Diagnosis of Helicobacter pylori infection and determination of clarithromycin resistance by fluorescence in situ hybridization from formalin-fixed, paraffin-embedded gastric biopsy specimens

Antibiotic Resistance of Helicobacter pylori in Turkey: A Systematic Review and Meta-Analysis

Turkey presents both a high prevalence of Helicobacter pylori infection and high prevalence of antibiotic resistance. In this study, we aimed to summarize recent data on H. pylori antibiotic resistance rates in this nation. After conducting searches in two national and international databases (ULAKBIM, EKUAL, and PubMed), a systematic review was conducted. A total of 197 original articles on antibiotic resistance of H. pylori in Turkey were collected. After screening for inclusion and exclusion criteria, to evaluate the H. pylori antibiotic resistance for the period 2005-2020, 20 eligible articles were included in the meta-analysis. Data analysis was performed using MedCalc 12.7.0. The number of isolated H. pylori strains in each study was weighted, and pooled proportion analysis was performed. This review included 20 Turkish studies, including 1,556 H. pylori strains. The overall resistance rates were as follows: clarithromycin (CLA), 26.7% (95% confidence interval [CI]: 20.5-33.5); metronidazole (MTZ), 28.4% (95% CI: 19.7-38.1); levofloxacin (LVX), 19.6% (95% CI: 9.9-31.7); tetracycline (TET), 0.7% (95% CI: 0.1-1.8); and amoxicillin (AMO), 1.3% (95% CI: 0.3-3.1). The reported results showed that Turkish H. pylori isolates are highly resistant to CLA, MTZ, and LVX, while exhibiting a low level of resistance toward AMO and TET.

Detection of Helicobacter pylori with clarithromycin resistance-associated mutations using peptide nucleic acid probe-based melting point analysis

BACKGROUND

Detection of Helicobacter pylori in gastric biopsy is important for appropriate treatment and prevention of gastric carcinoma and lymphoma. A novel peptide nucleic acid probe (PNA)-based real-time polymerase chain reaction (PCR) method was developed for detection of H pylori and A2142G/A2143G mutation of the 23S rRNA gene, which is associated with clarithromycin resistance.

METHODS

To evaluate the performance of the PNA probe-based PCR method, a total of 409 gastric biopsy samples were analyzed by PNA probe-based PCR and compared with other H pylori detection methods, including hematoxylin and eosin (HE) and Warthin-Starry (WS) staining, immunohistochemistry (IHC). A2142G/A2143G mutation of the 23S rRNA gene was tested by dual priming oligonucleotide (DPO)-based PCR and Sanger sequencing to evaluate PNA probe-based PCR.

RESULTS

Among 271 cases that were positive for H pylori on IHC which was considered as a standard method, 264 cases (97.4%) and 259 cases (95.6%) were positively detected by HE/WS and PNA probe-based qPCR, respectively. Of 100 H pylori-positive patients tested by IHC, H pylori was detected in 93 cases (93.0%) by PNA probe-based PCR, 86 cases (86.0%) by DPO-based PCR, and 93 cases (93.0%) by conventional PCR. The sensitivity, specificity, accuracy, positive predictive value, and negative predictive value of PNA probe-based qPCR were 93.0%, 94.9%, 93.9%, 94.9%, and 93.0%, respectively, which were all higher than those of DPO-based PCR. When Sanger sequencing was determined as a standard method to detect A2142G/A2143G mutations, the sensitivity of the PNA- and DPO-based methods was 100% and 94.4%, respectively, and the specificity was 100% for both methods.

CONCLUSION

PNA probe-based qPCR is an appropriate method for detecting H pylori and the clarithromycin resistance-associated mutation type.

Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory: a review

Early identification of microbial pathogens is essential for rational and conservative antibiotic use especially in the case of known regional resistance patterns. Here, we describe fluorescence in situ hybridization (FISH) as one of the rapid methods for easy identification of microbial pathogens, and its advantages and disadvantages for the diagnosis of pathogens in human infections in the laboratory diagnostic routine. Binding of short fluorescence-labeled DNA or nucleic acid-mimicking PNA probes to ribosomes of infectious agents with consecutive analysis by fluorescence microscopy allows identification of bacterial and eukaryotic pathogens at genus or species level. FISH analysis leads to immediate differentiation of infectious agents without delay due to the need for microbial culture. As a microscopic technique, FISH has the unique potential to provide information about spatial resolution, morphology and identification of key pathogens in mixed species samples. On-going automation and commercialization of the FISH procedure has led to significant shortening of the time-to-result and increased test reliability. FISH is a useful tool for the rapid initial identification of microbial pathogens, even from primary materials. Among the rapidly developing alternative techniques, FISH serves as a bridging technology between microscopy, microbial culture, biochemical identification and molecular diagnostic procedures.

