Comparison of invasive histological and molecular methods in the diagnosis of <i>Helicobacter pylori</i> from gastric biopsies of Sudanese patients: a cross-sectional study

Maram Elnosh; Hisham Altayb; Yousif Hamedelnil; Wafa Elshareef; Aliaa Abugrain; Esraa Osman; Aalaa Albasha; Abdelhamid Abdelhamid; Ehssan Moglad; Ahmed AbdAlla; Ahmed Ismail

doi:10.12688/f1000research.75873.2

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Research Article

Revised

Comparison of invasive histological and molecular methods in the diagnosis of Helicobacter pylori from gastric biopsies of Sudanese patients: a cross-sectional study

[version 2; peer review: 2 approved]

Maram Elnosh ¹, Hisham Altayb², Yousif Hamedelnil¹, [...] Wafa Elshareef³, Aliaa Abugrain⁴, Esraa Osman¹, Aalaa Albasha¹, Abdelhamid Abdelhamid¹, Ehssan Moglad⁵, Ahmed AbdAlla⁶, Ahmed Ismail^1,7

Maram Elnosh ¹, Hisham Altayb², [...] Yousif Hamedelnil¹, Wafa Elshareef³, Aliaa Abugrain⁴, Esraa Osman¹, Aalaa Albasha¹, Abdelhamid Abdelhamid¹, Ehssan Moglad⁵, Ahmed AbdAlla⁶, Ahmed Ismail^1,7

PUBLISHED 08 Jun 2022

Author details Author details

¹ Microbiology, College of Medical Laboratory Science, Sudan University of Science and Technology, Khartoum, State, 11111, Sudan
² Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, State, 21452, Saudi Arabia
³ Histopathology, The National Public Health Laboratory, Khartoum, State, 11111, Sudan
⁴ Histopathology, College of Medical Laboratory Science, Sudan University of Science and Technology, Khartoum, State, 11111, Sudan
⁵ Pharmaceutics, College of Pharmacy, Prince Sattam bin Abdulaziz University, Alkharj, State, 11942, Saudi Arabia
⁶ Parasitology and Medical Entomology, College of Medical Laboratory Science, Sudan University of Science and Technology, Khartoum, State, 11111, Sudan
⁷ Public Health Department, Ministry of Public Health, Doha, State, 122104, Qatar

Maram Elnosh
Roles: Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, Project Administration, Resources, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing

Hisham Altayb
Roles: Conceptualization, Methodology, Project Administration, Resources, Supervision, Validation, Writing – Review & Editing

Yousif Hamedelnil
Roles: Conceptualization, Supervision, Writing – Review & Editing

Wafa Elshareef
Roles: Investigation, Methodology

Aliaa Abugrain
Roles: Investigation, Methodology

Esraa Osman
Roles: Investigation, Methodology

Aalaa Albasha
Roles: Investigation, Methodology

Abdelhamid Abdelhamid
Roles: Investigation, Methodology

Ehssan Moglad
Roles: Conceptualization, Writing – Review & Editing

Ahmed AbdAlla
Roles: Writing – Review & Editing

Ahmed Ismail
Roles: Conceptualization, Writing – Review & Editing

OPEN PEER REVIEW

REVIEWER STATUS

Abstract

Background: The continuous rise in the number of patients suffering from Helicobacter pylori is probably due to the changes in modern life. Nowadays, patients suffering from gastrointestinal problems are diagnosed through invasive and non-invasive techniques. The choice of a diagnostic test is influenced by factors such as the tests' sensitivity and specificity, the clinical conditions, and the cost-effectiveness of the testing strategy. This study aimed to compare molecular detection methods of H. pylori by polymerase chain reaction (PCR) targeting the 16S rRNA, ureA and glmM genes with an invasive histopathological technique.
Methods: 290 gastric biopsies were collected using gastrointestinal endoscopy from patients with gastritis symptoms in different hospitals in Khartoum state. Two gastric biopsies were collected from each patient for PCR and histopathology.
Results: A total of 103 (35.5%) samples were positive by histopathological examination, 88 (30.3%) by 16S rRNA, 39 (13.4%) by glmM gene, and 56 (19.3%) by ureA gene. The highest sensitivity was observed in 16S rRNA (46.6%), followed by glmM (24.3%) and ureA (23.3%). While the best specificity was observed in glmM gene (92.5%), followed by ureA (82.3%) and 16S rRNA (78.6%).
Conclusion: PCR test targeting the 16S rRNA gene exhibited the best results for molecular detection of H. pylori compared to other genes.

Keywords

Helicobacter pylori, Histopathology, 16S rRNA, PCR, ureA, sensitivity, specificity, Khartoum.

Corresponding author: Maram Elnosh

Competing interests: No competing interests were disclosed.

Grant information: This study was funded by the Ministry of Higher Education and Scientific Research- Commission of Scientific Research and innovation- Sudan, grant No: 15/17.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Copyright: © 2022 Elnosh M et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

How to cite: Elnosh M, Altayb H, Hamedelnil Y et al. Comparison of invasive histological and molecular methods in the diagnosis of Helicobacter pylori from gastric biopsies of Sudanese patients: a cross-sectional study [version 2; peer review: 2 approved]. F1000Research 2022, 11:113 (https://doi.org/10.12688/f1000research.75873.2) First published: 28 Jan 2022, 11:113 (https://doi.org/10.12688/f1000research.75873.1) Latest published: 08 Jun 2022, 11:113 (https://doi.org/10.12688/f1000research.75873.2)

Revised Amendments from Version 1

There is some information about anther specimens and techniques were added to the introduction section. In the result section we added some information about signs and symptoms (table1), also we divided the age of study population into age groups (table1), and we bring out the age most susceptible to H. pylori infection, also we calculated the odds ratio of the tests which recorded in table2.

To read any peer review reports and author responses for this article, follow the "read" links in the Open Peer Review table.

