Helicobacter pylori detection in human biopsies: a competitive PCR assay with internal control reveals false results

Large-Scale Evaluation of ureC (glmM) and SSA Conventional PCR for Rapid Direct Detection of Helicobacter pylori in Gastric Biopsies as Compared to rpoB-based Quantitative Real-Time PCR

Background:

Conventional polymerase chain reaction (PCR)-based methods play a major role in the direct detection of H. pylori in clinical specimens, with time-saving as compared to culture-based methods. However, specificity and sensitivity vary among different varieties of these PCRs, which consequently could affect the accuracy of diagnosis of H. pylori infection. The study aimed to evaluate the utility of ureC (glmM) and SSA conventional PCR methods for rapid direct detection of H. pylori by comparing them with rpoB-based quantitative real-time PCR.

Methods:

A total of 402 non-repeated gastric biopsy specimens were subjected to DNA extraction followed by conventional ureC (glmM) and SSA PCR, and rpoB-based quantitative real-time PCR, which was used as the gold standard.

Results:

H. pylori was detected in 119 (29.6%), 126 (31.34%), and 187 (46.5%) of the tested specimens using ureC (glmM) PCR, SSA PCR, and real-time quantitative PCR, respectively. The specificity of the SSA PCR was higher than that of ureC (glmM) PCR (99.5% and 98.6%, respectively). The SSA PCR was more sensitive than the ureC (glmM), (66.8% and 62%, respectively). The diagnostic accuracy of SSA PCR (84.33%) was higher than that of ureC (glmM) PCR (81.59%).

Conclusion:

Overall, SSA PCR is more specific, sensitive, and diagnostically accurate than ureC (glmM) PCR, giving the SSA PCR assay superiority as a simple, rapid, and accurate diagnostic tool for direct detection of H. pylori in gastric tissue specimens.

Analysis of Helicobacter pylori Prevalence in Chittagong, Bangladesh, Based on PCR and CLO Test

The pathogenic bacterium Helicobacter pylori is a causative agent of gastric diseases in Bangladesh as well as throughout the world. This study aimed at analyzing the prevalence of H. pylori infection among dyspeptic patients in Chittagong, the second most populous city of Bangladesh, using 16S rRNA-based H. pylori-specific Polymerase Chain Reaction and Campylobacter-like organism test. We found that 67% of the population under study was positive for H. pylori infection. Gastric ulcer and duodenal ulcer disease showed statistically significant association with H. pylori infection; however, no association of H. pylori infection was observed in terms of age and gender. This study would play a crucial role in managing H. pylori-induced gastric diseases by understanding the current trend of H. pylori infection in the Chittagong region of Bangladesh.

Diagnosis of Helicobacter pylori: What should be the gold standard?

Since the discovery of Helicobacter pylori (H. pylori) in 1983, numerous detection methods for the presence of the bacterium have been developed. Each one of them has been associated with advantages and disadvantages. Noninvasive tests such as serology, ¹³C urea breath test (UBT) and stool antigen tests are usually preferred by the clinicians. Serology has its own limitation especially in endemic areas while ¹³C UBT is technically very demanding. The stool antigen detection method, although specific, is usually associated with poor sensitivity. The ¹³C UBT is believed to be specific, but with present revelation of the fact that stomach is colonized by many other urease producing bacteria makes it questionable. Histology, culture, rapid urease test and polymerase chain reaction (PCR) are the tests which are carried out on antral biopsies collected by invasive means. Histology has been proposed to be very sensitive and specific but the question is how by simply looking the morphology of the bacteria in the microscope, one can claim that the curved bacterium is exclusively H. pylori. Rapid urease test (RUT), the doctor’s test, is also challenged because the presence of other urease producing bacteria in the stomach cannot be denied. Moreover, RUT has been reported with poor sensitivity specially, when density of the bacterium is low. Isolation of H. pylori is essential to investigate its growth requirements, antibiotic susceptibility testing, studying virulence factor to develop vaccine and many more explorations. It has also got several disadvantages i.e., special condition for transporting, media, incubation and few days waiting for the colonies to appear, apart from the speed essentially needed to process the specimens. Till date, majority of the microbiological laboratories in the world are not equipped and trained to isolate such fastidious bacterium. The option left is PCR methods to detect H. pylori’s DNA in gastric mucosa, gastric juice, saliva, dental plaques and environmental specimens. There are speculations for false positivity due to detection of non-pylori Helicobacters due to genetic sharing; and false negativity due to low bacterial counts and presence of PCR inhibitors. However, specimen collection, transportation and processing do not require speed and special conditions. PCR based diagnosis may be considered as gold standard by designing primers extremely specific to H. pylori and targeting at least more than one conserved genes. Similarly specificity of PCR may be improved by use of internal Primers. Further, nested PCR will take care of false negatives by countering the effect of PCR inhibitors and low bacterial counts. Therefore, nested PCR based methods if performed properly, may be proposed as gold standard test.

