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Rosli NA, Al-Maleki AR, Loke MF, Chua EG, Alhoot MA, Vadivelu J. Polymorphism of virulence genes and biofilm associated with in vitro induced resistance to clarithromycin in Helicobacter pylori. Gut Pathog 2023; 15:52. [PMID: 37898785 PMCID: PMC10613384 DOI: 10.1186/s13099-023-00579-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND Clarithromycin-containing triple therapy is commonly used to treat Helicobacter pylori infections. Clarithromycin resistance is the leading cause of H. pylori treatment failure. Understanding the specific mutations that occur in H. pylori strains that have evolved antibiotic resistance can help create a more effective and individualised antibiotic treatment plan. However, little is understood about the genetic reprogramming linked to clarithromycin exposure and the emergence of antibiotic resistance in H. pylori. Therefore, this study aims to identify compensatory mutations and biofilm formation associated with the development of clarithromycin resistance in H. pylori. Clarithromycin-sensitive H. pylori clinical isolates were induced to develop clarithromycin resistance through in vitro exposure to incrementally increasing concentration of the antibiotic. The genomes of the origin sensitive isolates (S), isogenic breakpoint (B), and resistant isolates (R) were sequenced. Single nucleotide variations (SNVs), and insertions or deletions (InDels) associated with the development of clarithromycin resistance were identified. Growth and biofilm production were also assessed. RESULTS The S isolates with A2143G mutation in the 23S rRNA gene were successfully induced to be resistant. According to the data, antibiotic exposure may alter the expression of certain genes, including those that code for the Cag4/Cag protein, the vacuolating cytotoxin domain-containing protein, the sel1 repeat family protein, and the rsmh gene, which may increase the risk of developing and enhances virulence in H. pylori. Enhanced biofilm formation was detected among R isolates compared to B and S isolates. Furthermore, high polymorphism was also detected among the genes associated with biofilm production. CONCLUSIONS Therefore, this study suggests that H. pylori may acquire virulence factors while also developing antibiotic resistance due to clarithromycin exposure.
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Affiliation(s)
- Naim Asyraf Rosli
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Anis Rageh Al-Maleki
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Sana'a University, Sana'a, Yemen.
| | - Mun Fai Loke
- Camtech Biomedical Pte Ltd, Singapore, Singapore
| | - Eng Guan Chua
- School of Biomedical Sciences, Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Perth, WA, Australia
| | - Mohammed Abdelfatah Alhoot
- Faculty of Pharmacy, Airlangga University, Surabaya, 60155, Indonesia
- School of Graduate Studies, Management & Science University, Shah Alam, Selangor, Malaysia
| | - Jamuna Vadivelu
- Medical Education Research and Development Unit, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
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Menbari MN, Nasseri S, Menbari N, Mehdiabadi R, Alipur Y, Roshani D. The -160 (C>A) CDH1 Gene Promoter Polymorphism and Its Relationship with Survival of Patients with Gastric Cancer in
Kurdistan. Asian Pac J Cancer Prev 2017; 18:1561-1565. [PMID: 28669168 PMCID: PMC6373814 DOI: 10.22034/apjcp.2017.18.6.1561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Introduction: Gastric cancer (GC) is the fourth most common type of neoplasm and the second cause of malignancy-related death across much of the world. Complex multi-factorial processes are involved in its genesis, classified in two determinant clusters: non-genetic and genetic. Variation in CDH1 gene expression may play an important role in increasing risk of diffuse and intestinal subtypes of GC. This tumor suppressor gene, located on chromosome 16q22.1, encodes a trans membrane glycoprotein called epithelial cadherin (E-cadherin). Materials and Methods: In this historical cohort study, from June 2004 to Journey 2005 we collected 50 samples from Kurdish patients with stage II pathologically diagnosed gastric cancer that underwent surgery. Tumor tissues were paraffin-embedded along with 54 control samples from non-ulcer dyspepsia (NUD) cases undergoing upper gastrointestinal endoscopy. Three biopsies were captured by endoscopy from each individual’s gastric antrum. Result: The mean age of the patients was 59.5±2 years. Some 23 cases (53.4%) had the CC genotype, 19 AC and 1 AA. H.pylori infection was noted in 30 patients (69%). Survival rates of gastric cancer patients were 90.7% in the first year, 39.5% in the second year and 6.9% in the third year. Female patients had higher survival rates (P=0.004). Conclusion: In this study we found that frequencies of -160(C>A) CDH1 genotypes were not comparable in H.pylori-infected and H.pylori-uninfected subjects in both case and control groups. These findings suggest that -160 (C>A) CDH1 polymorphism is not related with H.pylori infection susceptibility. In addition we found no significant relationship between the CDH1 -160(C/A) promoter polymorphism with predisposition to gastric cancer.