Introduction

Helicobacter pylori (H. pylori) is a Gram-negative, microaerophilic, spiral, and motile bacterium that colonizes the human gastric mucosa.¹^,² It has been associated with the development of various clinical disorders of the upper gastrointestinal tract, such as aseptic ulcers, chronic gastritis, gastric adenocarcinoma and gastric mucosa-associated lymphoid tissue (MALT) lymphoma, which is classified as type I cancer-causing agent by the World Health Organization (WHO).³^–⁵ Its distribution is worldwide and affects more than 90% of the world population, but it is more common in developing countries with the highest prevalence found in Africa,⁶^,⁷ probably due to the possible transmission through the fecal-oral route and the unsafe sanitation conditions in these countries.¹^,⁸ Clinically, a variety of various invasive techniques (requiring endoscopy and biopsy which include, culture, histological examination, and rapid urease test, CLO (Campylobacter like organism) test, smear examination, and molecular studies such as polymerase chain reaction (PCR) and fluorescence in situ hybridization (FISH)) or noninvasive techniques (including serology, respiratory urea breath test, or the detection of fecal antigen) are often performed to detect H. pylori infection. FISH with 16S rRNA oligonucleotide probes has been used for detection and identification of H. pylori and detection of resistance to antimicrobials⁹^–¹¹ The sensitivity of any of those techniques in detecting H. pylori relays on how the density of the bacterial cells within the specimens taken by biopsy (recent use of disease-related medications, specifically antibiotics and proton-pump inhibitors (PPI) can reduce the density of the cells), pathologist expertise, also the type and quality of the stain used for detection purposes.¹⁰ Many studies reported that the gold standard method for the diagnosis is the detection of H. pylori in biopsy material.¹²^,¹³

Currently, many clinical laboratories use urease tests and histological analysis as a gold standard approach.¹³^,¹⁴ In routine practice, hematoxylin and eosin (H and E), Giemsa, and immunohistochemistry staining techniques are commonly used to identify H. pylori following endoscopy; however, these techniques normally fails in identifying low numbers or coccoid forms of bacteria.¹⁵

The polymerase Chain Reaction (PCR) method offers advantages over culture and histopathology because it can detect the coccoid form of the H. pylori. PCR which is highly specific and sensitive for the diagnosis of H. pylori from gastric biopsy, saliva, urine and stool specimen, as well as for detection of virulence and drug resistance genes especially clarithromycin resistance.¹⁶ The targets of these PCR methods include the 16S rRNA gene, the urease (ureA) gene, the ureC gene, renamed phosphoglucosaminemutase (glmM), the random chromosome sequence, and the 26-kDa species-specific antigen (SSA) gene. H. pylori ureA gene is an important virulence factor that ensures that bacteria can resist acidity of the gastric mucosa.¹⁷

In Sudan, many studies were carried out to investigate the seroprevalence of H. pylori using ELISA and rapid immunochromatographic tests.¹⁸ The prevalence of H. pylori infection was estimated to be 80% among patients with gastritis symptoms, 56% with duodenal ulcer, while 60% with duodenitis and 16% apparently healthy individuals.¹⁹ In another study in Eastern Sudan high prevalence of H. pylori infection, 80% among patients with gastritis and Barrett's esophagus was reported.²⁰ In Sudan and probably many third-world countries, the cost of diagnosis plays a major role rather than the accuracy of the diagnostic method. Hence, diagnosis of H. pylori infections is largely based on serology, detection of stool antigen and rarely endoscopy and culture. The present study aimed to compare the use of histopathology (gold standard method) with polymerase chain reaction (PCR) approach for the detection and prevalence of H. pylori infections in Khartoum State.

Methods

This was a cross-sectional study conducted at Khartoum State, Sudan between March 2018 to January 2020. The project was approved by the Ethics Committee of the Ministry of Health Research Department, Khartoum State (3/2018). The study aims were explained to the recruits, and a consent form was obtained and signed prior to sample collection.

Collection of biopsy specimens

Out of 290 male and female patients from all age groups who subjected for gastric biopsy through Oesophago-Gastro-Duodenoscopy (OGD) by physicians in different hospitals at Khartoum State (Khartoum locality and Omdurman locality) and suffering from dyspepsia and other gastritis-related symptoms were enrolled in this study in period between March 2018 to January 2020. Patients who had received antibiotics, PPI, H2 blockers, or colloidal bismuth sulfate within the previous two months of endoscopy for treatment of gastritis or peptic ulcer, patients with a history of gastric resection, patients with complicated peptic ulcer disease, i.e. hemorrhage, were excluded.⁴ Two biopsy specimens were collected from the antrum and the corpus of each patient, one sample was immediately placed in tubes containing saline and transported for molecular study, while the other was fixed in 10% buffered formalin for at least 24 hours and then embedded in paraffin wax for histopathological examination.

Histopathological identification of Helicobacter pylori

Hematoxylin and Eosin (H and E) staining and modified Giemsa staining were performed for all samples. Three sections for each specimen were deparaffinized and hydrated in descending grades of alcohol and cut in sequential 4 μm sections. One slide was stained by routine H and E stain, and the other slide was stained by modified Giemsa stain to demonstrate the presence of H. pylori. Cover slips with DPX mounted on slides and then later examined by a histopathologist and assigned to each morphological variable.

DNA extraction

DNA extraction of gastric biopsies was performed using the guanidine chloride method as described by Abd Al Rahem and Elhag.²¹ Biopsies were grounded by sterile blades and tips and then washed with phosphate buffer saline (PBS). 2 ml of lysis buffer were added, followed by 10 μl of proteinase K, 1 ml of guanidine chloride, and 300 μl of ammonium (NH₄) acetate, then vortexed and incubated at 65°C for 2 hours. The mixture was cooled to room temperature, and then 2 ml of pre-cooled chloroform was applied, vortexed, and centrifuged for 5 minutes at 3000 revolutions per minute (rpm). The upper layer of the mixture was moved to a new tube, and 10 ml of absolute cold ethanol were added, shaken, and held for 2 hours or overnight at −20°C. The tube was then centrifuged for 15–20 minutes at 3000 rpm, the supernatant was carefully removed, and the tube was inverted for 5 minutes on tissue paper. The pellet was washed with 70% ethanol, centrifuged for 5 minutes at 3000 rpm. The supernatant was poured away, allowing the pellet to dry for 10 minutes. Then re-suspended into 50 μl of distilled water, briefly vortexed, and held overnight at −20°C. The extracted DNA was stored at −80°C until use.

Polymerase chain reaction (PCR)

Three different primers were used for the detection of the bacteria, targeting specific H. pylori 16S rRNA (532 bp), glmM (294 bp), and ureA (217 bp). PCR was carried out in 25 μl of reaction mixture containing 5 μl of ready to use master mix (Taq DNA polymerase, dNTPs and MgCl₂) (Intron Biotechnology, Korea), 2 μl of DNA template, 1 μl of forward (F) primer, 1 μl of reverse (R) primer and 16μl distilled water (DW). For each batch of PCR assay, DW was used as negative control instead of the genomic DNA templates and known positive sample was used as positive control. The reaction mixtures were cycled in an automated thermocycler. The PCR for the specific H. pylori 16S rRNA gene was performed using the forward primer (5′-GCTAAGAGATCAGCCTATGTCC-3′) and reverse primer (5′-TGGCAATCAGCGTCAGGTAAT-3′). The PCR condition for the 16S rRNA gene was performed as follows: initial denaturation at 94°C for 3 minutes, 35 cycles of denaturation at 94°C for 30 seconds, annealing at 53°C for 30 seconds, extension at 72°C for 45 seconds, and a final extension at 72°C for 5 minutes.²² The PCR for the ureA gene of H. pylori was performed using the forward primer (5′-AACCGGATGATGTGATGGAT-3′) and reverse primer (5′-GGTCTGTCGCCAACATTTTT-3′) reported by Ye et al., which results in an amplicon of 217 bp. The PCR condition for the ureA gene was performed as follows: initial denaturation at 94°C for 3 minutes, 35 cycles of denaturation at 94°C for 30 seconds, annealing at 53°C for 30 seconds, extension at 72°C for 45 seconds, and a final extension at 72°C for 5 minutes.²²