Variation in number of cagA EPIYA-C phosphorylation motifs between cultured Helicobacter pylori and biopsy strain DNA

The Helicobacter pylori cagA gene encodes a cytotoxin which is activated by phosphorylation after entering the host epithelial cell. Phosphorylation occurs on specific tyrosine residues within EPIYA motifs in the variable 3'-region. Four different cagA EPIYA motifs have been defined according to the surrounding amino acid sequence; EPIYA-A, -B, -C and -D. Commonly, EPIYA-A and -B are followed by one or more EPIYA-C or -D motif. Due to observed discrepancies in cagA genotypes in cultured H. pylori and the corresponding DNA extracts it has been suggested that genotyping assays preferentially should be performed directly on DNA isolated from biopsy specimens. Gastric biopsies randomly selected from a Swedish cohort were homogenised and used for both direct DNA isolation and for H. pylori specific culturing and subsequent DNA isolation. In 123 of 153 biopsy specimens, the cagA EPIYA genotypes were in agreement with the corresponding cultured H. pylori strains. A higher proportion of mixed cagA EPIYA genotypes were found in the remaining 30 biopsy specimens. Cloning and sequencing of selected cagA EPIYA amplicons revealed variations in number of cagA EPIYA-C motifs in the mixed amplicons. The study demonstrates that culturing of H. pylori introduces a bias in the number of EPIYA-C motif. Consistent with other H. pylori virulence genotyping studies, we suggest that cagA EPIYA analysis should be performed using total DNA isolated from biopsy specimens.

PCR-based genotyping of Helicobacter pylori of Gambian children and adults directly from biopsy specimens and bacterial cultures

Background

Helicobacter pylori is an important agent of gastroduodenal disease in Africa and throughout the world. We sought to determine an optimum method for genotyping H. pylori strains from children and adults in The Gambia, West Africa.

Results

Virulence genes were amplified in 127 of 190 cases tested (121 adults and 6 children); each of 60 bacterial cultures, and 116 from DNA extracted directly from biopsies. The proportion of biopsies that were cagA+, the ratio of vacAs1/s2, and vacAm1/m2, and the proportion of mixed strain populations in individual subjects changed with age. Strains lacking virulence cagA and vacA genes and with apparently homogeneous (one predominant strain) infections were more common among infants than adults.

Conclusions

In order to detect the range of bacterial genotypes harbored by individual patients, direct PCR proved slightly superior to isolation of H. pylori by biopsy culture, but the techniques were complementary, and the combination of both culture and direct PCR produced the most complete picture. The seemingly higher virulence of strains from adult than infant infections in The Gambia merits further analysis.

Helicobacter pylori detection and antimicrobial susceptibility testing

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.

Helicobacter pylori genotypes identified in gastric biopsy specimens from Jordanian patients

BACKGROUND

The genetic diversity of Helicobacter pylori can be analyzed at two different levels: the genomic variation between strains originating from different individuals, and the variation in bacterial populations within an individual host. We reported for the first time the H. pylori genotypes in Jordanian patients with gastrointestinal diseases.

METHODS

Upper endoscopy was performed on 250 patients with symptoms of gastrointestinal diseases. Multiple gastric biopsy specimens were taken from the antrum. All the biopsies were tested by PCR for the H. pylori virulence genes vacA, cagA, and iceA, and 151 were tested by histology.