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Affiliation(s)
- Mohammad Nazir Menbari
- Cellular and Molecular Research Center, Kurdistan University of Medical
Sciences, Sanandaj, Iran.
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Molecular Epidemiology of Helicobacter pylori in Dental Plaque among Jordanians; A Probable Source for Infection and Treatment Failure. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2017. [DOI: 10.22207/jpam.11.1.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Puri A, Rai A, Dhanaraj PS, Lal R, Patel DD, Kaicker A, Verma M. An In Silico Approach for Identification of the Pathogenic Species, Helicobacter pylori and Its Relatives. Indian J Microbiol 2016; 56:277-86. [PMID: 27407291 PMCID: PMC4920758 DOI: 10.1007/s12088-016-0575-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 03/11/2016] [Indexed: 12/19/2022] Open
Abstract
Helicobacter is an economically important genus within the phylum Proteobacteria and include many species which cause many diseases in humans. With the conventional methods, it is difficult to identify them easily due to the high genetic similarity among its species. In the present study, 361 16S rRNA (rrs) gene sequences belonging to 45 species of genus Helicobacter were analyzed. Out of these, 264 sequences of 10 clinically relevant species (including Helicobacter pylori) were used. rrs gene sequences were analyzed to obtain a phylogenetic framework tree, in silico restriction enzyme analysis and species-specific conserved motifs. Protein sequences of another housekeeping gene, hsp60 were also subjected to phylogenetic analysis to supplement the data obtained using rrs sequences. Using these approaches, six out of ten species (including H. pylori) were easily segregated, whereas four species namely H. bilis, H. cinaedi, H. felis and Candidatus H. heilmannii were found to be heterogeneous. The above approaches have also helped in segregating unclassified sequences, thus proving them as an easy diagnostic method for identifying members of genus Helicobacter up to species level.
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Affiliation(s)
- Ayush Puri
- />Department of Zoology, Sri Venkateswara College, University of Delhi, South Campus, New Delhi, 110 021 India
| | - Arshiya Rai
- />Department of Zoology, Sri Venkateswara College, University of Delhi, South Campus, New Delhi, 110 021 India
| | - P. S. Dhanaraj
- />Department of Zoology, Sri Venkateswara College, University of Delhi, South Campus, New Delhi, 110 021 India
| | - Rup Lal
- />Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110 007 India
| | - Dev Dutt Patel
- />Department of Zoology, Sri Venkateswara College, University of Delhi, South Campus, New Delhi, 110 021 India
| | - Anju Kaicker
- />Department of Biochemistry, Sri Venkateswara College, University of Delhi, South Campus, New Delhi, 110 021 India
| | - Mansi Verma
- />Department of Zoology, Sri Venkateswara College, University of Delhi, South Campus, New Delhi, 110 021 India
- />Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110 007 India
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Talaei R, Souod N, Momtaz H, Dabiri H. Milk of livestock as a possible transmission route of Helicobacter pylori infection. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2015. [PMID: 26171135 DOI: 10.22037/ghfbb.v8isupplement.764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
AIM The current investigation aimed to evaluate ruminant raw milk as a reservoir source of Helicobacter pylori and analyze the diversity of cagA and vacA genotypes as H. pylori virulence factors to find any relationship between these genotypes in human and animal H. pylori strains. BACKGROUND The way of transmission of Helicobacter pylori as one of the most controversial bacteria in the world, which colonizes the human gastric tissue and is responsible for several gastric diseases is still unknown. The possibility of zoonotic transmission of H. pylori is feasible, but is not proven in ruminant reservoirs. METHODS Overall 210 cows, sheep, goats, camels and buffalos' raw milk samples and 100 human gastric biopsies were collected in this survey. We applied PCR assays to identify H. pylori, vacA and cagA genes. Statistical tests were applied for data analysis. RESULTS Totally 12(16%) cow, 8(13.79%) sheep, 2 (4.76%) goat, 2(13.33%), buffalo 4(20%) and 82 (82%) of human specimens were confirmed to be H. pylori positive. Among which s1a/m2 genotype was more frequent in isolated H. pylori strains and statistically significant between strains. Based on statistical analyses the s1b allele of sheep had a significant association with human strains. CONCLUSION The current survey was prompted by our previous report. According to both results we can conclude that sheep may act as a reservoir for H. pylori and transmit this bacterium to human via its milk. Extended assessments in other geographical regions and other animals are recommended.