The PCR for the glmM gene was performed using the forward primer (5′-GGATAAGCTTTTAGGGGTGTTAGGGG-3′) and reverse primer (5′-GCTTACTTTCTAACACTAACGCGC-3′).²³ The PCR condition for the glmM gene was performed as follows: initial denaturation at 94°C for 3 minutes, 35 cycles of denaturation at 94°C for 30 seconds, annealing at 58°C for 30 seconds, extension at 72°C for 30 seconds, and a final extension at 72°C for 3 minutes.

After amplification, 5 μl of the product was run in electrophoreses on a 1.5% agarose gel containing Ethidium bromide (0.5 μg/ml), then visualized under an ultraviolet illuminator and photographed. A 100-bp DNA ladder was used as a size marker (Intron Biotechnology, Korea).

Statistical analysis

Statistical analysis was done using IBM Statistical Package for Social Sciences (SPSS) software version 20.0 (RRID: SCR_019096 URL: https://www.ibm.com/products/spss-statistics). Chi-squared test was done for the analysis of categorical variables. A p-value of <0.05 was considered statistically significant.

Results

The sociodemographic and clinical data of 290 patients recruited in this study are shown in Table 1.

Table 1. Sociodemographic and clinical data for participated patients.

Patients characters (n=290)	Number (%)
Sex
Males	159 (54.8)
Females	131 (45.1)
Age (years)
14-29	72 (24.8%)
30-49	117 (40.3%)
50 years and older	101 (34.8%)
Residence*
Khartoum locality	175 (60.3)
Omdurman locality	115 (39.7)
Endoscopy
gastritis	194 (66.9)
gastric ulcer	29 (10.0)
duodenal ulcer	27 (9.3)
esophagitis	13 (4.5)
normal gastric mucosa	27 (9.3)
Signs and symptoms
Dyspepsia	118 (40.7)
Vomiting	26 (9.0)
Dysphagia	22 (7.6)
Abdominal pain	72 (24.8)
Acidity	52 (17.9)

* Samples were collected from two localities in Khartoum State.

Histopathological identification of Helicobacter pylori

Gastric biopsies were obtained from 290 patients suffering from various gastric conditions through Oesophago-Gastro-Duodenoscopy (OGD). H. pylori were clearly detected in positive samples as curved bacilli on the surface of the gastric epithelial cells; the bacteria appear as light bluish rods in H and E slides with varying sizes (3–6 μ) on the luminal surface of mucosal cells. In Giemsa’s stain H. pylori appear dark blue in a light blue background.³

From a total of 290 samples, H. pylori were found in 103 samples (35.5%). The highest number of positive H. pylori samples were observed in the active chronic gastritis followed by patients of the duodenal ulcer, gastric ulcer, and normal gastric findings in the following frequencies: 75 (25.9%), 13 (4.5%), 6 (2.1%) and 6 (2.1%) respectively, while the lowest frequency was noticed in patients with esophagitis 3 (1.0%) cases.

Patients enrolled in the study were divided into three age groups: young adults 14-29 years, middle-aged adults 30-49 years, and old-aged adults 50 years and older. The detection of H. pylori infection was 27 (9.3%), 45 (15.5%), and 31 (10.7%), respectively. The prevalence of H. pylori increased gradually with age, but it was statistically insignificant (p = 0.451).

Detection of H. pylori 16S rRNA, glmM, and ureA genes of H. pylori by PCR

Among the samples analyzed by the PCR method for H. pylori 88 (30.3%) were positive using H. pylori 16S rRNA gene, 39 (13.4%) samples were positive using glmM gene, 56 (19.3%) samples were positive using ureA gene, and the rest of samples 234 (80.7%) were negative (Figure 1).

Figure 1. PCR amplification of H. pylori on agarose gel electrophoresis 1.5%.

a. 16S rRNA gene. Lane 8 marker (100–1500 bp), lane 7 positive control, lanes 2–5 contain positive samples (532 bp), lanes 1 and 6 are negative samples. b. glmM gene, lane 5 marker (100–1500 bp), lane 4 positive control, lanes 1,6, and 7 contain amplicons of glmM (294 bp), lanes 2 and 3 are negative samples. c. ureA gene. Lane 1 marker (100–1500 bp), lane 8 positive control, lanes 4 and 7 contain amplicons of ureA (217 bp), lanes 2, 3, 5, and 6 are negative samples.

Considering the histology as a gold standard, the PCR method using 16S rRNA were the most sensitive methods (46.6%). The PCR method using glmM gene were the most specific method (92.5%). The PPV, NPV and odds ratio of each method are noted in Table 2.

Table 2. Comparison between histopathological approach and various PCR methods used for the diagnosis of H. pylori infections in this study.

PCR methods		Histopathological technique		p-value	Odds ratio	Sensitivity (%)	Specificity (%)	PPV (%)	NPV (%)
PCR methods		Positive	Negative	p-value	Odds ratio	Sensitivity (%)	Specificity (%)	PPV (%)	NPV (%)
16S rRNA	Positive	48	40	<0.05	3.207	46.6	78.6	54.5	72.8
16S rRNA	Negative	55	147	<0.05	3.207	46.6	78.6	54.5	72.8
glmM	Positive	25	14	<0.05	3.961	24.3	92.5	64.1	68.9
glmM	Negative	78	173	<0.05	3.961	24.3	92.5	64.1	68.9
ureA	Positive	24	32	0.201	1.472	23.3	82.3	42.9	66.2
ureA	Negative	79	155	0.201	1.472	23.3	82.3	42.9	66.2
Total		103	187

Discussion

Currently, there are many diagnostic methods for the diagnosis of H. pylori infections; each method has its advantages and disadvantages, so it is recommended to use at least a combination of two methods based on different principles to detect colonization by H. pylori.²⁴ Although, the culture method is regarded as the most appropriate technique, it has limitations, particularly in case of slow-growing or fastidious bacteria, due to complicated identification and time-consuming methods. In addition to the need for immediate transport of the biopsy specimens to the designated laboratory to assure the viability of H. pylori and prevent the formation of coccoid forms of the microorganism.²⁴^–²⁶ The histological technique and culturing of gastric biopsy specimens have been considered a gold standard method under optimal conditions.²⁴

