylori infection in Peruvian shantytown residents. H. pylori isolates from 63 participants were cultured, and five single colonies and a pool of additional colonies from each participant were analyzed by ERIC-PCR and by RAPD tests with four 10-nucleotide primers (one primer per reaction). There was 94% agreement between the ERIC and RAPD profiles in classifying sets of isolates as uniform versus closely related but not identical versus probably unrelated, indicating a high kappa statistic of 0.8942. Subtle differences in related ERIC or RAPD patterns likely reflect gene transfer between strains, recombination, and/or mutation, whereas markedly different patterns reflect infection by unrelated strains. At least half of infected shantytown residents seemed to carry more than one H. pylori strain, although in 19 of 31 persons, the strains were closely related. Three RAPD tests, each with a different primer, were needed to achieve the sensitivity of one ERIC test. ERIC-PCR constitutes a resource- and time-efficient method for H. pylori strain differentiation.
authors.affiliation: Departamento de Microbiología, Universidad Peruana Cayetano Heredia, Lima, Peru.
authors.forename: S Alison
authors.initials: SA
authors.lastname: Finger
authors.forename: Billie
authors.initials: B
authors.lastname: Velapatiño
authors.forename: Margaret
authors.initials: M
authors.lastname: Kosek
authors.forename: Livia
authors.initials: L
authors.lastname: Santivañez
authors.forename: Daiva
authors.initials: D
authors.lastname: Dailidiene
authors.forename: Willi
authors.initials: W
authors.lastname: Quino
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Balqui
authors.forename: Phabiola
authors.initials: P
authors.lastname: Herrera
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Berg
authors.forename: Robert H
authors.initials: RH
authors.lastname: Gilman
mesh_terms: D015373:Bacterial Typing Techniques; D016172:DNA Fingerprinting / Q000379:methods*; D004269:DNA, Bacterial / Q000032:analysis; D021901:DNA, Intergenic / Q000032:analysis; D016481:Helicobacter Infections / Q000382:microbiology*; D016480:Helicobacter pylori / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods*; D019105:Random Amplified Polymorphic DNA Technique / Q000379:methods*; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D004269:DNA, Bacterial; D021901:DNA, Intergenic