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Affiliation(s)
- Ramin Talaei
- Shahid Modaress Hospital, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Negar Souod
- Young Researchers and Elite Club, Islamic Azad University, Central Tehran Branch, Tehran, Iran
| | - Hassan Momtaz
- Department of Microbiology, Faculty of Veterinary Medicine, Islamic Azad University, ShahreKord Branch, ShahreKord, Iran
| | - Hossein Dabiri
- Department of Clinical Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Agarwal S, Jithendra KD. Presence of Helicobacter pylori in subgingival plaque of periodontitis patients with and without dyspepsia, detected by polymerase chain reaction and culture. J Indian Soc Periodontol 2013; 16:398-403. [PMID: 23162336 PMCID: PMC3498711 DOI: 10.4103/0972-124x.100919] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2010] [Accepted: 04/11/2012] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Helicobacter pylori is an important gastrointestinal pathogen that is strongly associated with gastritis as well as peptic ulcer disease. Antimicrobial therapy frequently fails to cure H. pylori infection, which suggests there may be sanctuary sites where the organism resides. This study was aimed to assess the role of oral cavity as a reservoir of H. pylori by evaluating the occurrence of the organism in subgingival plaque of dyspeptic patients by polymerase chain reaction as well as culture. MATERIALS AND METHODS Thirty chronic periodontitis patients whose biopsy specimens were found to be H. pylori positive with rapid urease test and histopathologic examination were considered as cases and 20 chronic periodontitis patients who never had any symptoms of gastritis or peptic ulcer were taken as controls. Subgingival plaque samples were collected and sent to microbiological laboratory for detection of H. pylori by 16S rRNA based polymerase chain reaction as well as culture. RESULTS 60% of the samples were found to be positive with polymerase chain reaction in the case group when compared to 15% in the controls. Also, 30% of the cases were found to be positive with culture compared to none in controls. CONCLUSION A higher frequency of detection of H. pylori in those patients with positive antral biopsy report was seen. Also, polymerase chain reaction was found to be more sensitive than culture for detection. Thus, we conclude that detection of H. pylori in dental plaque of dyspeptic patients cannot be neglected and might represent a risk factor for recolonization of stomach after systemic eradication therapy.
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Affiliation(s)
- Sangita Agarwal
- Department of Periodontology, People's Dental Academy, Bhopal, Madhya Pradesh, India
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Liu H, Rahman A, Semino-Mora C, Doi SQ, Dubois A. Specific and sensitive detection of H. pylori in biological specimens by real-time RT-PCR and in situ hybridization. PLoS One 2008; 3:e2689. [PMID: 18648543 PMCID: PMC2481290 DOI: 10.1371/journal.pone.0002689] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Accepted: 06/02/2008] [Indexed: 12/13/2022] Open
Abstract
PCR detection of H. pylori in biological specimens is rendered difficult by the extensive polymorphism of H. pylori genes and the suppressed expression of some genes in many strains. The goal of the present study was to (1) define a domain of the 16S rRNA sequence that is both highly conserved among H. pylori strains and also specific to the species, and (2) to develop and validate specific and sensitive molecular methods for the detection of H. pylori. We used a combination of in silico and molecular approaches to achieve sensitive and specific detection of H. pylori in biologic media. We sequenced two isolates from patients living in different continents and demonstrated that a 546-bp domain of the H. pylori 16S rRNA sequence was conserved in those strains and in published sequences. Within this conserved sequence, we defined a 229-bp domain that is 100% homologous in most H. pylori strains available in GenBank and also is specific for H. pylori. This sub-domain was then used to design (1) a set of high quality RT-PCR primers and probe that encompassed a 76-bp sequence and included at least two mismatches with other Helicobacter sp. 16S rRNA; and (2) in situ hybridization antisense probes. The sensitivity and specificity of the approaches were then demonstrated by using gastric biopsy specimens from patients and rhesus monkeys. This H. pylori-specific region of the 16S rRNA sequence is highly conserved among most H. pylori strains and allows specific detection, identification, and quantification of this bacterium in biological specimens.