Prevalence of Primary Antimicrobial Resistance of H. pylori in Turkey: A Systematic Review

BACKGROUND

The prevalence of clarithromycin resistance has increased to the 20% or more in different regions of the world. Clarithromycin resistance is known to be responsible for most of the treatment failures in Helicobacter pylori (H. pylori) infection. The aim of this systematic review was to summarize the prevalence of primary antibiotic resistance (amoxicillin, clarithromycin, metronidazole, levofloxacin, tetracycline) of H. pylori strains in different geographical regions of Turkey.

MATERIAL AND METHODS

An Internet search was performed using PubMed and the ULAKBIM Turkish Medical Database. The terms "primary antibiotic resistance (separately; amoxicillin, clarithromycin, metronidazole, levofloxacin, tetracycline) of H. pylori" with and without "Turkey" or "different geographical regions of Turkey" were searched among articles published in both English and Turkish language within the time span from 1999 to 2015. Data analysis was performed using MedCalc 12.7.0. Each article was weighted according to the number of isolated H. pylori strains. Pooled proportion analysis was performed.

RESULTS

Twenty-one Turkish studies including 1059 H. pylori strains were included in this review. The overall primary antibiotic resistance rates of H. pylori strains isolated in Turkey were as follows: amoxicillin 3 (0.971%), clarithromycin 425 (24.864%), metronidazole 75 (33.747%), tetracycline 2 (3.511%), and levofloxacin 31 (23.769%).

CONCLUSIONS

Primary antibiotic resistance against H. pylori in Turkey shows differences between geographical regions and population densities. There is an increase in primary resistance rates to clarithromycin and metronidazole in different years. The data are not sufficient for tetracycline, amoxicillin, and levofloxacin. High clarithromycin resistance rates were mostly detected in overpopulated cities like Ankara (north), Izmir (west), Istanbul (west), and Bursa (west).

Mechanisms of Helicobacter pylori antibiotic resistance and molecular testing

Antibiotic resistance in Helicobacter pylori (H.pylori) is the main factor affecting the efficacy of current treatment methods against infection caused by this organism. The traditional culture methods for testing bacterial susceptibility to antibiotics are expensive and require 10–14 days. Since resistance to clarithromycin, fluoroquinolone, and tetracycline seems to be exclusively caused by specific mutations in a small region of the responsible gene, molecular methods offer an attractive alternative to the above-mentioned techniques. The technique of polymerase chain reaction (PCR) is an accurate and rapid method for the detection of mutations that confer antibiotic resistance. This review highlights the mechanisms of antibiotic resistance in H. pylori and the molecular methods for antibiotic susceptibility testing.

Virulence factors and antibiotic resistance in children with Helicobacter pylori gastritis

OBJECTIVES

There are limited data regarding the pattern of Helicobacter pylori (Hp) antibiotic resistance and virulence factors in children. Evaluation of prevalence of drug resistance and virulence-factor genotype in children with Hp gastritis and to investigate whether there is any relation between drug resistance and genotype were our aims in this study.

METHODS

Ninety-eight children with polymerase chain reaction-positive Hp gastritis were included. Antimicrobial susceptibility was tested by disc diffusion method and polymerase chain reaction assays were used for the determination of virulence factors.

RESULTS

The resistance rates to clarithromycin, metronidazole, and amoxicillin were 23.5%, 11.7%, and 3.9%, respectively. All strains carried vacA genotype, and 51%, 70.4%, 49%, 34.7%, and 25.5% were cagA-, cagE-, babA2-, iceA1-, and iceA2-positive, respectively. Of those 98 specimens, 81.6%, 19.4%, 38.8%, and 63.3% carried vacAs1, vacAs2, vacAm1, and vacAm2, respectively. Dominant vacA type was s1am2 (32.7%), followed by s1am1 (14.3%) and s2m2 (12.2%). Significant rates of clarithromycin resistance were observed in cagE-, iceA1-, babA2-, and vacAs1c-positive groups. In those with metronidazole resistance, vacAs1 and vacAs1c were more common (P < 0.05).

CONCLUSIONS

The cagE-positive and vacA s1a/m2 genotypes, which are correlated with increased antibiotic resistance, were predominant in our population. In countries where Hp infection is prevalent, studies focusing on virulence factors and antibiotic susceptibility may provide anticipation of the prognosis and may be helpful to reduce morbidity and mortality.