Histological staining enables identifying bacteria and evaluating the type and intensity of the gastric mucosa's inflammation and associated pathology, such as, atrophic gastritis (AG), intestinal metaplasia (IM), and gastric cancer or lymphoma.²⁷

In this study, the prevalence of H. pylori infection was 35.5%. H. pylori was detected in (103/290) patients using histopathological examination with 35.5% sensitivity. There are many previous studies done in this field with various pictures of the disease. Mohamed et al. reported that 16/69 (23.2%) positive patients for H. pylori infection among Sudanese patients with colon polyps and colon cancer patients.¹⁸ Redéen et al. reported that 97/304 (31.9%) positive patients for H. pylori infection.²⁸ In another study, Salman et al. reported that 115/210 (54.7%) samples were positive for H. pylori via histopathology, 57 (62.6%) of positive H. pylori samples were observed in patients with chronic gastritis, 11 (50%) with adenocarcinoma and 31 (44.2%) with superficial gastritis, while only one H. pylori-positive out of 5 cases observed in atrophy gastritis patient.²⁹ Histopathology is the first diagnostic method for detection of H. pylori and is still widely used as the main diagnostic tool; nevertheless, it has limitations including higher cost, longer turnaround time, and inter-observer variation assessment; experience and skills of the pathologist do matter for the specificity and sensitivity of histopathological diagnosis of H. pylori,² false-positive results can occur due to presence of structures similar to H. pylori²⁴ and failure to detect all the positive samples might occur in case of intestinal metaplasia.²⁹ The density and irregular distribution of H. pylori can vary at different sites on the gastric mucosa, which might lead to sampling error.²⁴^,²⁷ Moreover, the sensitivity of histology may decrease in patients taking antisecretory therapy, such as, proton pump inhibitor (PPI).²⁷

Molecular tests should be applied as replacements to the traditional method for the identification of H. pylori, which are sensitive, rapid, and precise techniques for the specific recognition of H. pylori from gastric biopsy specimens and to discover particular mutations related to antimicrobial resistance.²⁴^–²⁶

In this study, identification of H. pylori was applied to all biopsies by PCR using specific primers. Specific H. pylori 16S rRNA gene is a conserved region of prokaryotic DNA that allows specific identification. However, H. pylori 16S rRNA gene's sensitivity and specificity were 46.6% and 78.6%, respectively. The glmM gene shows 24.3% sensitivity and 92.5% specificity. In our study, the ureA gene showed the lowest sensitivity (23.3%), and 82.3% specificity. Our result aligned with a study conducted by AlNaji et al. in 2018, which found that the glmM gene is 38.8% lower than the 16S rRNA gene 95.9%.³⁰ Helaly et al. reported similar results (38.5%) for glmM gene.³¹ This low percent of glmM (ureC) gene may be due to sequence polymorphism or/in variation to the diversity of strains within the patients that reported in previous studies.³⁰ Also, housekeeping genes are affected by geographical regions and point mutations, Intragenic and recombination are another potential factors.³²

The ureA gene is a housekeeping gene that is needed for urease enzyme activity. Espinoza et al. demonstrated that the amplification of the ureA gene was noticed in (86.36%) which was lower than that of the glmM gene (100%).¹⁷ Smith et al. reported that ureA gene PCR had a very poor specificity and sensitivity.³³ The possible reasons for poor sensitivity of ureA and ureC (glmM) genes for the detection of H. pylori may be that both of them are single-step PCR and thus unable to identify the lower number of bacteria or they were unable to counteract PCR inhibitors in the clinical specimens.³⁴

The 16S rRNA gene is a useful and commonly used for the primary finding of H. pylori use Hp1, Hp2 primers with sensitivity up to 100%.³⁰ Sugimoto et al. and Farhadkhani et al. reported that the detection of H. pylori 16S rRNA gene was greater than the ureA gene. They determined that the difference could be due to discrepancy in the primer specificity and sensitivity. Using of 16S rRNA gene for the detection of H. pylori might be more sensitive but could not be as specific as ureA gene.³⁵^,³⁶ The poor specificity may be explained by sequence conservation across the bacterial genera and also by possible amplification of nonspecifically human DNA.³⁴ Yet, no 100% specificity or sensitivity for primer sets amplifies H. pylori ureA and 16SrRNA genes.³⁵^,³⁶

Conclusions

Many tests already exist in the world for diagnosis of H. pylori infections. The study results suggest that H. pylori 16S rRNA gene detection by the PCR method could be used to diagnose H. pylori infections. To avoid false-positive results and increase specificity, we recommend using two conserved target genes to detect H. pylori infections.

Data availability

Underlying data

Figshare: Underlying data for ‘Comparison of invasive histological and molecular methods in the diagnosis of Helicobacter pylori from gastric biopsies of Sudanese patients: a cross-sectional study’.

The project contains the following underlying data:

- Raw data collected from patients with gastritis symptoms: https://doi.org/10.6084/m9.figshare.17072012.v2.³⁷
- Raw gel electrophoresis images: [PCR amplification of H. pylori on agarose gel electrophoresis 1.5%]: https://doi.org/10.6084/m9.figshare.18482015.v1.³⁸

Data are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).

