Helicobacter ISSN 1523-5378 © 2007 The Authors 136 Journal compilation © 2007 Blackwell Publishing Ltd, Helicobacter 12 : 136–141 Blackwell Publishing Ltd Oxford, UK HEL Helicobacter 1083-4389 © 2007 The Authors Journal compilation © 2007 Blackwell Publishing Ltd 12 2 Original Article H. pylori and FISH Yilmaz et al. Detection of Helicobacter pylori and Determination of Clarithromycin Susceptibility Using Formalin-Fixed, Paraffin-Embedded Gastric Biopsy Specimens by Fluorescence In Situ Hybridization Özlem Yilmaz, * Ebru Demiray, † Sait Tümer, ‡ O G uz Altungöz, ‡ Kutsal Yörüko G lu, § Müjde Soytürk ¶ and ˆ lkay 6 im 5 ek ¶ * Department of Microbiology and Clinical Microbiology, † Department of Medical Biology and Genetics, ‡ Department of Pathology, § Department of Gastroenterology, Faculty of Medicine, Dokuz Eylül University, Inciralti, Izmir, Turkey Abstract Background:Clarithromycin resistance and poor compliance to therapy are often responsible for Helicobacter pylori eradication therapy failure. Aim: To evaluate fluorescence in situhybridization (FISH) as a nonculture method to simultaneously detect H. pylori and to identify clarithromycin resistance. Methods: Fifty-four patients with dyspepsia (17 male, 37 female subjects; mean age, 46.5; range, 21–78 years) were studied. Two antrum and corpus biopsies were taken from each patient. Positive rapid urease test (RUT) and histopathologic examinations defined H. pylori positivity. A total of 108 formalin-fixed paraffin-embedded gastric mucosal biopsies were examined retrospectively by the FISH (seaFAST H. pylori Combi-Kit) method. Results: Forty-five patients (83.3%) were H. pylori positive and 43 (95.5%) were also positive by FISH. There were two false-positive FISH results. Fourteen patients (31.1%) had clarithromycin-susceptible strains, 4 (8.9%) resistant strains, and 27 (60%) both susceptible and resistant strains. Conclusion: FISH results correlated well with H. pylori infection and were able to identify clarithromycin-susceptible and -resistant strains. This technique will be helpful in determining the bacterial density and the success of treatment where clarithromycin has been widely used in populations to increase the efficacy of the treatment and to clarify the treatment failure in vitro. Keywords Helicobacter pylori , fluorescence in situ hybridization (FISH), clarithromycin resistance. Reprint request to : Özlem Yilmaz, Department of Microbiology and Clinical Microbiology, Faculty of Medicine, Dokuz Eylül University, Izmir, Turkey. Tel.: 00 90 232 4124506; Fax: 00 90 232 2590541; E-mail: ozlem.yilmaz@deu.edu.tr Helicobacter pylori is etiologically associated with gastritis, gastric and duodenal ulcers, gastric adenocarcinoma, and mucosa-associated lymphoid tissue (MALT) lymphoma [1,2]. The most widely used triple therapy consists of a proton pump inhibitor (PPI) in combination with two antibiotics: amoxicillin, and clarithromycin or metronidazole [3–6]. Although clarithromycin is a key component of most treatment recommendations to eradicate H. pylori [7], resistance has become increasingly widespread and is a frequent cause of treatment failure [4]. The main factors for treatment failure are low compliance with drug intake and bacterial resistance to the antibiotics used in the regimen [6]. Resistance of H. pylori to clarithromycin is mainly due to point mutations in the 23S rRNA, which eliminates the binding sites and prevents macrolides from binding to the ribosome. Point mutations include an adenine-to-guanine transition at positions A2142G, A2143G, and A2144G or an adenine-to-cytosine transversion at position A2142C and A2143C, which are included in the peptidyltrans- ferase-encoding region of the 23S rRNA [3,5,8–12]. Muta- tions A2142G and A2143G are most often observed; the A2142C mutation being less common [13]. Other point mutations A2115G, G2141A, and T2717C have been also reported but these mutations appear to be very rare [14– 17]. As expected, clarithromycin resistance is associated