SMI notes: Investigation of infectious causes of dyspepsia (SMI B 55)
drsuryabrata@gmail.comThere are 2 SMIs related to H pylori- Identification of Helicobacter spp. (SMI ID26) & Investigation of infectious causes of dyspepsia (SMI B55).
Available tests for the diagnosis of H. pylori infection
There are 4 major types of tests that we can use to test for H pylori.
1. Urea breath test (UBT)
- This is the most accurate test.
- It is recommended for both initial tests for someone who never had a test for H pylori before and repeat tests after a course of treatment if indicated.
2. Stool antigen test (SAT)
- Two methods are available – Lab-based ELISA and near-patient (immunochromatography) test.
- Lab-based ELISA using monoclonal antibodies have high accuracy for both primary diagnosis and post-treatment diagnosis.
- Near-patient tests are less reliable.
- Use a fresh faecal sample.
3. Serology – antibody test (HiG)
- Only IgG is tested by ELISA as H pylori are considered to be a chronic infection.
- not recommended for most patients, and positives should be confirmed by a second test such as UBT, SAT or biopsy.
- has a very good negative predictive value at current (it is reliable when it is negative, less so when it is positive); low prevalence in the developed countries.
- most useful in patients with acute gastrointestinal bleeding (and atrophy or gastric malignancy), to confirm negative UBT or SAT. Blood and PPI use interacts with UBT/SAT.
- Blood serology is less predictive and results are variable for current infection. It should not be used in the elderly, children or post-treatment.
- Near-patient serology tests are not recommended.
4. Microscopy and culture of gastric biopsy
- Gastric biopsy should be considered
1. after 1st failure and if an endoscopy is being done.
2. on all cases if there is a 2nd treatment failure.
3. In areas where clarithromycin resistance is >20% (The Maastricht IV consensus report). - A biopsy is taken from the site of inflammation – most commonly gastric antrum, then the main body, and in cases of duodenal ulcer – duodenal biopsy.
- 90% sensitivity was reported if the two biopsies are examined.
- Ideally, samples should be taken before the antibiotic, but due to the NICE test and treat strategy – most samples would be from cases of treatment failure.
- A period of at least two weeks should have elapsed since the last dose of antimicrobial therapy before the collection of the specimen.
Other tests
- PCR for identification and clarithromycin resistance,
- histology
- MALDI- ToF
Laboratory processing of H pylori
Laboratory safety
- Containment level 2.
- Laboratory procedures that give rise to infectious aerosols must be conducted in a microbiological safety cabinet.
Transporting media
- Dent’s transport medium.
- Alternatively isotonic saline.
- Process within 6 hours, if not store at 4 degrees C covered with 1mL brain-heart infusion broth for 48 hrs.
Stain
- Organisms may be stained using Giemsa or Gram stain. Use carbol fuchsin or Sandiford’s counter stain
- Stain smears from blood cultures with acridine orange rather than Gram stain.
- Gram-negative, long, thin, straight or slightly curved to spiral-shaped rods. It could be spiral/helical and even coccoid (in older cultures).
Plate selection
- H pylori selective media or Dent selective media: blood agar with dent supplement (vancomycin, trimethoprim, cefsoludin and amphotericin B). Incubation is microaerophilic, with 3-5% H2 @35 degrees C for 10 days.
- Chocolate/blood agar
- If the urease test has not been performed (i.e. UBT), use Christenson’s Urea broth.
Colony
- Small (1mm), grey, translucent and maybe slightly haemolytic after 3-5 days. Longer incubation may show swarming colonies.
Identification
- Catalase, and oxidase positive; Urease reaction is variable for different species, but H pylori is strongly positive.
- PCR & MALI ToF (depend on the database).
Sensitivity test
- Use MIC. Report – Amoxicillin, clarithromycin, metronidazole, levofloxacin, tetracycline.
- Rifampicin is the 2nd line.
- EUCAST breakpoints available.
Other tests that can be done on biopsy
- Histology and urease test.
H pylori resistance rate in the UK
| ANTIBIOTIC | RESISTANCE RATE |
|---|---|
| Metronidazole | 22-88% |
| Clarithromycin | 3-68% |
| Levofloxacin | 17% |
| Amoxicillin, rifampicin, tetracycline | 3% |
| Rifabutin | <1% |