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25. Dong Z, Chen B, Pan H, et al.: Detection of microbial 16S rRNA gene in the serum of patients with gastric cancer. Front. Oncol. 2019; 9: 608. PubMed Abstract | Publisher Full Text
26. Kisa O, Albay A, Mas MR, et al.: The evaluation of diagnostic methods for the detection of Helicobacter pylori in gastric biopsy specimens. Diagn. Microbiol. Infect. Dis. 2002; 43(4): 251–255. Publisher Full Text
27. Lee JY, Kim N: Diagnosis of Helicobacter pylori by invasive test: histology. Annals of translational medicine. 2015; 3(1).
28. Redéen S, Petersson F, Törnkrantz E, et al.: Reliability of diagnostic tests for Helicobacter pylori infection. Gastroenterol. Res. Pract. 2011; 2011: 1–6. PubMed Abstract | Publisher Full Text
29. Salman KD, Al-Thwaini AN, Askar BA: Evaluation of glmM Gene in Diagnosis of Helicobacter pylori with Another Invasive Methods. Iran. J. Biotechnol. 2019; 18(3).
30. AlNaji HA, Omran R, AlSherify A: Molecular Detection of Helicobacter pylori Infection in Gastric Biopsy Specimens by PCR. Journal of University of Babylon for Pure and Applied Sciences. 2018; 26(2): 109–118.
31. Helaly GH, El-Afandy NM, Hassan AA, et al.: Diagnostic Value of Housekeeping [glmM] Gene Expression in Antral Biopsies in Comparison to Rapid Urease Test and Histological Detection of Helicobacter Pylori Infection Egyptian. J. Med. Microbiol. 2009; 18(4).
32. Raymond J, Thiberge J-M, Chevalier C, et al.: Genetic and transmission analysis of Helicobacter pylori strains within a family. Emerg. Infect. Dis. 2004; 10(10): 1816–1821. PubMed Abstract | Publisher Full Text | Free Full Text
33. Smith S, Oyedeji K, Arigbabu A, et al.: Comparison of three PCR methods for detection of Helicobacter pylori DNA and detection of cagA gene in gastric biopsy specimens. World J Gastroenterol: WJG. 2004; 10(13): 1958–1960. PubMed Abstract | Publisher Full Text | Free Full Text
34. Singh V, Mishra S, Rao G, et al.: Evaluation of nested PCR in detection of Helicobacter pylori targeting a highly conserved gene: HSP60. J. Helicobacter. 2008; 13(1): 30–34. PubMed Abstract | Publisher Full Text
35. Farhadkhani M, Nikaeen M, Hassanzadeh A, et al.: Potential transmission sources of Helicobacter pylori infection: detection of H. pylori in various environmental samples. J. Environ. Health Sci. Eng. 2019; 17(1): 129–134. PubMed Abstract | Publisher Full Text
36. Sugimoto M, Wu J-Y, Abudayyeh S, et al.: Unreliability of results of PCR detection of Helicobacter pylori in clinical or environmental samples. J. Clin. Microbiol. 2009; 47(3): 738–742. PubMed Abstract | Publisher Full Text
37. Maram E, Altayb Hisham N, Fadalla HY, et al.: Comparison of invasive histological and molecular methods in the diagnosis of Helicobacter pylori from gastric biopsies of Sudanese patients: a cross-sectional study. figshare. Dataset. 2021. Publisher Full Text
38. Maram E, Altayb Hisham N, Fadalla HY, et al.: Comparison of invasive histological and molecular methods in the diagnosis of Helicobacter pylori from gastric biopsies of Sudanese patients: a cross-sectional study. figshare. Figure. 2022. Publisher Full Text

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VERSION 2 PUBLISHED 28 Jan 2022

Author details Author details

¹ Microbiology, College of Medical Laboratory Science, Sudan University of Science and Technology, Khartoum, State, 11111, Sudan
² Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, State, 21452, Saudi Arabia
³ Histopathology, The National Public Health Laboratory, Khartoum, State, 11111, Sudan
⁴ Histopathology, College of Medical Laboratory Science, Sudan University of Science and Technology, Khartoum, State, 11111, Sudan
⁵ Pharmaceutics, College of Pharmacy, Prince Sattam bin Abdulaziz University, Alkharj, State, 11942, Saudi Arabia
⁶ Parasitology and Medical Entomology, College of Medical Laboratory Science, Sudan University of Science and Technology, Khartoum, State, 11111, Sudan
⁷ Public Health Department, Ministry of Public Health, Doha, State, 122104, Qatar

Maram Elnosh
Roles: Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, Project Administration, Resources, Software, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing

Hisham Altayb
Roles: Conceptualization, Methodology, Project Administration, Resources, Supervision, Validation, Writing – Review & Editing

Yousif Hamedelnil
Roles: Conceptualization, Supervision, Writing – Review & Editing

Wafa Elshareef
Roles: Investigation, Methodology

Aliaa Abugrain
Roles: Investigation, Methodology

Esraa Osman
Roles: Investigation, Methodology

Aalaa Albasha
Roles: Investigation, Methodology

Abdelhamid Abdelhamid
Roles: Investigation, Methodology

Ehssan Moglad
Roles: Conceptualization, Writing – Review & Editing

Ahmed AbdAlla
Roles: Writing – Review & Editing

Ahmed Ismail
Roles: Conceptualization, Writing – Review & Editing

Competing interests

No competing interests were disclosed.

Grant information

This study was funded by the Ministry of Higher Education and Scientific Research- Commission of Scientific Research and innovation- Sudan, grant No: 15/17.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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https://doi.org/10.12688/f1000research.75873.2

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Elnosh M, Altayb H, Hamedelnil Y et al. Comparison of invasive histological and molecular methods in the diagnosis of Helicobacter pylori from gastric biopsies of Sudanese patients: a cross-sectional study [version 2; peer review: 2 approved]. F1000Research 2022, 11:113 (https://doi.org/10.12688/f1000research.75873.2)

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Reviewer Report 21 Jun 2022

Maxime Pichon, Infectious Agents Department, CHU Poitiers, Poitiers, France; INSERM U1070 Pharmacology of Antimicrobial Agents and Antibiotic Resistance, Poitiers, France

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https://doi.org/10.5256/f1000research.134815.r140058

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Reviewer Report 10 Jun 2022

Stella Ifeanyi Smith, Department of Molecular Biology and Biotechnology, Nigeria Institute of Medical Research, Lagos, Nigeria

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https://doi.org/10.5256/f1000research.134815.r140059

I have gone through the manuscript and noted the changes made following my query. However, I still noted a few areas that need minor corrections, e.g.:

Under the introduction, fourth line from the bottom of the first

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Reviewer Report 25 May 2022

Stella Ifeanyi Smith, Department of Molecular Biology and Biotechnology, Nigeria Institute of Medical Research, Lagos, Nigeria

Approved with Reservations

https://doi.org/10.5256/f1000research.79802.r136292

In the Introduction section, the authors have described invasive histological methods of diagnosis and compared them with basic molecular biology methods and did not include other molecular methods that have been used for H. pylori diagnosis and simultaneous detection of ... Continue reading

In the Introduction section, the authors have described invasive histological methods of diagnosis and compared them with basic molecular biology methods and did not include other molecular methods that have been used for H. pylori diagnosis and simultaneous detection of resistance including the Fluorescence in situ Hybridization (FISH). These other molecular methods should be included in this section.

Under the results table, it is expected to see the age of patients by groups, e.g. 1–10 years, and that immediately brings out the age most susceptible to H. pylori infection. I also want to believe still under Table 1, that the two hospitals were randomly chosen. The socio-demographic and clinical data are too scanty, kindly give more information.

Helicobacter pylori should be italicized and some H. pylori have the species name starting with a capital letter, so the species name should start with small letters, not capital letters as the authors have written in some.

In the conclusion, the authors have written 'urgent need…', there are several available methods now which can be utilized to suit the particular country of origin depending on costs and accuracy. It would have been interesting to see the molecular method compared with both histology and or stool antigen test at the least since histology is not as specific as stool antigen test or urea breath test (the latter might be out of reach due to high cost).

I, therefore, approve with reservations after my suggestions above have been incorporated into the manuscript.

Is the work clearly and accurately presented and does it cite the current literature?

Partly
Is the study design appropriate and is the work technically sound?

Partly
Are sufficient details of methods and analysis provided to allow replication by others?

