Methods for detection of antibiotic resistant h.pylori

A method for obtaining H. pylori DNA from a fecal sample, the method comprising:

• a) exposing a first part of the fecal sample to an anti-H. pylori antibody;
• b) separating H. pylori bound to the anti-H. pylori antibody from fecal material in the first part of the fecal sample;
• c) extracting H. pylori DNA from the H. pylori separated from the first fecal material;
• d) exposing a second part of the fecal sample to a DNA probe that binds to H. pylori DNA;
• e) extracting the H. pylori DNA from the second part of the fecal sample;
• and
• f) pooling the H. pylori DNA obtained from the first part of the fecal sample and the H. pylori DNA obtained from the second part of the fecal sample.

A method for treating H. pylori infection in a subject, the method comprising:

• a) obtaining a sample from the subject;
• b) obtaining a threshold level of H. pylori DNA from the sample;
• c) amplifying a region of the H. pylori DNA to generate multiple copies of the region of the H. pylori DNA;
• d) sequencing the multiple copies of the region of the H. pylori DNA;
• e) comparing sequences of the multiple copies of the region of the H. pylori DNA to one or more reference sequences;
• f) detecting a mutation in the multiple copies of the region of H. pylori DNA;
• g) determining a number of the multiple copies of the region of the H. pylori DNA with the mutation, wherein antibiotic resistant H. pylori is present in the sample when the number of the multiple copies of the region of the H. pylori DNA with the mutation is above a predetermined amount;
• and
• h) administering to the subject one or more antibiotics to which the H. pylori lacks resistance.