A culture-free whole-genome sequencing approach for rapid detection and characterization of Helicobacter pylori in gastric biopsies

Helicobacter pylori is a gastric pathogen with a high worldwide prevalence and a significant clinical burden. Chronic infection leads to chronic gastritis and can progress to other disorders such as ulcers, MALT lymphoma or gastric adenocarcinoma. The emergence of multi-resistant strains is responsible for increasing failure rates of first-line combination therapies and the WHO classified H. pylori as a high priority organism for the development of novel antibiotics in 2017. Current clinical guidelines for the eradication of H. pylori typically recommend antibiotic susceptibility testing only after unsuccessful first-line treatments. However, culture-based susceptibility testing of H. pylori can take up to two weeks and thus empirical drug therapies are generally started before results are available.

To address this clinical situation, we developed a microbial enrichment pipeline allowing us to sequence whole H. pylori genomes from DNA directly extracted from gastric biopsies obtained during routine endoscopy. The pipeline comprises multiple rounds of enrichment with native genomic DNA, sequencing libraries and real-time Nanopore sequencing. Using this approach, we were able to obtain complete H. pylori genomes with 5-10x coverage, representing a 50 to 100-fold enrichment of the low-abundance bacterial DNA within gastric tissue samples. The resulting genomic data can then be used for further characterization relevant to clinical diagnosis or public health surveillance. In particular, we performed a genotype-based analysis to predict susceptibility to clinically relevant antibiotics and obtained accuracies ranging from 93% (clarithromycin) to 62% (metronidazole).

In summary, our approach allows for quick determination of antibiotic susceptibility in H. pylori which can ultimately be implemented as a rapid diagnostic test to optimize therapeutic efficiency and curtail the development of antibiotic resistance in this pathogen.