Partly
If applicable, is the statistical analysis and its interpretation appropriate?

Yes
Are all the source data underlying the results available to ensure full reproducibility?

Yes
Are the conclusions drawn adequately supported by the results?

Partly

Competing Interests: No competing interests were disclosed.

Reviewer Expertise: Molecular epidemiology of infectious diseases including Helicobacter pylori

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

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Reviewer Report 11 Feb 2022

Maxime Pichon, Infectious Agents Department, CHU Poitiers, Poitiers, France; INSERM U1070 Pharmacology of Antimicrobial Agents and Antibiotic Resistance, Poitiers, France

Approved with Reservations

https://doi.org/10.5256/f1000research.79802.r121551

The manuscript by Maram Elnosh et al. describes interesting data on the comparison between histology and molecular biology for the detection of Helicobacter pylori in gastric biopsies. If the publication is suitable for the editor, modifications remain to be made ... Continue reading

The manuscript by Maram Elnosh et al. describes interesting data on the comparison between histology and molecular biology for the detection of Helicobacter pylori in gastric biopsies. If the publication is suitable for the editor, modifications remain to be made before indexing.

Introduction:

The introduction needs to be completed, adding information about testing another sample, non-invasive such as stool - for example, see Pichon et al., 2020¹ which demonstrates that invasive sampling is not the sole solution in recent times, especially searching for resistance to primary-line antibiotic resistance. In addition, this reference could provide information on the detection of CLA resistance, not described in this study without good reason.

Methods:

The authors should justify the number of patients they included and their inclusion period.
Because the authors use a very homemade extraction and PCR process, they must use positive and negative controls. Please describe the results obtained.
Specify the manufacturers' information for the DNA ladder.

Results:

Table 1: Specify if age is min-max or IQR.
Table 1: Specify the impact of the two different locations.
Italicize all gene names.
The last sentence in the results section of the manuscript should be reworded. The sentence could lead the reader to misunderstand the results. Moreover, the authors indicate a p-value equal to 0 that is statistically impossible, so they have to limit their conclusion to p-value < threshold.
Evaluation of the concordance between the different PCRs tested in this manuscript would be interesting (to be calculated and discussed).
Table 2: Prefer likelihood ratio instead of PPV and NPV as prevalence was specific.

Conclusion:

Rephrase the first sentence, as many tests already exist in the world there is no urgency.

Is the work clearly and accurately presented and does it cite the current literature?

Partly
Is the study design appropriate and is the work technically sound?

Partly
Are sufficient details of methods and analysis provided to allow replication by others?

Partly
If applicable, is the statistical analysis and its interpretation appropriate?

Yes
Are all the source data underlying the results available to ensure full reproducibility?

Yes
Are the conclusions drawn adequately supported by the results?

Partly

References

1. Pichon M, Pichard B, Barrioz T, Plouzeau C, et al.: Diagnostic Accuracy of a Noninvasive Test for Detection of Helicobacter pylori and Resistance to Clarithromycin in Stool by the Amplidiag H. pylori+ClariR Real-Time PCR Assay. Journal of Clinical Microbiology. 2020; 58 (4). Publisher Full Text

Competing Interests: No competing interests were disclosed.

Reviewer Expertise: Medical microbiology

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

CITE

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Maxime Pichon, CHU Poitiers, Poitiers, France; INSERM U1070 Pharmacology of Antimicrobial Agents and Antibiotic Resistance, Poitiers, France
Stella Ifeanyi Smith, Nigeria Institute of Medical Research, Lagos, Nigeria

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21 Jun 2022 | for Version 2

Maxime Pichon, Infectious Agents Department, CHU Poitiers, Poitiers, France; INSERM U1070 Pharmacology of Antimicrobial Agents and Antibiotic Resistance, Poitiers, France

12 Views Cite this report Responses(0)

Approved

The manuscript has been appropriately revised.

Competing Interests

No competing interests were disclosed.

Reviewer Expertise

Medical microbiology

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

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11 Views

10 Jun 2022 | for Version 2

Stella Ifeanyi Smith, Department of Molecular Biology and Biotechnology, Nigeria Institute of Medical Research, Lagos, Nigeria

11 Views Cite this report Responses(0)

Approved

I have gone through the manuscript and noted the changes made following my query. However, I still noted a few areas that need minor corrections, e.g.:

Under the introduction, fourth line from the bottom of the first paragraph: should the word not be 'relies' and not 'relays' as written in the manuscript?
Still under introduction, third paragraph, line 1: polymerase chain reaction, i.e. the c and r should start with small letters.
Still under the third paragraph, line 2 statement: should be 'PCR is' and not 'PCR which is'.

These are minor corrections which does not affect the decision, which is approved.

Competing Interests

No competing interests were disclosed.

Reviewer Expertise

Molecular epidemiology of infectious diseases

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

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14 Views

25 May 2022 | for Version 1

Stella Ifeanyi Smith, Department of Molecular Biology and Biotechnology, Nigeria Institute of Medical Research, Lagos, Nigeria

14 Views Cite this report Responses(0)

Approved With Reservations

In the Introduction section, the authors have described invasive histological methods of diagnosis and compared them with basic molecular biology methods and did not include other molecular methods that have been used for H. pylori diagnosis and simultaneous detection of resistance including the Fluorescence in situ Hybridization (FISH). These other molecular methods should be included in this section.

Under the results table, it is expected to see the age of patients by groups, e.g. 1–10 years, and that immediately brings out the age most susceptible to H. pylori infection. I also want to believe still under Table 1, that the two hospitals were randomly chosen. The socio-demographic and clinical data are too scanty, kindly give more information.

Helicobacter pylori should be italicized and some H. pylori have the species name starting with a capital letter, so the species name should start with small letters, not capital letters as the authors have written in some.

In the conclusion, the authors have written 'urgent need…', there are several available methods now which can be utilized to suit the particular country of origin depending on costs and accuracy. It would have been interesting to see the molecular method compared with both histology and or stool antigen test at the least since histology is not as specific as stool antigen test or urea breath test (the latter might be out of reach due to high cost).

I, therefore, approve with reservations after my suggestions above have been incorporated into the manuscript.

Is the work clearly and accurately presented and does it cite the current literature?

Partly
Is the study design appropriate and is the work technically sound?

Partly
Are sufficient details of methods and analysis provided to allow replication by others?

Partly
If applicable, is the statistical analysis and its interpretation appropriate?

Yes
Are all the source data underlying the results available to ensure full reproducibility?

Yes
Are the conclusions drawn adequately supported by the results?

Partly

Competing Interests

No competing interests were disclosed.

