{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T03:09:22Z","timestamp":1793502562730,"version":"4.5.0"},"update-to":[{"DOI":"10.12688\/f1000research.75873.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,6,8]],"date-time":"2022-06-08T00:00:00Z","timestamp":1654646400000}}],"reference-count":38,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2022,6,8]],"date-time":"2022-06-08T00:00:00Z","timestamp":1654646400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The Ministry of Higher Education and Scientific Research- Commission of Scientific Research and innovation- Sudan","award":["15\/17"],"award-info":[{"award-number":["15\/17"]}]}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns3:p>\n                    <ns3:bold>Background:<\/ns3:bold>\n                    The continuous rise in the number of patients suffering from\n                    <ns3:italic>Helicobacter pylori<\/ns3:italic>\n                    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\n                    <ns3:italic>H. pylori<\/ns3:italic>\n                    by polymerase chain reaction (PCR) targeting the\n                    <ns3:italic>16S rRNA, ureA<\/ns3:italic>\n                    and\n                    <ns3:italic>glmM<\/ns3:italic>\n                    genes with an invasive histopathological technique.\n                  <\/ns3:p>\n                  <ns3:p>\n                    <ns3:bold>Methods:<\/ns3:bold>\n                    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.\n                  <\/ns3:p>\n                  <ns3:p>\n                    <ns3:bold>Results<\/ns3:bold>\n                    : A total of 103 (35.5%) samples were positive by histopathological examination, 88 (30.3%) by\n                    <ns3:italic>16S rRNA<\/ns3:italic>\n                    , 39 (13.4%) by\n                    <ns3:italic>glmM<\/ns3:italic>\n                    gene, and 56 (19.3%) by\n                    <ns3:italic>ureA<\/ns3:italic>\n                    gene. The highest sensitivity was observed in\n                    <ns3:italic>16S rRNA<\/ns3:italic>\n                    (46.6%), followed by\n                    <ns3:italic>glmM<\/ns3:italic>\n                    (24.3%) and\n                    <ns3:italic>ureA<\/ns3:italic>\n                    (23.3%). While the best specificity was observed in\n                    <ns3:italic>glmM<\/ns3:italic>\n                    gene (92.5%), followed by\n                    <ns3:italic>ureA<\/ns3:italic>\n                    (82.3%) and\n                    <ns3:italic>16S rRNA<\/ns3:italic>\n                    (78.6%).\n                  <\/ns3:p>\n                  <ns3:p>\n                    <ns3:bold>Conclusion<\/ns3:bold>\n                    : PCR test targeting the\n                    <ns3:italic>16S rRNA<\/ns3:italic>\n                    gene exhibited the best results for molecular detection of\n                    <ns3:italic>H. pylori<\/ns3:italic>\n                    compared to other genes.\n                  <\/ns3:p>","DOI":"10.12688\/f1000research.75873.2","type":"journal-article","created":{"date-parts":[[2022,6,8]],"date-time":"2022-06-08T10:05:23Z","timestamp":1654682723000},"page":"113","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":7,"title":["Comparison of invasive histological and molecular methods in the diagnosis of Helicobacter pylori from gastric biopsies of Sudanese patients: a cross-sectional study"],"prefix":"10.12688","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4675-5295","authenticated-orcid":false,"given":"Maram","family":"Elnosh","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hisham","family":"Altayb","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yousif","family":"Hamedelnil","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wafa","family":"Elshareef","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aliaa","family":"Abugrain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esraa","family":"Osman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9501-7264","authenticated-orcid":false,"given":"Aalaa","family":"Albasha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abdelhamid","family":"Abdelhamid","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ehssan","family":"Moglad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5463-9892","authenticated-orcid":false,"given":"Ahmed","family":"AbdAlla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7325-1674","authenticated-orcid":false,"given":"Ahmed","family":"Ismail","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2022,6,8]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"13-19","DOI":"10.5935\/1676-2444.20170003","article-title":"Molecular technique for detection and identification of Helicobacter pylori in clinical specimens: a comparison with the classical diagnostic method.","volume":"53","author":"J Nevoa","year":"2017","journal-title":"Jornal Brasileiro de Patologia e Medicina Laboratorial."