title: Fast and accurate quantitative detection of Helicobacter pylori and identification of clarithromycin resistance mutations in H. pylori isolates from gastric biopsy specimens by real-time PCR.
abstract: Rapid identification of patients infected with clarithromycin-resistant Helicobacter pylori without the need for culture can help to avoid useless prescriptions of clarithromycin. We developed and tested a routine real-time quantitative PCR assay dedicated to that purpose. One hundred ninety-six consecutive gastric biopsy specimens were examined by culture, histology performed by a trained physician, and rapid PCR with the LightCycler apparatus. Infection was defined as (i) positivity of culture, (ii) positivity of histology, or (iii) positivity of PCR if confirmed by positivity of a concomitant indirect test (serology or urea breath test). Susceptibility to clarithromycin was tested by E-test and PCR. The prevalence of infection was 33.7% (66 of 196 samples). The sensitivities of culture, histology, and PCR were 90.9% (60 of 66 samples), 87.9% (58 of 66 samples), and 97.0% (64 of 66 samples), respectively. The specificity of PCR was 94.6% (123 of 130 samples). The linearity of the PCR results was achieved over a 6-log range of input DNA, and we were able to accurately quantify as few as 300 bacteria and to qualitatively detect as few as 30 bacteria per DNA sample. For clarithromycin susceptibility testing, there was 98.2% (55 of 56 samples) concordance between E-test and PCR. Forty-eight strains were clarithromycin susceptible, and 9 strains were clarithromycin resistant. The single discrepancy concerned a culture which was a mixture of mutant and wild type, with a susceptible-to-resistant ratio of 11.5: the resistant population was detected by E-test but not by PCR. Our PCR assay is accurate for fast detection of H. pylori as well as of clarithromycin resistance and is also able to objectively determine bacterial density.
authors.affiliation: Laboratoire de Bactériologie, Centre Hospitalo-Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris, Université Paris XII, Créteil, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Lascols
authors.forename: Dominique
authors.initials: D
authors.lastname: Lamarque
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Costa
authors.forename: Christiane
authors.initials: C
authors.lastname: Copie-Bergman
authors.forename: Jeanne-Marie
authors.initials: JM
authors.lastname: Le Glaunec
authors.forename: Lionel
authors.initials: L
authors.lastname: Deforges
authors.forename: Claude-James
authors.initials: CJ
authors.lastname: Soussy
authors.forename: Jean-Claude
authors.initials: JC
authors.lastname: Petit
authors.forename: Jean-Charles
authors.initials: JC
authors.lastname: Delchier
authors.forename: Jacques
authors.initials: J
authors.lastname: Tankovic
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001706:Biopsy; D017291:Clarithromycin / Q000494:pharmacology*; D003470:Culture Media; D004275:DNA, Ribosomal / Q000032:analysis; D024881:Drug Resistance, Bacterial / Q000235:genetics; D016481:Helicobacter Infections / Q000382:microbiology*; D016480:Helicobacter pylori / Q000187:drug effects / Q000254:growth & development / Q000302:isolation & purification; D006801:Humans; D008826:Microbial Sensitivity Tests; D009154:Mutation; D016133:Polymerase Chain Reaction / Q000379:methods*; D012338:RNA, Ribosomal, 23S / Q000235:genetics*; D013270:Stomach / Q000382:microbiology*; D013997:Time Factors
chemical_list: D000900:Anti-Bacterial Agents; D003470:Culture Media; D004275:DNA, Ribosomal; D012338:RNA, Ribosomal, 23S; D017291:Clarithromycin