Reviewer Expertise

Molecular epidemiology of infectious diseases including Helicobacter pylori

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

Respond to this report

Responses (0)

Back to all reports

Reviewer Report

30 Views

11 Feb 2022 | for Version 1

Maxime Pichon, Infectious Agents Department, CHU Poitiers, Poitiers, France; INSERM U1070 Pharmacology of Antimicrobial Agents and Antibiotic Resistance, Poitiers, France

30 Views Cite this report Responses(0)

Approved With Reservations

The manuscript by Maram Elnosh et al. describes interesting data on the comparison between histology and molecular biology for the detection of Helicobacter pylori in gastric biopsies. If the publication is suitable for the editor, modifications remain to be made before indexing.

Introduction:

The introduction needs to be completed, adding information about testing another sample, non-invasive such as stool - for example, see Pichon et al., 2020¹ which demonstrates that invasive sampling is not the sole solution in recent times, especially searching for resistance to primary-line antibiotic resistance. In addition, this reference could provide information on the detection of CLA resistance, not described in this study without good reason.

Methods:

The authors should justify the number of patients they included and their inclusion period.
Because the authors use a very homemade extraction and PCR process, they must use positive and negative controls. Please describe the results obtained.
Specify the manufacturers' information for the DNA ladder.

Results:

Table 1: Specify if age is min-max or IQR.
Table 1: Specify the impact of the two different locations.
Italicize all gene names.
The last sentence in the results section of the manuscript should be reworded. The sentence could lead the reader to misunderstand the results. Moreover, the authors indicate a p-value equal to 0 that is statistically impossible, so they have to limit their conclusion to p-value < threshold.
Evaluation of the concordance between the different PCRs tested in this manuscript would be interesting (to be calculated and discussed).
Table 2: Prefer likelihood ratio instead of PPV and NPV as prevalence was specific.

Conclusion:

Rephrase the first sentence, as many tests already exist in the world there is no urgency.

Is the work clearly and accurately presented and does it cite the current literature?

Partly
Is the study design appropriate and is the work technically sound?

Partly
Are sufficient details of methods and analysis provided to allow replication by others?

Partly
If applicable, is the statistical analysis and its interpretation appropriate?

Yes
Are all the source data underlying the results available to ensure full reproducibility?

Yes
Are the conclusions drawn adequately supported by the results?

Partly

References

1. Pichon M, Pichard B, Barrioz T, Plouzeau C, et al.: Diagnostic Accuracy of a Noninvasive Test for Detection of Helicobacter pylori and Resistance to Clarithromycin in Stool by the Amplidiag H. pylori+ClariR Real-Time PCR Assay. Journal of Clinical Microbiology. 2020; 58 (4). Publisher Full Text

Competing Interests

No competing interests were disclosed.

Reviewer Expertise

Medical microbiology

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

Respond to this report

Responses (0)

[1] 1. Nevoa JC, Rodrigues RL, Menezes GL, et al.: Molecular technique for detection and identification of Helicobacter pylori in clinical specimens: a comparison with the classical diagnostic method. Jornal Brasileiro de Patologia e Medicina Laboratorial. 2017; 53(1): 13–19. Publisher Full Text

[2] 2. Khalifehgholi M, Shamsipour F, Ajhdarkosh H, et al.: Comparison of five diagnostic methods for Helicobacter pylori. Iran. J. Microbiol. 2013; 5(4): 396–401. PubMed Abstract

[3] 3. Loharamtaweethong K, Puripat N: Comparison of Immunohistochemistry and Conventional Stains for Helicobacter Pylori Detection in Gastric Biopsies of Patients Receiving Proton Pump Inhibitors. J. Health Sci. Med. Res. 2020; 38(4): 321–330. Publisher Full Text

[4] 4. Rajan A, Ganguli P, Pathak N, et al.: Correlation of serology with morphological changes in gastric biopsy of H. pylori infection. Int. J. Res. Med. Sci. 2017; 5(5): 1851–1857. Publisher Full Text

[5] 5. Gao C, Du S-Y, Fang L, et al.: Eradication treatment of Helicobacter pylori infection based on molecular pathologic antibiotic resistance. Infect. Drug Resist. 2020; Volume 13: 69–79. PubMed Abstract | Publisher Full Text

[6] 6. Idris AB, Idris EB, Ataelmanan AE, et al.: First insights into the molecular basis association between promoter polymorphisms of the IL1B gene and Helicobacter pylori infection in the Sudanese population: computational approach. BMC Microbiol. 2021; 21(1): 1–15. Publisher Full Text

[7] 7. Zamani M, Ebrahimtabar F, Zamani V, et al.: Systematic review with meta-analysis: the worldwide prevalence of Helicobacter pylori infection. Aliment. Pharmacol. Ther. 2018; 47(7): 868–876. PubMed Abstract | Publisher Full Text

[8] 8. Eldeen LAT, Mohamed MA, Awad MM, et al.: A variety of Helicobacter pylori strains colonize the stomach of non-bleeding Egyptian patients with upper gastrointestinal disorders. Bull. Natl. Res. Cent. 2019; 43(1): 1–8. Publisher Full Text

[9] 9. Akanda M, Rahman A: Comparative study of different methods for detection of Helicobacter pylori in gastric biopsies. Dinajpur Med. Col. J. 2011; 4(1): 1–6.

[10] 10. Mawlood AH, Kawther RS, Balaky STJ: Evaluation of Invasive and Non-Invasive Methods for the Diagnosis of H. pylori in Dyspepsia Patients. Diyala J. Med. 2019; 16(2): 55–63. Publisher Full Text

[11] 11. Wang Y-K, Kuo F-C, Liu C-J, et al.: Diagnosis of Helicobacter pylori infection: Current options and developments. World J. Gastroenterol: WJG. 2015; 21(40): 11221–11235. PubMed Abstract | Publisher Full Text

[12] 12. Hasosah M: Accuracy of invasive and noninvasive methods of Helicobacter pylori infection diagnosis in Saudi children. Saudi Journal of Gastroenterology: Official Journal of the Saudi Gastroenterology Association. 2019; 25(2): 126–131. PubMed Abstract | Publisher Full Text

[13] 13. Cosgun Y, Yildirim A, Yucel M, et al.: Evaluation of invasive and noninvasive methods for the diagnosis of Helicobacter pylori infection. Asian Pacific Journal of Cancer Prevention: APJCP. 2016; 17(12): 5265–5272. PubMed Abstract

[14] 14. Ahmad F, Jaffar R, Khan I: Helicobacter Pylori detection in chronic gastritis: A comparison of staining methods. J. Ayub Med. Coll. Abbottabad. 2011; 23(2): 112–114.