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Affiliation(s)
- Hui Liu
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Arifur Rahman
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Cristina Semino-Mora
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Sonia Q. Doi
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Andre Dubois
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- * E-mail:
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Detection and Analysis of Helicobacter pylori DNA in the Gastric Juice, Saliva, and Urine by Nested PCR. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s1348-8643(08)80003-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Singh V, Mishra S, Rao GRK, Jain AK, Dixit V, Gulati AK, Mahajan D, McClelland M, Nath G. Evaluation of nested PCR in detection of Helicobacter pylori targeting a highly conserved gene: HSP60. Helicobacter 2008; 13:30-4. [PMID: 18205663 PMCID: PMC2752369 DOI: 10.1111/j.1523-5378.2008.00573.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVE To comparatively evaluate a new nested set of primers designed for the detection of Helicobacter pylori targeting a highly conserved heat shock protein gene (Hsp60). METHODS A total of 60 subjects having peptic ulcer diseases were tested for the detection of H. pylori using rapid urease test (RUT), histology, culture, and polymerase chain reaction (PCR) in their antral biopsy specimens. A newly designed Hsp60 gene-based primer set was evaluated against commonly used PCR primers for detection of H. pylori. RESULTS Forty-six of the 60 study subjects were found positive for culture isolation and all the 46 culture-positive specimens were also positive with Hsp60 gene PCR. Of the 46 culture-positive specimens, 44 were positive for 16S rRNA gene, ureC gene, RUT, and histology whereas only 29 were positive with ureA gene PCR. Of the 14 culture-negative subjects, 10 were positive with 16S rRNA gene, 4 were positive with ureC (glmM) gene PCR, and 2 were positive with RUT and 1 was positive on histology. CONCLUSION This study shows that nested amplification targeting Hsp60 gene is the most sensitive and specific with LR+ and LR- values of proportional, variant and 0, respectively, when compared with the other three PCR methods. Also, HSP60 gene-specific nested protocol was the most appropriate for detection of H. pylori in clinical specimens. This is particularly valuable because it can be used as a noninvasive method for detecting H. pylori infection in young children and also, in follow-up studies with peptic ulcer patients, on samples like feces and saliva.
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Affiliation(s)
- Varsha Singh
- Department of Biochemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Shrutkirti Mishra
- Department of Biochemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - GRK Rao
- Department of Biochemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Ashok Kumar Jain
- Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - V.K. Dixit
- Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Anil Kumar Gulati
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Divya Mahajan
- Department of Biochemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Michael McClelland
- Cell and Molecular Biology Laboratory, Sidney Kimmel Cancer Center, San Diego, CA, USA
| | - Gopal Nath
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India.,Corresponding author & Reprint request Mailing address: Gopal Nath Professor, Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005,India. Phone: 91-9335058394 Fax: 91-542 2367568
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Mégraud F, Lehours P. Helicobacter pylori detection and antimicrobial susceptibility testing. Clin Microbiol Rev 2007; 20:280-322. [PMID: 17428887 PMCID: PMC1865594 DOI: 10.1128/cmr.00033-06] [Citation(s) in RCA: 463] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The discovery of Helicobacter pylori in 1982 was the starting point of a revolution concerning the concepts and management of gastroduodenal diseases. It is now well accepted that the most common stomach disease, peptic ulcer disease, is an infectious disease, and all consensus conferences agree that the causative agent, H. pylori, must be treated with antibiotics. Furthermore, the concept emerged that this bacterium could be the trigger of various malignant diseases of the stomach, and it is now a model for chronic bacterial infections causing cancer. Most of the many different techniques involved in diagnosis of H. pylori infection are performed in clinical microbiology laboratories. The aim of this article is to review the current status of these methods and their application, highlighting the important progress which has been made in the past decade. Both invasive and noninvasive techniques will be reviewed.
