Application of 16S rRNA gene sequencing in <i>Helicobacter pylori</i> detection

Szymczak, Aleksander; Ferenc, Stanisław; Majewska, Joanna; Miernikiewicz, Paulina; Gnus, Jan; Witkiewicz, Wojciech; Dąbrowska, Krystyna

doi:10.7717/peerj.9099

Cited by 13 publications

(14 citation statements)

References 62 publications

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“…PCR can be considered as either an invasive or non-invasive method for detecting H. pylori depending on the applied material. It demonstrates up to 95% sensitivity and 95% specificity [38]. Molecular methods are more expensive than other methods, and the laboratory must have appropriate equipment and experience.…”

Section: Molecular Invasive and Non-invasive Methods For H Pylorimentioning

confidence: 99%

Current Helicobacter pylori Diagnostics

et al. 2021

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The high prevalence of Helicobacter pylori and the variety of gastroduodenal diseases caused by this pathogen necessitate the use of only accurate methods both for the primary diagnosis and for monitoring the eradication effectiveness. There is a broad spectrum of diagnostic methods available for detecting H. pylori. All methods can be classified as invasive or non-invasive. The need for upper endoscopy, different clinical circumstances, sensitivity and specificity, and accessibility defines the method chosen. This article reviews the advantages and disadvantages of the current options and novel developments in diagnostic tests for H. pylori detection. The progress in endoscopic modalities has made it possible not only to diagnose precancerous lesions and early gastric cancer but also to predict H. pylori infection in real time. The contribution of novel endoscopic evaluation technologies in the diagnosis of H. pylori such as visual endoscopy using blue laser imaging (BLI), linked color imaging (LCI), and magnifying endoscopy is discussed. Recent studies have demonstrated the capability of artificial intelligence to predict H. pylori status based on endoscopic images. Non-invasive diagnostic tests such as the urea breathing test and stool antigen test are recommended for primary diagnosis of H. pylori infection. Serology can be used for initial screening and epidemiological studies. The histology showed its value in detecting H. pylori and provided more information about the degree of gastric mucosa inflammation and precancerous lesions. Molecular methods are mainly used in detecting antibiotic resistance of H. pylori. Cultures from gastric biopsies are the gold standard and recommended for antibiotic susceptibility tests.

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Section: Molecular Invasive and Non-invasive Methods For H Pylorimentioning

confidence: 99%

Current Helicobacter pylori Diagnostics

et al. 2021

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“…Our study supports and extends, using an expanded sample size and the number of routine tests, a previous Polish study of 40 patients who were tested with histological assessment, polymerase chain reaction (PCR) detection of urease ( ureA specific primers), and 16S rRNA gene sequencing. They reported that 17.5% of infections were detected by only 16S rRNA sequencing but not with PCR or histology/IHC methods 25 . A recent Spanish study reported that using droplet digital polymerase chain reaction detected low‐density H .…”

Section: Discussionmentioning

confidence: 99%

“…logical assessment, polymerase chain reaction (PCR) detection of urease (ureA specific primers), and 16S rRNA gene sequencing. They reported that 17.5% of infections were detected by only 16S rRNA sequencing but not with PCR or histology/IHC methods 25. A recent Spanish study reported that using droplet digital polymerase chain reaction detected low-density H. pylori infection in 36% of patientsF I G U R E 1 ROCcurve of Helicobacterpylori detection based on 16S rRNA operational taxonomic units (OTUs, red line) Abbreviations: 16S rRNA, 16S ribosomal ribonucleic acid; HpN, H. pylori-negative; HpP, H. pyloripositive; OTUs, operational taxonomic units; RA, relative abundance.…”

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confidence: 99%

Advantage of 16S rRNA amplicon sequencing in Helicobacter pylori diagnosis

et al. 2021

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Background 16S rRNA amplicon sequencing is an accurate method of detecting microbial infection without culture. It is unclear if sequencing has additional benefits over routine diagnostic methods for Helicobacter pylori testing. Methods We enrolled Mongolian volunteers with dyspepsia. Using routine diagnostic methods, positive H. pylori was defined as positive results on histology/immunohistochemistry, culture, rapid urease test, or serology; negative H. pylori was defined by negative results from all these tests. We performed 16S rRNA sequencing on gastric biopsy specimens and calculated cutoffs for operational taxonomic units (OTUs) and relative abundance (RA) to define positive results using ROC curves. Results We examined 161 individuals with a mean age of 43.6 years, and 64.6% were women. Using routine diagnostic methods, 122 (75.8%) participants were H. pylori positive, the sensitivity and specificity for 16S rRNA sequencing were 94.3% and 82.1% or 93.4% and 82.1% when cutoff values were set to 1113 (OTU number) or 4.4% RA, respectively (both p < .001). When combining the validated values, the concordance rate was high (91.1%); however, 16S rRNA sequencing had additional positive yield in 9 cases (5.6%) compared with routine diagnostic methods, and much greater additional positive yield compared to histopathology/IHC, culture, RUT, serology separately with 12 (7.4%), 37 (23.0%) and 43 (26.7%). Conclusion 16S rRNA amplicon sequencing detects potentially important proportion of H. pylori‐positive cases that test negative with routine diagnostic methods. The quantitative number of H. pylori can help to understand how it can be changing by diseases and RA give opportunity to understand how H. pylori communicate with other microbiota.

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“…PCR including the assay targeting the 16S rRNA gene confirmed to be a far more sensitive method for H pylori detection in gastric biopsies compared to other methods 18 …”

Section: Invasive Testsmentioning

confidence: 98%

Review: Diagnosis of Helicobacter pylori infection

2020

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New endoscopic techniques, especially linked colour imaging (LCI) and blue laser imaging (BLI), were extensively evaluated this year either for the diagnosis of Helicobacter pylori gastritis or the detection of early gastric cancer (EGC). In the first case, the studies followed a similar protocol. Endoscopy was performed with the new imaging technique as well as white light imaging (WLI) on a group of patients for whom the H pylori status was established by various methods. Several images were obtained from different parts of the stomach and submitted blindly to a group of endoscopists (at least 4) for evaluation. The first aim was to determine the sensitivity and specificity of the new method vs WLI. LCI always performed better than WLI with sensitivity and specificity for LCI ranging from 83.8% to 85.4% and 79.5% to 99.5%, respectively (Table 1). The difficulty stemmed from the fact that there are different stages of H pylori gastritis, from active inflammation to atrophy and intestinal metaplasia, which exhibit very different aspects. Nevertheless in their study, Wang et al concluded that identification of H pylori gastritis by LCI was especially reliable in the corpus. 1 In another study by Jiang et al, using a score of 3.5 as the cutoff value, sensitivity and specificity were 83.8% and 99.5%, respectively, for the diagnosis of H pylori gastritis among 358 patients. 2 Ono et al 3

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Application of 16S rRNA gene sequencing in Helicobacter pylori detection

Cited by 13 publications

References 62 publications

Current Helicobacter pylori Diagnostics

Current Helicobacter pylori Diagnostics

Advantage of 16S rRNA amplicon sequencing in Helicobacter pylori diagnosis

Review: Diagnosis of Helicobacter pylori infection

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