<i>Helicobacter pylori</i> culture positivity and antimicrobial susceptibility profiles (Vancouver, Canada)
Bibliographic record
Abstract
INTRODUCTION: Helicobacter pylori is associated with gastrointestinal diseases including gastritis and peptic ulcers. Despite its significance, there is a scarcity of antimicrobial susceptibility testing (AST) data available for this organism in North America. OBJECTIVES: The aim of this study was to assess the AST profile and identify factors associated with H. pylori culture positivity in a cohort of patients with refractory H. pylori undergoing gastric biopsies. METHODS: We retrospectively reviewed gastric biopsy specimens received for culture between July 2009 and February 2023. We analyzed specimen transport time, Gram smear results, direct urease test findings, culture positivity and AST profiles. Using gradient strip methodology and European Committee on Antimicrobial Susceptibility Testing breakpoints, AST was conducted for amoxicillin, clarithromycin, metronidazole, levofloxacin and tetracycline. RESULTS: Of 579 biopsy samples received for H. pylori culture, 228 (39.4%) tested positive. Samples transported within <1 h had significantly higher odds (1.81 times, P < 0.015) of being culture positive compared to those with longer transport times. Smear-positive samples had substantially higher odds (18.8 times, P < 0.001) of culture positivity compared to smear-negative. Urease-positive samples demonstrated notably higher odds (7.7 times, P < 0.001) of culture positivity compared to urease-negative samples. The collection of isolates from gastric biopsies showed susceptibility rates of 97.3% to amoxicillin, 99.1% to tetracycline, 50.4% to levofloxacin, 25.9% to metronidazole and 12.9% to clarithromycin. CONCLUSIONS: Short sample transport time was associated with improved H. pylori recovery rates. In this cohort of refractory H. pylori cases, susceptibility rates were high for amoxicillin and tetracycline and low for clarithromycin, metronidazole and levofloxacin. Susceptibility rates remained stable over time.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.007 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".