},{"key":"ref2","first-page":"396-401","article-title":"Comparison of five diagnostic methods for Helicobacter pylori.","volume":"5","author":"M Khalifehgholi","year":"2013","journal-title":"Iran. J. Microbiol."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"321-330","DOI":"10.31584\/jhsmr.2020752","article-title":"Comparison of Immunohistochemistry and Conventional Stains for Helicobacter Pylori Detection in Gastric Biopsies of Patients Receiving Proton Pump Inhibitors.","volume":"38","author":"K Loharamtaweethong","year":"2020","journal-title":"J. Health Sci. Med. Res."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"1851-1857","DOI":"10.18203\/2320-6012.ijrms20171599","article-title":"Correlation of serology with morphological changes in gastric biopsy of H. pylori infection.","volume":"5","author":"A Rajan","year":"2017","journal-title":"Int. J. Res. Med. Sci."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"69-79","DOI":"10.2147\/IDR.S232169","article-title":"Eradication treatment of Helicobacter pylori infection based on molecular pathologic antibiotic resistance.","volume":"13","author":"C Gao","year":"2020","journal-title":"Infect. Drug Resist."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"1-15","DOI":"10.1186\/s12866-020-02072-3","article-title":"First insights into the molecular basis association between promoter polymorphisms of the IL1B gene and Helicobacter pylori infection in the Sudanese population: computational approach.","volume":"21","author":"A Idris","year":"2021","journal-title":"BMC Microbiol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"868-876","DOI":"10.1111\/apt.14561","article-title":"Systematic review with meta-analysis: the worldwide prevalence of Helicobacter pylori infection.","volume":"47","author":"M Zamani","year":"2018","journal-title":"Aliment. Pharmacol. Ther."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"1-8","DOI":"10.1186\/s42269-019-0224-5","article-title":"A variety of Helicobacter pylori strains colonize the stomach of non-bleeding Egyptian patients with upper gastrointestinal disorders.","volume":"43","author":"L Eldeen","year":"2019","journal-title":"Bull. Natl. Res. Cent."},{"key":"ref9","first-page":"1-6","article-title":"Comparative study of different methods for detection of Helicobacter pylori in gastric biopsies.","volume":"4","author":"M Akanda","year":"2011","journal-title":"Dinajpur Med. Col. J."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"55-63","DOI":"10.26505\/DJM.16024460122","article-title":"Evaluation of Invasive and Non-Invasive Methods for the Diagnosis of H. pylori in Dyspepsia Patients.","volume":"16","author":"A Mawlood","year":"2019","journal-title":"Diyala J. Med."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"11221-11235","DOI":"10.3748\/wjg.v21.i40.11221","article-title":"Diagnosis of Helicobacter pylori infection: Current options and developments.","volume":"21","author":"Y Wang","year":"2015","journal-title":"World J. Gastroenterol: WJG."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"126-131","DOI":"10.4103\/sjg.SJG_288_18","article-title":"Accuracy of invasive and noninvasive methods of Helicobacter pylori infection diagnosis in Saudi children.","volume":"25","author":"M Hasosah","year":"2019","journal-title":"Saudi Journal of Gastroenterology: Official Journal of the Saudi Gastroenterology Association."},{"key":"ref13","first-page":"5265-5272","article-title":"Evaluation of invasive and noninvasive methods for the diagnosis of Helicobacter pylori infection.","volume":"17","author":"Y Cosgun","year":"2016","journal-title":"Asian Pacific Journal of Cancer Prevention: APJCP."