Development of a high throughput human stool specimen processing method for a molecular Helicobacter pylori clarithromycin resistance assay
DNA, Bacterial
Genotype
Helicobacter pylori
Science
Q
R
Microbial Sensitivity Tests
Polymerase Chain Reaction
Anti-Bacterial Agents
Body Fluids
Helicobacter Infections
High-Throughput Screening Assays
3. Good health
Feces
03 medical and health sciences
0302 clinical medicine
Clarithromycin
Drug Resistance, Bacterial
Medicine
Humans
Research Article
DOI:
10.1371/journal.pone.0224356
Publication Date:
2019-12-16T13:31:51Z
AUTHORS (2)
ABSTRACT
It has become critical to detect Helicobacter pylori (H. pylori) infection due to the link to gastric cancer with some strains. These strains are also increasing in resistance to antibiotics with clarithromycin leading the way as the first line treatment. Resistance to clarithromycin has been shown to correlate with the A2142G, A2142C, and A2143G mutations on the rrl gene. In the last few decades, non-invasive specimens, such as stool, have been a reliable alternate to gastric biopsy for immunoassay tests. More recently, it has been proven feasible for stool to be used in molecular based tests. Many of the core laboratories in the United States need a high throughput sample preparation to run this test. Here, a high throughput assay is compared to a previously published manual sample prep H. pylori molecular based assay. Using the Magna Pure 96 (Roche), at least 96 stool species and 96 biopsy specimens can be tested in an 8-hour shift of a clinical lab. The high throughput sample prep had a positive percent agreement (PPA) of 87% compared to the manual sample prep using the same testing configuration. The genotype predictions from the high throughput assay matched genotype predictions from the manual sample prep with the same stool sample 92% of the time. A concordance rate of 89% was observed with genotype predictions from the high throughput assay of the same patient stool and biopsy. In stool samples from the high throughput assay, there was 100% concordance between the quantitative polymerase chain reaction (qPCR)-derived genomic prediction and DNA sequencing data. The high throughput workflow can get more patients tested faster in addition to detection of mutations associated with clarithromycin resistance.
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