Five methods for detection of Helicobacter pylori in the Turkish population

AIM: To compare culture analysis, Helicobacter pylori (H. pylori) stool antigen (HpSA) test, polymerase chain reaction (PCR) and fluorescence in situ hybridization (FISH) for H. pylori detection.

METHODS: One hundred and thirty-two consecutive adult dyspeptic patients receiving diagnostic endoscopy at the department of gastroenterology were enrolled in this study. Culture and histological examination were performed on biopsy specimens. PCR and FISH tests were applied to histopathological samples. Stool samples that were simultaneously collected were tested for the H. pylori antigen using the HpSA test and bacterial DNA using stool PCR.

RESULTS: H. pylori was positively identified by histological examination in 85/132 (64.4%) of the patients, while positive samples were found in 56 (42.4%), 64 (48.5%), 98 (74.2%), 28 (21.2%) and 81 (61.4%) of the patients by culture, HpSA, PCR, stool PCR and FISH methods, respectively. The results of the culture, biopsy PCR, HpSA and FISH tests, with the exception of the stool PCR, were found to correlate with the histological examination as a gold standard.

CONCLUSION: The HpSA test is a rapid, simple, and noninvasive test for monitoring therapy. FISH is an accurate, rapid, cost-effective, and easy-to-use test for H. pylori detection.

Molecular diagnostic techniques

Clinical microbiology laboratories increasingly rely on molecular diagnostic techniques. The various formats of nucleic acid amplification are the most frequently used molecular tests in the diagnosis of infectious diseases. In many clinical settings, polymerase chain reaction (PCR) is clearly the method of choice due to its exquisite sensitivity and specificity. Today, many conventional PCR methods are being replaced by real-time PCR, which allows more rapid detection and quantification of the PCR product, as well as detection of different strains of the pathogen by melting curve analysis. The ability to measure the quantity of microbe by quantitative PCR has become increasingly important, providing information on the progression and prognosis of disease, and effectiveness of treatment. Other widely used molecular diagnostic techniques are isothermal amplification methods and nucleic acid hybridization techniques. Microarray is a technique which holds promise and has an exceptional sensitivity and the capacity to detect several pathogens simultaneously. However, microarrays are currently too expensive to be adapted for routine diagnostics, and their diagnostic use requires broad-based nucleic acid amplification prior to analysis which is not well established. Several molecular methods can be used for genotyping, which allows the identification of different subtypes of the pathogen; genotyping plays a role in the risk assessment and management of infections. Clinicians need to recognize the enhanced accuracy and speed of the molecular diagnostic techniques for the diagnosis of infections, but also to understand their limitations. Laboratory results should always be interpreted in the context of the clinical presentation of the patient, and appropriate site, quality, and timing of specimen collection are required for reliable test results.

Fluorescence in situ hybridization confirms clearance of visible Helicobacter spp. associated with gastritis in dogs and cats

BACKGROUND

The results of studies examining the role of Helicobacter spp. in the pathogenesis of canine and feline gastritis are inconclusive. Furthermore, data evaluating the effectiveness of medical therapy for eradication of Helicobacter infection are limited.

AIM

To detect Helicobacter spp. in mucosal biopsies of dogs and cats diagnosed with gastritis, with fluorescence in situ hybridization (FISH).

ANIMALS

Three dogs and 2 cats with signs of chronic gastrointestinal disease.

METHODS

Dogs and cats infected with Helicobacter spp. were treated with triple antimicrobial therapy and fed an elimination diet for 21 days. Helicobacter spp. status in endoscopic (3 dogs, 1 cat) or surgical biopsies (1 cat) of gastric mucosa was compared pre- and posttreatment in each animal by histology, FISH analysis, and polymerase chain reaction (PCR).

RESULTS

Gastritis of varying severity with intraglandular spiral bacteria was observed in all animals. Pretreatment diagnostic tests confirmed the presence of mucosal Helicobacter spp. in all animals by FISH and histopathology and in 4/5 animals by PCR. Rapid resolution of vomiting episodes was observed in all animals. Gastric biopsies performed after triple therapy revealed clearance of visible Helicobacter spp. by histopathology and negative FISH analysis, as well as PCR in all animals.

CONCLUSIONS AND CLINICAL IMPORTANCE

Application of FISH to routine biopsy specimens enabled rapid and specific identification of Helicobacter spp. within the gastric mucosa of dogs and cats. Although medical therapy was useful in resolution of clinical signs and clearance of visible Helicobacter spp. in gastric biopsies, gastric inflammation persisted.