},{"key":"ref14","first-page":"112-114","article-title":"Helicobacter Pylori detection in chronic gastritis: A comparison of staining methods.","volume":"23","author":"F Ahmad","year":"2011","journal-title":"J. Ayub Med. Coll. Abbottabad."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"1-13","DOI":"10.1155\/2018\/9064952","article-title":"Diagnosis of Helicobacter pylori using invasive and noninvasive approaches.","volume":"2018","author":"A Talebi Bezmin Abadi","year":"2018","journal-title":"J. Pathog."},{"key":"ref16","first-page":"34-41","article-title":"Detecting the Helicobacter pylori 16S rRNA gene in dyspepsia patients using real-time PCR.","volume":"51","author":"R Syahniar","year":"2019","journal-title":"Acta Med. Indones."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"1650-1652","DOI":"10.1128\/JCM.00461-10","article-title":"Detection of the glmM gene in Helicobacter pylori isolates with a novel primer by PCR.","volume":"49","author":"M Espinoza","year":"2011","journal-title":"J. Clin. Microbiol."},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1-6","DOI":"10.1186\/s13104-020-05159-2","article-title":"Prevalence of Helicobacter pylori among Sudanese patients diagnosed with colon polyps and colon cancer using immunohistochemistry technique.","volume":"13","author":"A Mohamed","year":"2020","journal-title":"BMC. Res. Notes."},{"key":"ref19","first-page":"255-258","article-title":"Association of Helicobacter pylori infection with life style chronic diseases and body-index.","volume":"4","author":"O Hamid","year":"2014","journal-title":"J. Sci."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"115-119","DOI":"10.1016\/S2222-1808(14)60326-1","article-title":"Sero-prevalence and factors associated with Helicobacter pylori infection in Eastern Sudan.","volume":"4","author":"T Abdallah","year":"2014","journal-title":"Asian Pac. J. Trop. Dis."},{"key":"ref21","article-title":"Molecular Detection of Helicobacter pylori in Drinking Water in Khartoum State (Sudan).","volume":"3","author":"S Abd Al Rahem","year":"2018","journal-title":"African J. Med. Sci."},{"key":"ref22","article-title":"The role of DNA supercoiling in the coordinated regulation of gene expression in Helicobacter pylori.","author":"F Ye","year":"2004"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"976-980","DOI":"10.1128\/JCM.41.3.976-980.2003","article-title":"Heterogeneity of cag genotypes in Helicobacter pylori isolates from human biopsy specimens.","volume":"41","author":"M Tomasini","year":"2003","journal-title":"J. Clin. Microbiol."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"903-908","DOI":"10.1590\/S1517-83822012000300008","article-title":"Evaluation of diagnostic methods for the detection of Helicobacter pylori in gastric biopsy specimens of dyspeptic patients.","volume":"43","author":"I Ramis","year":"2012","journal-title":"Braz. J. Microbiol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"608","DOI":"10.3389\/fonc.2019.00608","article-title":"Detection of microbial 16S rRNA gene in the serum of patients with gastric cancer.","volume":"9","author":"Z Dong","year":"2019","journal-title":"Front. Oncol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"251-255","DOI":"10.1016\/S0732-8893(02)00409-1","article-title":"The evaluation of diagnostic methods for the detection of Helicobacter pylori in gastric biopsy specimens.","volume":"43","author":"O Kisa","year":"2002","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref27","article-title":"Diagnosis of Helicobacter pylori by invasive test: histology.","volume":"3","author":"J Lee","year":"2015","journal-title":"Annals of translational medicine."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"1-6","DOI":"10.1155\/2011\/940650","article-title":"Reliability of diagnostic tests for Helicobacter pylori infection.","volume":"2011","author":"S Red\u00e9en","year":"2011","journal-title":"Gastroenterol. Res. Pract."},{"key":"ref29","article-title":"Evaluation of glmM Gene in Diagnosis of Helicobacter pylori with Another Invasive Methods.","volume":"18","author":"K Salman","year":"2019","journal-title":"Iran. J. Biotechnol."},{"key":"ref30","first-page":"109-118","article-title":"Molecular Detection of Helicobacter pylori Infection in Gastric Biopsy Specimens by PCR.","volume":"26","author":"H AlNaji","year":"2018","journal-title":"Journal of University of Babylon for Pure and Applied Sciences."