RESULTS

The biopsies positive for H. pylori by PCR were 110/250 (44%), and by histology 117/151 (77.5%), and these results were highly associated (P < 0.02). Analyses of virulence genes revealed that iceA2 (73.6%) was the predominant genotype, the vacAs2 allele was more frequently identified than the vacAs1 allele, while the cagA genotype was low (26.4%). The presence of certain genotypes might be associated with each other, but the presence of certain genotypes was not significantly associated with the age, or gender of the patient.

CONCLUSION

The results illustrate the geographic nature of the genetic diversity of H. pylori, as the identified genotypes are similar to those reported in neighboring countries. This study provides a baseline data of H. pylori genotypes identified in gastric biopsy specimens from Jordan, serving as a powerful epidemiological tool for prospective investigations to better understand the genetic diversity of this pathogen.

Development and use of an internal positive control for detection of Bordetella pertussis by PCR

An internal control of amplification was constructed by recombinant PCR to detect PCR inhibitors. This exogenous DNA was included in the reaction mixture and coamplified with the target gene. This detection was successfully applied to the diagnosis of whooping cough by amplification of a fragment of Bordetella pertussis IS481.

Molecular-phylogenetic analyses of human gastrointestinal microbiota

Molecular-phylogenetic methods have revolutionized the analysis of complex microbial communities. Polymerase chain reaction amplification and phylogenetic analysis of small-subunit ribosomal RNA gene sequences allow microbes to be identified objectively, even in the absence of cultivation. Furthermore, the sequence information obtained by these means can be used to design sequence-based tools for identifying, tracking, and diagnosing the presence of microbes in complex samples. In this article, we summarize this approach and review its application to the study of the human gastrointestinal microbiota. Although just beginning, molecular-phylogenetic surveys of human gut microbes have revealed that most microbes identified in the gastrointestinal tract represent novel, previously undescribed species. A full description of the microbial constituents of the human gut will set the groundwork for interpreting how the gastrointestinal microbiota influence the health of the host.

Detection of herpes simplex virus and varicella-zoster virus in clinical swabs: frequent inhibition of PCR as determined by internal controls

BACKGROUND

PCR-based detection of microorganisms is widely used for diagnostic purposes. Most routine PCR applications do not control for inhibition of PCR, thus leading to false-negative results.

METHODS AND RESULTS

One hundred eighteen swab samples obtained from skin and mucosa were investigated for the presence of herpes simplex virus (HSV), varicella-zoster virus (VZV), and the control gene betaglobin by internally controlled PCR with purified and unpurified DNA in parallel. With unpurified DNA, inhibition of PCR was detected in 23% of betaglobin PCRs, 25% of VZV PCRs, and 16% of HSV PCRs versus 3% each for purified DNA. Approximately 20% of the samples with positive results for HSV or VZV had negative or inhibited results using unpurified DNA.

CONCLUSION

These results indicate that PCR from clinical swab specimens should be performed exclusively with internal controls because the positive control alone cannot exclude PCR inhibition in individual samples. Purification of DNA will decrease, but not exclude, PCR inhibition.

Enhanced Polymerase Chain Reaction Methods for Detecting and Quantifying Phytophthora infestans in Plants

ABSTRACT Sensitive and specific primer sets for polymerase chain reaction (PCR) for Phytophthora infestans, the oomycete that causes late blight of potato and tomato, were developed based on families of highly repeated DNA. The performance of these primers was compared to those developed previously for the internal transcribed spacer (ITS) of ribosomal DNA. The detection limit using the new primers is 10 fg of P. infestans DNA, or 0.02 nuclei. This is about 100 times more sensitive than ITS-directed primers. Nested polymerase chain reaction (PCR) allows the measurement of down to 0.1 fg of DNA using the new primers. To enhance the reliability of diagnostic assays, an internal positive control was developed using an amplification mimic. The mimic also served as a competitor for quantitative PCR, which was used to assess the growth of P. infestans in resistant and susceptible tomato. A key dimension of this study was that two laboratories independently checked the specificity and sensitivity of each primer set; differences were noted that should be considered when PCR is adopted for diagnostic applications in any system.