Detection of the drug-resistant gene of Helicobacter pylori

Antibiotic-resistant Helicobacter pylori (H. pylori) and the resistance rate are increased due to the wide use of antibiotics. At present, the detection of antibiotic-resistant H. pylori is focused on the clarithromycin and metronidazole resistance testing using PCR-based molecular biology techniques. However, PCR-restriction fragment length polymorphism and real-time PCR in combination with melting curve analysis techniques have a broad prospect in detecting drug-resistant clarithromycin. They can detect it from tissue biopsy and stool samples, and thus can be used in detecting the resistance of a wide range of antibiotics. Western blot and PCR- restriction fragment length polymorphism can also detect the resistance of metronidazole, and can therefore develop into the routine procedures for detecting drug-resistant H. pylori.

Application of polymerase chain reaction-based assays for rapid identification and antibiotic resistance screening of Helicobacter pylori in gastric biopsies

The benefits of using a multiplex detection polymerase chain reaction (PCR) assay for Helicobacter pylori speciation and 2 real-time probe hybridization assays determining clarithromycin and tetracycline susceptibilities in gastric biopsies from 171 dyspeptic patients were investigated. Overall, 70 of 71 H. pylori culture-positive biopsies were PCR positive. For the 100 culture-negative biopsies, PCR identified a further 29 H. pylori positives (17% overall) and presence of resistance markers for clarithromycin (20/28) and tetracycline (2/28). The results demonstrated that PCR testing was valuable in providing improved detection rates and antibiotic susceptibility information when H. pylori culture was unsuccessful.

Progress in developing accurate tests for the diagnosis of Helicobacter pylori infection

Helicobacter pylori is a chronic infectious agent as defined the major pathogen causing gastritis, gastric and duodenal ulcer, gastric carcinoma and mucosa-associated lymphoid tissue lymphoma, however little is known about its role in functional dyspepsia. H. pylori is the only microorganism known to inhabit the human stomach and the gastric mucosal cells. Chronic H. pylori infection of the stomach is increasingly recognized as a major risk factor for the development of gastroduodenal disease. H. pylori can be detected by non-invasive and invasive methods, the latter requiring endoscopy.

Detection of clarithromycin-resistant Helicobacter pylori in frozen gastric biopsies from pediatric patients by a commercially available fluorescent in situ hybridization

Clarithromycin resistance is an important factor of eradication failure. A commercially available fluorescent in situ hybridization (FISH) kit (creaFAST) was used to detect H. pylori infection and the resistance to clarithromycin in frozen biopsies. A total of 33 biopsies, H. pylori culture-positive, obtained from pediatric patients were retrospectively studied. Clarithromycin resistance was compared with MICs detected by E-test from H. pylori clinical isolates. All culture-positive biopsies were positive by FISH. Detection of clarithromycin resistance showed sensitivity of 90%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 86.7% compared with results obtained by E-test. Discrepant results were 2 biopsies, clarithromycin-susceptible by FISH but intermediate by E-test. In conclusion, FISH technology is a rapid, easy-to-implement, and reliable cultivation-independent method for routine application; however, when frozen biopsies are studied, some modification of the recommended procedure should be used to obtain better results.

Development and application of a novel peptide nucleic acid probe for the specific detection of Helicobacter pylori in gastric biopsy specimens

In this work, a fluorescence in situ hybridization (FISH) method for the rapid detection of Helicobacter pylori using a novel peptide nucleic acid (PNA) probe is reported. Laboratory testing with several different bacterial species, including other Helicobacter spp., has shown that this probe is highly specific for H. pylori strains. In addition, the PNA FISH method has been successfully adapted for detection of the pathogen in paraffin-embedded gastric biopsy specimens.

Diagnosis of Helicobacter pylori: invasive and non-invasive tests

Helicobacter pylori infection can be diagnosed by invasive techniques requiring endoscopy and biopsy (e.g. histological examination, culture and rapid urease test) and by non-invasive techniques, such as serology, the urea breath test, urine/blood or detection of H. pylori antigen in stool specimen. Some non-invasive tests, such as the urea breath test and the stool antigen test, detect active infection: these are called 'active tests'. Non-invasive tests (e.g. serology, urine, near-patient tests) are markers of exposure to H. pylori but do not indicate if active infection is ongoing; these are 'passive tests'. Non-invasive test-and-treat strategies are widely recommended in the primary care setting. The choice of appropriate test depends on the pre-test probability of infection, the characteristics of the test being used and its cost-effectiveness.

