I think that two of many papers from my group may be useful for you (attachment). The advantage is that these techniques may be performed in paraffined samples.

We routinely use a stool PCR in children for the detection of clarithromycin resistance: H. pylori ClariRes Assay (CE-IVD) (http://www.ingenetix.com/en/human-med/real-time-pcr-detection-bacteria-human-pathogens/h-pylori-clarires-ceivd)

1. Claudia Schabereiter-Gurtner, Alexander M. Hirschl, Brigitte Dragosics, Peter Hufnagl, Sonja Puz, Zsuzsanna Kovách, Manfred Rotter and Athanasios Makristathis. 2004. Novel real-time PCR assay for detection of Helicobacter pylori infection and simultaneous clarithromycin susceptibility testing in stool and biopsy specimens. J. Clin. Microbiol. 42:4512-8.

2. Vécsei A, Innerhofer A, Binder C, Gizci H, Hammer K, Bruckdorfer A, Riedl S, Gadner H, Hirschl AM, Makristathis A. 2010. Stool polymerase chain reaction for Helicobacter pylori detection and clarithromycin susceptibility testing in children. Clin. Gastroenterol. Hepatol. 8:309-312.

3. Vécsei A, Innerhofer A, Graf U, Binder C, Giczi H, Hammer K, Bruckdorfer A, Hirschl AM, Makristathis A. 2011. Helicobacter pylori eradication rates in children upon susceptibility testing based on noninvasive stool polymerase chain reaction versus gastric tissue culture. J. Pediatr. Gastroenterol. Nutr. 53:65-70.

Many thanks to Cristina, Ierardi, Amin and Andreas. 

Your helpful assistance and illustrious contributions are much appreciated.

Best Regards

Sayed

Dear Amin

Many thanks for your offer.  It's much appreciated.  Our Pathology Service is currently undergoing a huge transformation.  It is merging with the pathology service at a neighbouring teaching hospital trust and moving to a newly refurbished larger campus.  At this moment in time we are sorting out the logistics.  I shall call upon your expertise in due course.

Best regards

Sayed

Sayed Bukhari MD FRCPath

East Midlands, UK