title: Novel Helicobacter pylori sequencing test identifies high rate of clarithromycin resistance.
abstract: OBJECTIVE
  Eradication therapy selection for Helicobacter pylori gastritis requires knowledge of the local resistance rate to clarithromycin. There is minimal population-based or regional data in the United States on pediatric clarithromycin resistance. Although commercial methods such as fluorescence in situ hybridization and DNA probe assays are available in Europe for the evaluation of H pylori 23S rRNA mutations associated with resistance, clinical testing for 23S rRNA in the United States is not widely available. This study examined a single pediatric institution's clarithromycin resistance rate by a DNA polymerase chain reaction/sequencing assay applied to archived gastric biopsy specimens.
  
  
  METHODS
  From the period 2010 to 2012, 38 H pylori-infected gastric biopsies were examined from archived formalin-fixed paraffin-embedded (FFPE) material. The 23S rRNA gene of H pylori was polymerase chain reaction amplified and sequenced for the identification of point mutations that are associated with clarithromycin therapeutic resistance.
  
  
  RESULTS
  By 23S rRNA gene sequencing, 50% (n=19) of the specimens contained H pylori with mutations significant for clarithromycin resistance.
  
  
  CONCLUSIONS
  This study is consistent with other pediatric reports suggesting significant H pylori clarithromycin resistance in the United States. Furthermore, the method used in this study can be used by hospital-based clinical laboratories to assess local clarithromycin resistance from archived biopsy material.
authors.affiliation: *Department of Pathology †Division of Pediatric Gastroenterology, Children's Medical Center, University of Texas Southwestern Medical Center, Dallas.
authors.forename: Midori
authors.initials: M
authors.lastname: Mitui
authors.forename: Ashish
authors.initials: A
authors.lastname: Patel
authors.forename: N Kristine
authors.initials: NK
authors.lastname: Leos
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Doern
authors.forename: Jason Y
authors.initials: JY
authors.lastname: Park
mesh_terms: D000293:Adolescent; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D002648:Child; D002675:Child, Preschool; D017291:Clarithromycin / Q000494:pharmacology*; D004252:DNA Mutational Analysis / Q000379:methods; D017931:DNA Primers; D004269:DNA, Bacterial / Q000032:analysis; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D005260:Female; D016481:Helicobacter Infections / Q000188:drug therapy*; D016480:Helicobacter pylori / Q000187:drug effects* / Q000235:genetics*; D006801:Humans; D008297:Male; D016133:Polymerase Chain Reaction; D012338:RNA, Ribosomal, 23S / Q000235:genetics; D019233:Retreatment; D012680:Sensitivity and Specificity; D017211:Treatment Failure; D055815:Young Adult
chemical_list: D000900:Anti-Bacterial Agents; D017931:DNA Primers; D004269:DNA, Bacterial; D012338:RNA, Ribosomal, 23S; D017291:Clarithromycin