Review: Diagnostic accuracy of <scp>PCR</scp>‐based detection tests for <i>Helicobacter Pylori</i> in stool samples

Khadangi, Fatemeh; Yassi, Maryam; Kerachian, Mohammad Amin

doi:10.1111/hel.12444

Cited by 38 publications

(28 citation statements)

References 49 publications

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“…This does not contradict the fact that H pylori DNA and antigens can be detected routinely in feces. 42 An important limitation of our study is that the analysis reflects the gut microbiota composition at a given moment of the digestive process (all individuals were fasting at the time of sampling). At present, we are unaware of temporary variations of microbial communities related to the different phases of digestion, which are characterized by profound changes in GI motility and in secretions following nutrients intake.…”

Section: Discussionmentioning

confidence: 99%

Analysis of Transcriptionally Active Bacteria Throughout the Gastrointestinal Tract of Healthy Individuals

Vasapolli¹,

et al. 2019

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See Covering the Cover synopsis on page 907; see editorial on page 927. BACKGROUND & AIMS:The microbiome varies along the human gastrointestinal (GI) tract with exposure to luminal and mucosal factors. We analyzed active bacterial communities at 8 locations along the GI tract using high-throughput sequencing techniques. METHODS: We collected saliva, mucosal, and fecal samples from healthy adults (10 men and 11 women; mean age, 59 ± 12.3 years) who underwent upper and lower GI tract endoscopy in Germany from December 2015 through September 2016. Biopsies were taken from stomach, antrum, corpus, duodenum, terminal ileum, ascending colon, and descending colon. RNA was extracted from all samples and reverse transcribed into complementary DNA; V1-V2 regions of 16S ribosomal RNA genes were amplified and sequenced on an Illumina MiSeq platform. Abundances of the taxa in all taxonomic ranks in each sample type were used to construct sample-similarity matrices with the Bray-Curtis algorithm. Significant differences between a priori-defined groups were evaluated using analysis of similarity. RESULTS: After taxonomic annotation, 4045 phylotypes, belonging to 169 genera and 14 different phyla, were identified. Each subject had a different bacterial community. We identified distinct microbial consortia in saliva, upper GI tract, lower GI tract, and fecal samples. The predominant genera in the upper GI tract (Gemella, Veillonella, Neisseria, Fusobacterium, Streptococcus, Prevotella, Pseudomonas, and Actinomyces) were almost absent from the lower GI tract, where the microbial communities mainly comprised Faecalibacterium, Ruminococcus, and Bacteroides. The bacterial communities in the upper GI tract were characterized by greater richness and heterogeneity (measured by the Shannon index) than those in the lower GI tract. We detected Helicobacter pylori in only the upper GI tract. CON-CLUSIONS: In an analysis of saliva, mucosal, and fecal samples from 21 healthy adults, we found each individual, and each GI region, to have a different bacterial community. The fecal microbiome is not representative of the mucosal microbiome. We propose a systematic method to analyze the bacterial communities of the GI tract.

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Section: Discussionmentioning

confidence: 99%

Analysis of Transcriptionally Active Bacteria Throughout the Gastrointestinal Tract of Healthy Individuals

Vasapolli¹,

et al. 2019

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“…Despite its sensitivity to a relatively small number of H pylori , PCR tests are not considered appropriate for verifying the success of a treatment, which is particularly related to the risk of detection of killed bacteria . This opinion prevails despite the recent conclusion from a meta‐analysis that the sensitivity and specificity of stool PCR tests are relatively in the same range as other diagnostic methods …”

Section: Introductionmentioning

confidence: 99%

“…7 This opinion prevails despite the recent conclusion from a meta-analysis that the sensitivity and specificity of stool PCR tests are relatively in the same range as other diagnostic methods. 11 There are several PCR modifications that can help to increase the sensitivity and specificity of detection, including real-time PCR that provides fast detection and quantitation of target DNA. [12][13][14][15] However, this procedure has several disadvantages: high equipment cost, high technical skill, increased risk of false-negative results due to the human error as a result of improper assay development, and incorrect data analysis.…”