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Affiliation(s)
- Francis Mégraud
- INSERM U853, and Université Victor Segalen Bordeaux 2, and Laboratoire de Bactériologie, Hôpital Pellegrin, Place Amélie Raba-Léon, 33076 Bordeaux cedex, France.
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Paimela HM, Oksala NK, Kääriäinen IP, Carlson PJ, Kostiala AA, Sipponen PI. Faecal antigen tests in the confirmation of the effect of Helicobacter eradication therapy. Ann Med 2006; 38:352-6. [PMID: 16938804 DOI: 10.1080/07853890600630567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The frequent occurrence of Helicobacter pylori infection requires significant health care resources after eradication therapy. Therefore the non-invasive testing methods are required to alleviate the increased work-load of health care personnel and to allow an easy control of eradication therapy. Conventionally, the effect of eradication therapy has been confirmed with 13C-urea breath test 4-6 weeks after a completed eradication. AIM To assess the applicability of Helicobacter pylori stool antigen tests as alternatives to the breath test in the control of the effect of eradication therapy. METHODS Fifty patients were diagnosed Helicobacter-positive by endoscopy and histology as well as by rapid urease test from mucosal specimen. Four weeks after an eradication therapy the patients were subjected to 13C-urea breath test as well as to faecal Helicobacter pylori antigen tests with mono- and polyclonal primary antibodies. RESULTS The monoclonal and polyclonal stool tests had 94% and 88% sensitivity, and 100% and 97% specificity, respectively, in the detection of Helicobacter pylori infection as compared to the 13C-urea breath test. The non-invasive test results were completely parallel in patients with various grades of mucosal atrophy or intestinal metaplasia. CONCLUSIONS Monoclonal faecal Helicobacter pylori antigen test is slightly superior to the polyclonal test regarding the sensitivity in the detection of stool Helicobacter antigens. Due to their sufficient sensitivity and specificity, and to their practicability and cost-effectiveness, they can be recommended for non-invasive testing of Helicobacter pylori infection as alternatives to the 13C-urea breath test.
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Affiliation(s)
- Hannu M Paimela
- Department of Surgery, Helsinki University Central Hospital, Jorvi Hospital, Espoo, Finland.
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Lim CY, Lee KH, Cho MJ, Chang MW, Kim SY, Myong NH, Lee WK, Rhee KH, Kook YH. Detection of Helicobacter pylori in gastric mucosa of patients with gastroduodenal diseases by PCR-restriction analysis using the RNA polymerase gene (rpoB). J Clin Microbiol 2003; 41:3387-91. [PMID: 12843100 PMCID: PMC165300 DOI: 10.1128/jcm.41.7.3387-3391.2003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A novel PCR restriction analysis method using the RNA polymerase beta-subunit- coding gene (rpoB) was employed to both detect and identify Helicobacter pylori in biopsy specimens and culture isolates. The rpoB DNAs (458 bp) were specifically amplified by PCR with the Helicobacter-specific primers (HF and HR). Based on the determined rpoB sequences of the culture isolates, an H. pylori-specific restriction site, Tru9I, was found. H. pylori can be identified by observing two discernible DNA fragments (288 and 138 bp) after Tru9I digestion and agarose gel electrophoresis. The rpoB PCR and subsequent restriction analysis (PRA) enabled the specific detection and identification of H. pylori in biopsy specimens from patients with gastroduodenal diseases. The rpoB PRA conferred a compatible or a slightly higher positive rate (53.7%) than did the Campylobacter-like organism (CLO) test (50.4%) and glmM PCR (48.8%), suggesting that it is useful for diagnosing an H. pylori infection without culture in the clinical laboratory.