},{"key":"ref31","article-title":"Diagnostic Value of Housekeeping [glmM] Gene Expression in Antral Biopsies in Comparison to Rapid Urease Test and Histological Detection of Helicobacter Pylori Infection Egyptian.","volume":"18","author":"G Helaly","year":"2009","journal-title":"J. Med. Microbiol."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"1816-1821","DOI":"10.3201\/eid1010.040042","article-title":"Genetic and transmission analysis of Helicobacter pylori strains within a family.","volume":"10","author":"J Raymond","year":"2004","journal-title":"Emerg. Infect. Dis."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"1958-1960","DOI":"10.3748\/wjg.v10.i13.1958","article-title":"Comparison of three PCR methods for detection of Helicobacter pylori DNA and detection of cagA gene in gastric biopsy specimens.","volume":"10","author":"S Smith","year":"2004","journal-title":"World J Gastroenterol: WJG."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"30-34","DOI":"10.1111\/j.1523-5378.2008.00573.x","article-title":"Evaluation of nested PCR in detection of Helicobacter pylori targeting a highly conserved gene: HSP60.","volume":"13","author":"V Singh","year":"2008","journal-title":"J. Helicobacter."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"129-134","DOI":"10.1007\/s40201-018-00333-y","article-title":"Potential transmission sources of Helicobacter pylori infection: detection of H. pylori in various environmental samples.","volume":"17","author":"M Farhadkhani","year":"2019","journal-title":"J. Environ. Health Sci. Eng."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"738-742","DOI":"10.1128\/JCM.01563-08","article-title":"Unreliability of results of PCR detection of Helicobacter pylori in clinical or environmental samples.","volume":"47","author":"M Sugimoto","year":"2009","journal-title":"J. Clin. Microbiol."},{"key":"ref37","doi-asserted-by":"publisher","DOI":"10.6084\/m9.figshare.17072012.v2","article-title":"Comparison of invasive histological and molecular methods in the diagnosis of Helicobacter pylori from gastric biopsies of Sudanese patients: a cross-sectional study. figshare.","author":"E Maram","year":"2021","journal-title":"Dataset."},{"key":"ref38","doi-asserted-by":"publisher","DOI":"10.6084\/m9.figshare.18482015.v1","article-title":"Comparison of invasive histological and molecular methods in the diagnosis of Helicobacter pylori from gastric biopsies of Sudanese patients: a cross-sectional study. figshare.","author":"E Maram","year":"2022","journal-title":"Figure."}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/11-113\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/11-113\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/11-113\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,6,21]],"date-time":"2022-06-21T09:00:32Z","timestamp":1655802032000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/11-113\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,8]]},"references-count":38,"URL":"https:\/\/doi.org\/10.12688\/f1000research.75873.2","relation":{"has-review":[{"id-type":"doi","id":"10.5256\/f1000research.134815.r140059","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.134815.r140058","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.134815.r140058","asserted-by":"object"},{"id-type":"doi","id":"10.5256\/f1000research.134815.r140059","asserted-by":"object"}]},"ISSN":["2046-1402"],"issn-type":[{"value":"2046-1402","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,6,8]]},"assertion":[{"value":"Indexed","URL":"https:\/\/f1000research.com\/articles\/11-113\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.134815.r140058, Maxime Pichon, Infectious Agents Department, CHU Poitiers, Poitiers, France, 21 Jun 2022, version 2, indexed","URL":"https:\/\/f1000research.com\/articles\/11-113\/v2#referee-response-140058","order":0,"name":"referee-response-140058","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.134815.r140059, Stella Ifeanyi Smith, Department of Molecular Biology and Biotechnology, Nigeria Institute of Medical Research, Lagos, Nigeria, 10 Jun 2022, version 2, indexed","URL":"https:\/\/f1000research.com\/articles\/11-113\/v2#referee-response-140059","order":1,"name":"referee-response-140059","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"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.","order":2,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}