Section: Introductionmentioning

confidence: 99%

Diagnostic reliability of nested PCR depends on the primer design and threshold abundance ofHelicobacter pyloriin biopsy, stool, and saliva samples

et al. 2020

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Background The aim of this work was to find a reliable nested PCR for the detection of Helicobacter pylori in biopsy, stool, and saliva specimens. Materials and Methods Novel nested PCR was elaborated and validated on 81 clinical biopsy, stool, and saliva samples from the same individual and compared to available H pylori assays: histology, rapid urease test (RUT), stool antigen test (SAT), 13C‐urea breath test (UBT). Results The efficiency and selectivity of 17 published nested polymerase chain reactions (PCR) available for Helicobacter pylori detection were re‐evaluated. Most of them had serious limitations and mistakes in primer design. Hence, we elaborated a nested PCR for the unambiguous identification of H pylori in biopsy, stool, and saliva, using primers targeted to variable regions of the 16S ribosomal RNA (rRNA) gene. Moreover, we determined the detection limit by adding a known number of cells. This number was as low as 0.5 cells in a PCR vial, but due to the DNA isolation procedures, it required 1‐5 × 103 cells/g or ml of specimen. The sensitivity for nested PCR from stomach biopsies was on the same scale as 13C‐UBT (93.8%), but it was much lower in amplifications from stool (31.3%). Sequencing of all obtained PCR products exclusively confirmed H pylori‐specific DNA sequences. Conclusions Elaborated nested PCR assay can serve as an auxiliary method for controversial samples (patients with bleeding or taking proton‐pump inhibitor) in laboratories with basic equipment. The sensitivity and specificity for the amplification from gastric biopsies was almost like 13C‐UBT. Despite the good sensitivity, the threshold occurrence and the ability to survive in the oral cavity aside from and independent of the stomach is the reason why H pylori DNA cannot be reliably detected in saliva, stool, and some biopsy samples.

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“…In this setting, the THD fecal test has shown sensitivity and specificity above 90% [ 17 ] and a 100% concordance for the point mutations conferring resistance to clarithromycin between stools and gastric biopsy samples [ 18 ]. While a recent meta-analysis [ 19 ] identified the bacterial 23S ribosomal RNA subunit gene as the most accurate marker for diagnosis of infection using molecular tests on stool samples, with 82% sensitivity and 99% specificity, there are no data about the detection of gyrA mutations in stools. On this basis, we retrospectively reviewed our experience about genotypic resistance analysis in stools to both clarithromycin and levofloxacin in the last four years in order to evaluate time trends, both in naive and failure patients.…”

Section: Introductionmentioning

confidence: 99%

Helicobacter pylori Primary and Secondary Genotypic Resistance to Clarithromycin and Levofloxacin Detection in Stools: A 4-Year Scenario in Southern Italy

et al. 2020

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Antibiotic resistance has become an emerging problem for treating Helicobacter pylori (H. pylori) infection. Clarithromycin and levofloxacin are two key antibiotics used for its eradication. Therefore, we reviewed our experience with genotypic resistance analysis in stools to both clarithromycin and levofloxacin in the last four years to evaluate time trends, both in naive and failure patients. Patients collected a fecal sample using the THD fecal test device. Real-time polymerase chain reaction was performed to detect point mutations conferring resistance to clarithromycin (A2142C, A2142G, and A2143G in 23S rRNA) and levofloxacin (substitutions at amino acid position 87 and 91 of gyrA). One hundred and thirty-five naive patients were recruited between 2017–2020. Clarithromycin resistance was detected in 37 (27.4%). The time trend did not show any significant variation from 2017 to 2020 (p = 0.33). Primary levofloxacin resistance was found in 26 subjects (19.2%), and we observed a dramatic increase in rates from 2017 (10%) to 2018 (3.3%), 2019 (20%), and 2020 (37.8%). Ninety-one patients with at least one eradication failure were recruited. Secondary resistance to clarithromycin and levofloxacin was found in 59 (64.8%) and 45 patients (59.3%), respectively. In conclusion, our geographic area has a high risk of resistance to clarithromycin. There is also a progressive spreading of levofloxacin-resistant strains.

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Review: Diagnostic accuracy of PCR‐based detection tests for Helicobacter Pylori in stool samples

Cited by 38 publications

References 49 publications

Analysis of Transcriptionally Active Bacteria Throughout the Gastrointestinal Tract of Healthy Individuals

Analysis of Transcriptionally Active Bacteria Throughout the Gastrointestinal Tract of Healthy Individuals

Diagnostic reliability of nested PCR depends on the primer design and threshold abundance ofHelicobacter pyloriin biopsy, stool, and saliva samples

Helicobacter pylori Primary and Secondary Genotypic Resistance to Clarithromycin and Levofloxacin Detection in Stools: A 4-Year Scenario in Southern Italy

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