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Affiliation(s)
- Chang-Young Lim
- Department of Internal Medicine, Dankook University College of Medicine, Cheonan, 330-715, Korea
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Chisholm SA, Owen RJ, Teare EL, Saverymuttu S. PCR-based diagnosis of Helicobacter pylori infection and real-time determination of clarithromycin resistance directly from human gastric biopsy samples. J Clin Microbiol 2001; 39:1217-20. [PMID: 11283030 PMCID: PMC87913 DOI: 10.1128/jcm.39.4.1217-1220.2001] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A novel PCR detection assay that amplifies the Helicobacter pylori-specific vacuolating cytotoxin gene (vacA) and thus enables rapid diagnosis of infection is described. Additionally, a real-time probe hybridization melting point analysis assay to detect all three mutations in the 23S rRNA gene associated with clarithromycin resistance was applied directly to antral gastric biopsy samples. Comparison with culture and an alternative PCR assay targeting the 16S rrn gene showed that the vacA assay was sensitive and specific when tested on biopsy samples from 121 patients. Clarithromycin susceptibilities could be determined in the majority (92.3%) of culture-positive gastric biopsy samples analyzed, four of which generated melting peaks indicative of clarithromycin resistance by either an A-->G or A-->C mutation. The presence of the mutations correlated with the clarithromycin disk diffusion sensitivities of matched cultures. This PCR-based system was simple to perform and could be completed in 3 to 4 h, thereby overcoming the delays associated with conventional culture methods for H. pylori identification and susceptibility testing.
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Affiliation(s)
- S A Chisholm
- Laboratory of Enteric Pathogens, Central Public Health Laboratory, London NW9 5HT, United Kingdom
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Thoreson AC, Borre M, Andersen LP, Jørgensen F, Kiilerich S, Scheibel J, Rath J, Krogfelt KA. Helicobacter pylori detection in human biopsies: a competitive PCR assay with internal control reveals false results. FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY 1999; 24:201-8. [PMID: 10378421 DOI: 10.1111/j.1574-695x.1999.tb01283.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A polymerase chain reaction assay (PCR) for the diagnosis of Helicobacter pylori in human gastric biopsies was developed. To prevent false-negative results while performing PCR on human tissues, an internal control is necessary. Primer set ACT1-ACT2 which specifically amplifies a 542-bp fragment of the 16S rRNA gene of H. pylori was used. dUTP and hot-start were used to prevent false-positives from carryover of previous products and avoid non-specific extension products. A competitive internal control DNA fragment was constructed to detect the presence of inhibitors. Biopsies from 101 unselected patients with gastric symptoms were tested. PCR results were compared with results from microscopy of histological sections and conventional culturing for H. pylori. Forty-two percent of the biopsies were found to contain compounds inhibiting the PCR. The addition of the internal control assures the performance of the PCR assay and is an important quality control parameter.
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Affiliation(s)
- A C Thoreson
- Department of Gastrointestinal Infections, Statens Serum Institut, Copenhagen, Denmark
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Lu JJ, Perng CL, Shyu RY, Chen CH, Lou Q, Chong SK, Lee CH. Comparison of five PCR methods for detection of Helicobacter pylori DNA in gastric tissues. J Clin Microbiol 1999; 37:772-4. [PMID: 9986850 PMCID: PMC84550 DOI: 10.1128/jcm.37.3.772-774.1999] [Citation(s) in RCA: 144] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Five different PCR methods for the detection of Helicobacter pylori were evaluated. The results of this study indicate that of the five PCR methods examined, the ureC (glmM) gene PCR is the most sensitive and specific for the detection of H. pylori in gastric biopsy specimens.
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Affiliation(s)
- J J Lu
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan.
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Song Q, Haller B, Schmid RM, Adler G, Bode G. Helicobacter pylori in dental plaque: a comparison of different PCR primer sets. Dig Dis Sci 1999; 44:479-84. [PMID: 10080137 DOI: 10.1023/a:1026680618122] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This study was designed to compare different primer sets for PCR analysis of H. pylori in the same series of 40 dental plaque samples. Three pairs of primers, HPU1/HPU2, HP1/HP2, and EHC-U/EHC-L, directed to the urease A gene, 16S rRNA gene, or 860-bp DNA of H. pylori, respectively, were used. Our results demonstrate that EHC-L/EHC-U were more specific and sensitive for H. pylori added to saliva or dental plaque than HPU1/HPU2 and HP1/HP2. The detection rates for H. pylori DNA in dental plaque samples from randomly selected adult patients from the Dental Clinic of the University of Ulm were 26.5% (9/34) for HPU1/HPU2, 78.9% (30/38) for HP1/HP2, and 100% (40/40) for EHC-U/EHC-L (P < 0.001). Nested PCR using primers directed to the 860-bp DNA of H. pylori further confirmed the presence of H. pylori DNA (40/40) in all these samples. Our results indicate that primers EHC-U/EHC-L are to be recommended for PCR detection of H. pylori in the oral cavity.