Detection of Helicobacter pylori and determination of clarithromycin susceptibility using formalin-fixed, paraffin-embedded gastric biopsy specimens by fluorescence in situ hybridization

BACKGROUND

Clarithromycin resistance and poor compliance to therapy are often responsible for Helicobacter pylori eradication therapy failure.

AIM

To evaluate fluorescence in situ hybridization (FISH) as a nonculture method to simultaneously detect H. pylori and to identify clarithromycin resistance.

METHODS

Fifty-four patients with dyspepsia (17 male, 37 female subjects; mean age, 46.5; range, 21-78 years) were studied. Two antrum and corpus biopsies were taken from each patient. Positive rapid urease test (RUT) and histopathologic examinations defined H. pylori positivity. A total of 108 formalin-fixed paraffin-embedded gastric mucosal biopsies were examined retrospectively by the FISH (seaFAST H. pylori Combi-Kit) method.

RESULTS

Forty-five patients (83.3%) were H. pylori positive and 43 (95.5%) were also positive by FISH. There were two false-positive FISH results. Fourteen patients (31.1%) had clarithromycin-susceptible strains, 4 (8.9%) resistant strains, and 27 (60%) both susceptible and resistant strains.

CONCLUSION

FISH results correlated well with H. pylori infection and were able to identify clarithromycin-susceptible and -resistant strains. This technique will be helpful in determining the bacterial density and the success of treatment where clarithromycin has been widely used in populations to increase the efficacy of the treatment and to clarify the treatment failure in vitro.

Diagnosis of Helicobacter pylori infection

A growing interest in non-invasive tests for the detection of Helicobacter pylori has been observed recently, reflecting a large number of studies published this year. New tests have been validated, and the old ones have been used in different clinical situations or for different purposes. Stool antigen tests have been extensively evaluated in pre- and post-treatment settings both in adults and children, and the urea breath test has been studied as a predictor of bacterial load, severity of gastric inflammation, and response to eradication treatment. Several studies have also explored the usefulness of some serologic markers as indicators of the gastric mucosa status. With regard to invasive tests, molecular methods are being used more and more, but the breakthrough this year was the direct in vivo observation of H. pylori during endoscopy.

Liquid chromatographic-electrospray tandem mass spectrometric determination of clarithromycin in human plasma

A rapid, sensitive and specific LC-MS-MS method has been developed for the determination of clarithromycin (CLA) in human plasma using roxithromycin (ROX) as the internal standard. Samples were prepared via liquid-liquid extraction with methyl tert-butyl ether (MTBE) and chromatographed on a Supelco RP(18) (4.6 x 50 mm, 3 microm particle size) column with a mobile phase consisting of acetonitrile:methanol:60 mM (pH 3.5) ammonium acetate buffer (32.5:32.5:35) at a constant flow rate of 0.8 mL/min. The run time was 3 min with retention times of approximately 1.65 and 1.70 min for CLA and ROX, respectively. Detection was performed on a PE Sciex API 365 mass spectrometer equipped with a turboionspray ionization source in multiple reaction monitoring (MRM) mode. The MRM pairs were m/z 748.5 --> m/z 158.2 for CLA and m/z 837.7 --> m/z 679.3 for ROX, respectively, with dwell times of 200 ms for each transition. The validated calibration curve range was 5.00-5000 ng/mL, based on 0.100 mL plasma sample volume with signal-to-noise ratio (S/N) greater than 60 for CLA at the lower limit of quantification level (5.00 ng/mL). The correlation coefficients (r(2)) of the calibration curves were better than or equal to 0.996. The inter-day (n = 18) precision and accuracy of the quality control (QC) samples were less than 3.58% RSD (relative standard deviation) and -10.8% bias, respectively. The intra-day (n = 6) precision and accuracy of the quality control samples were less than 5.0 and 12.6%, respectively. There was no significant deviation from the nominal values after a 10-fold dilution of high concentration QC samples using blank matrix. The QC samples were stable when left on the bench for 24 h or after three freeze-thaw cycles. The processed samples were also stable in HPLC autosampler at 10C for over 72 h. No matrix ionization suppression was observed when extracted blank matrix or reconstitution solvent was injected onto the system with post-column infusion of clarithromycin and roxithromycin. No carryover was observed when an extracted blank plasma sample was injected immediately after a 5000 ng/mL ULOQ (the upper limit of quantification) standard. The mean recovery was 81.5 and 78.3%, respectively, for clarithromycin and internal standard.