[15] 15. Talebi Bezmin Abadi A: Diagnosis of Helicobacter pylori using invasive and noninvasive approaches. J. Pathog. 2018; 2018: 1–13. PubMed Abstract | Publisher Full Text

[16] 16. Syahniar R, Wahid MH, Syam AF, et al.: Detecting the Helicobacter pylori 16S rRNA gene in dyspepsia patients using real-time PCR. Acta Med. Indones. 2019; 51(1): 34–41. PubMed Abstract

[17] 17. Espinoza MGC, Vazquez RG, Mendez IM, et al.: Detection of the glmM gene in Helicobacter pylori isolates with a novel primer by PCR. J. Clin. Microbiol. 2011; 49(4): 1650–1652. PubMed Abstract | Publisher Full Text

[18] 18. Mohamed AK, Elhassan NM, Awhag ZA, et al.: Prevalence of Helicobacter pylori among Sudanese patients diagnosed with colon polyps and colon cancer using immunohistochemistry technique. BMC. Res. Notes. 2020; 13(1): 1–6.

[19] 19. Hamid O, Eldaif W: Association of Helicobacter pylori infection with life style chronic diseases and body-index. J. Sci. 2014; 4(4): 255–258.

[20] 20. Abdallah TM, Mohammed HB, Mohammed MH, et al.: Sero-prevalence and factors associated with Helicobacter pylori infection in Eastern Sudan. Asian Pac. J. Trop. Dis. 2014; 4(2): 115–119. Publisher Full Text

[21] 21. Abd Al Rahem SA, Elhag WI: Molecular Detection of Helicobacter pylori in Drinking Water in Khartoum State (Sudan). African J. Med. Sci. 2018; 3(5).

[22] 22. Ye F: The role of DNA supercoiling in the coordinated regulation of gene expression in Helicobacter pylori.2004.

[23] 23. Tomasini ML, Zanussi S, Sozzi M, et al.: Heterogeneity of cag genotypes in Helicobacter pylori isolates from human biopsy specimens. J. Clin. Microbiol. 2003; 41(3): 976–980. PubMed Abstract | Publisher Full Text | Free Full Text

[24] 24. Ramis IB, Moraes EP, Fernandes MS, et al.: Evaluation of diagnostic methods for the detection of Helicobacter pylori in gastric biopsy specimens of dyspeptic patients. Braz. J. Microbiol. 2012; 43(3): 903–908. PubMed Abstract | Publisher Full Text

[25] 25. Dong Z, Chen B, Pan H, et al.: Detection of microbial 16S rRNA gene in the serum of patients with gastric cancer. Front. Oncol. 2019; 9: 608. PubMed Abstract | Publisher Full Text

[26] 26. Kisa O, Albay A, Mas MR, et al.: The evaluation of diagnostic methods for the detection of Helicobacter pylori in gastric biopsy specimens. Diagn. Microbiol. Infect. Dis. 2002; 43(4): 251–255. Publisher Full Text

[27] 27. Lee JY, Kim N: Diagnosis of Helicobacter pylori by invasive test: histology. Annals of translational medicine. 2015; 3(1).

[28] 28. Redéen S, Petersson F, Törnkrantz E, et al.: Reliability of diagnostic tests for Helicobacter pylori infection. Gastroenterol. Res. Pract. 2011; 2011: 1–6. PubMed Abstract | Publisher Full Text

[29] 29. Salman KD, Al-Thwaini AN, Askar BA: Evaluation of glmM Gene in Diagnosis of Helicobacter pylori with Another Invasive Methods. Iran. J. Biotechnol. 2019; 18(3).

[30] 30. AlNaji HA, Omran R, AlSherify A: Molecular Detection of Helicobacter pylori Infection in Gastric Biopsy Specimens by PCR. Journal of University of Babylon for Pure and Applied Sciences. 2018; 26(2): 109–118.

[31] 31. Helaly GH, El-Afandy NM, Hassan AA, et al.: Diagnostic Value of Housekeeping [glmM] Gene Expression in Antral Biopsies in Comparison to Rapid Urease Test and Histological Detection of Helicobacter Pylori Infection Egyptian. J. Med. Microbiol. 2009; 18(4).

[32] 32. Raymond J, Thiberge J-M, Chevalier C, et al.: Genetic and transmission analysis of Helicobacter pylori strains within a family. Emerg. Infect. Dis. 2004; 10(10): 1816–1821. PubMed Abstract | Publisher Full Text | Free Full Text

[33] 33. Smith S, Oyedeji K, Arigbabu A, et al.: Comparison of three PCR methods for detection of Helicobacter pylori DNA and detection of cagA gene in gastric biopsy specimens. World J Gastroenterol: WJG. 2004; 10(13): 1958–1960. PubMed Abstract | Publisher Full Text | Free Full Text

[34] 34. Singh V, Mishra S, Rao G, et al.: Evaluation of nested PCR in detection of Helicobacter pylori targeting a highly conserved gene: HSP60. J. Helicobacter. 2008; 13(1): 30–34. PubMed Abstract | Publisher Full Text

[35] 35. Farhadkhani M, Nikaeen M, Hassanzadeh A, et al.: Potential transmission sources of Helicobacter pylori infection: detection of H. pylori in various environmental samples. J. Environ. Health Sci. Eng. 2019; 17(1): 129–134. PubMed Abstract | Publisher Full Text

[36] 36. Sugimoto M, Wu J-Y, Abudayyeh S, et al.: Unreliability of results of PCR detection of Helicobacter pylori in clinical or environmental samples. J. Clin. Microbiol. 2009; 47(3): 738–742. PubMed Abstract | Publisher Full Text

[37] 37. Maram E, Altayb Hisham N, Fadalla HY, et al.: Comparison of invasive histological and molecular methods in the diagnosis of Helicobacter pylori from gastric biopsies of Sudanese patients: a cross-sectional study. figshare. Dataset. 2021. Publisher Full Text

[38] 38. Maram E, Altayb Hisham N, Fadalla HY, et al.: Comparison of invasive histological and molecular methods in the diagnosis of Helicobacter pylori from gastric biopsies of Sudanese patients: a cross-sectional study. figshare. Figure. 2022. Publisher Full Text

Comparison of invasive histological and molecular methods in the diagnosis of Helicobacter pylori from gastric biopsies of Sudanese patients: a cross-sectional study

Abstract

Keywords

Revised Amendments from Version 1

Introduction

Methods

Collection of biopsy specimens

Histopathological identification of Helicobacter pylori

DNA extraction

Polymerase chain reaction (PCR)

Statistical analysis

Results

Table 1. Sociodemographic and clinical data for participated patients.

Histopathological identification of Helicobacter pylori

Detection of H. pylori 16S rRNA, glmM, and ureA genes of H. pylori by PCR

Figure 1. PCR amplification of H. pylori on agarose gel electrophoresis 1.5%.

Table 2. Comparison between histopathological approach and various PCR methods used for the diagnosis of H. pylori infections in this study.

Discussion

Conclusions

Data availability

Underlying data

References

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