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Affiliation(s)
- Q Song
- Department of Internal Medicine I, University of Ulm, Germany
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Leung WK. Evaluation of 16S rRNA gene PCR with primers Hp1 and Hp2 for detection of Helicobacter pylori. J Clin Microbiol 1998; 36:603. [PMID: 9466789 PMCID: PMC104590 DOI: 10.1128/jcm.36.2.603-603.1998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Abstract
Helicobacter pylori is a gram-negative bacterium which causes chronic gastritis and plays important roles in peptic ulcer disease, gastric carcinoma, and gastric lymphoma. H. pylori has been found in the stomachs of humans in all parts of the world. In developing countries, 70 to 90% of the population carries H. pylori. In developed countries, the prevalence of infection is lower. There appears to be no substantial reservoir of H. pylori aside from the human stomach. Transmission can occur by iatrogenic, fecal-oral, and oral-oral routes. H. pylori is able to colonize and persist in a unique biological niche within the gastric lumen. All fresh isolates of H. pylori express significant urease activity, which appears essential to the survival and pathogenesis of the bacterium. A variety of tests to diagnose H. pylori infection are now available. Histological examination of gastric tissue, culture, rapid urease testing, DNA probes, and PCR analysis, when used to test gastric tissue, all require endoscopy. In contrast, breath tests, serology, gastric juice PCR, and urinary excretion of [15N]ammonia are noninvasive tests that do not require endoscopy. In this review, we highlight advances in the detection of the presence of the organism and methods of differentiating among types of H. pylori, and we provide a background for appropriate chemotherapy of the infection.
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Abstract
Helicobacter pylori is a gram-negative bacterium which causes chronic gastritis and plays important roles in peptic ulcer disease, gastric carcinoma, and gastric lymphoma. H. pylori has been found in the stomachs of humans in all parts of the world. In developing countries, 70 to 90% of the population carries H. pylori. In developed countries, the prevalence of infection is lower. There appears to be no substantial reservoir of H. pylori aside from the human stomach. Transmission can occur by iatrogenic, fecal-oral, and oral-oral routes. H. pylori is able to colonize and persist in a unique biological niche within the gastric lumen. All fresh isolates of H. pylori express significant urease activity, which appears essential to the survival and pathogenesis of the bacterium. A variety of tests to diagnose H. pylori infection are now available. Histological examination of gastric tissue, culture, rapid urease testing, DNA probes, and PCR analysis, when used to test gastric tissue, all require endoscopy. In contrast, breath tests, serology, gastric juice PCR, and urinary excretion of [15N]ammonia are noninvasive tests that do not require endoscopy. In this review, we highlight advances in the detection of the presence of the organism and methods of differentiating among types of H. pylori, and we provide a background for appropriate chemotherapy of the infection.
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Affiliation(s)
- B E Dunn
- Department of Pathology, Medical College of Wisconsin, Milwaukee 53226-0509, USA
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Lou Q, Chong SK, Fitzgerald JF, Siders JA, Allen SD, Lee CH. Rapid and effective method for preparation of fecal specimens for PCR assays. J Clin Microbiol 1997; 35:281-3. [PMID: 8968926 PMCID: PMC229557 DOI: 10.1128/jcm.35.1.281-283.1997] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We have developed a novel method for the preparation of fecal specimens for PCR assays. Approximately 100 mg of solid stool or 200 microliters of liquid fecal sample was thoroughly suspended in 1 ml of water. Fecal debris was removed by low-speed centrifugation (2,800 x g for 2 min). The supernatant was then boiled for 10 min in a water bath and further clarified by high-speed centrifugation (12,000 x g for 5 min). Fifty microliters of the clarified supernatant was then purified by Sepharose CL-6B spin column chromatography, and a portion of the purified supernatant was used for PCR. By this method, stools containing enterotoxigenic Escherichia coli H10407 were amplified by colonization factor antigen I fimbrial gene PCR, with a sensitivity of 100 organisms per reaction. The method was also effective for processing stool specimens for Clostridium difficile toxin A and B gene PCRs. This method is rapid, effective, and simple to perform and will improve the applications of PCR to stool specimens for diagnostic purposes.
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Affiliation(s)
- Q Lou
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis 46202, USA
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