Evaluation of rapid molecular methods for detection of clarithromycin resistance in Helicobacter pylori

Helicobacter pylori infection and antibiotic resistance - from biology to clinical implications

Helicobacter pylori is a major human pathogen for which increasing antibiotic resistance constitutes a serious threat to human health. Molecular mechanisms underlying this resistance have been intensively studied and are discussed in this Review. Three profiles of resistance - single drug resistance, multidrug resistance and heteroresistance - seem to occur, probably with overlapping fundamental mechanisms and clinical implications. The mechanisms that have been most studied are related to mutational changes encoded chromosomally and disrupt the cellular activity of antibiotics through target-mediated mechanisms. Other biological attributes driving drug resistance in H. pylori have been less explored and this could imply more complex physiological changes (such as impaired regulation of drug uptake and/or efflux, or biofilm and coccoid formation) that remain largely elusive. Resistance-related attributes deployed by the pathogen cause treatment failures, diagnostic difficulties and ambiguity in clinical interpretation of therapeutic outcomes. Subsequent to the increasing antibiotic resistance, a substantial drop in H. pylori treatment efficacy has been noted globally. In the absence of an efficient vaccine, enhanced efforts are needed for setting new treatment strategies and for a better understanding of the emergence and spread of drug-resistant bacteria, as well as for improving diagnostic tools that can help optimize current antimicrobial regimens.

Macrolide resistance in microorganisms at antimicrobial-free Swine farms

To investigate the relationship between agricultural antimicrobial use and resistance, a variety of methods for quantification of macrolide-lincosamide-streptogramin B (MLS(B)) resistance were applied to organic swine farm manure samples. Fluorescence in situ hybridization was used to indirectly quantify the specific rRNA methylation resulting in MLS(B) resistance. Using this method, an unexpectedly high prevalence of ribosomal methylation and, hence, predicted MLS(B) resistance was observed in manure samples from two swine finisher farms that reported no antimicrobial use (37.6% +/- 6.3% and 40.5% +/- 5.4%, respectively). A culture-based method targeting relatively abundant clostridia showed a lower but still unexpectedly high prevalence of resistance at both farms (27.7% +/- 11.3% and 11.7% +/- 8.6%, respectively), while the prevalence of resistance in cultured fecal streptococci was low at both farms (4.0%). These differences in the prevalence of resistance across microorganisms suggest the need for caution when extrapolating from data obtained with indicator organisms. A third antimicrobial-free swine farm, a breeder-to-finisher operation, had low levels of MLS(B) resistance in manure samples with all methods used (<9%). Tetracycline antimicrobials were detected in manure samples from one of the finisher farms and may provide a partial explanation for the high level of MLS(B) resistance. Taken together, these findings highlight the need for a more fundamental understanding of the relationship between antimicrobial use and the prevalence of antimicrobial resistance.

Rapid screening of clarithromycin resistance in Helicobacter pylori by pyrosequencing

Helicobacter pylori infections can be effectively treated with clarithromycin, a macrolide, in combination with other antibiotics, such as amoxicillin, tetracycline or metronidazole. The failure of H. pylori eradication is mainly associated with macrolide-resistant strains. Three point mutations (A2142G/C, A2143G, T2182C) in the peptidyltransferase region of domain V of the 23S rRNA have been described as being associated with clarithromycin resistance. Therefore, the determination of clarithromycin resistance by pyrosequencing was evaluated. H. pylori from 81 gastric biopsies was cultured and clarithromycin resistance was determined by Etest, as well as by pyrosequencing technology (PSQ 96 system; Biotage). The respective mutations were set in relation to the MIC measured in μg ml−1 by Etest. In this study, point mutations in positions 2142 and 2143 were associated with clarithromycin resistance. Mutations in position 2182 did not contribute to clarithromycin resistance. In addition, from 22 out of the 81 biopsies, clarithromycin resistance was determined directly without culturing H. pylori to save additional time. Identical results were obtained as compared to resistance testing with pure H. pylori strains. All results obtained by pyrosequencing were evaluated by Sanger sequencing. The data show that pyrosequencing to detect point mutation is a fast and reliable method for determining clarithromycin resistance in H. pylori, and provides the same results as the Etest.

Basis for the management of drug-resistant Helicobacter pylori infection

The discovery that most stomach diseases are a consequence of an Helicobacter pylori infection has completely changed the management of stomach diseases. Antibacterials are the treatment of choice in addition to proton pump inhibitors (PPIs) or ranitidine bismuth. We are now faced with the problem of antimicrobial resistance, which is the main cause of treatment failure. H. pylori acquires resistance essentially via point mutations, and today this phenomenon is found with most antibacterials. The most important resistance to consider is that to clarithromycin, since it is the first-choice antibacterial and clarithromycin resistance is highly clinically significant. Quadruple therapy or triple therapies with amoxicillin-metronidazole or tetracycline-metronidazole and a PPI or ranitidine bismuth can then be used despite a possible resistance to metronidazole if the strain is resistant to clarithromycin. Resistance to both clarithromycin and metronidazole may lead to the use of other combinations, i.e. amoxicillin-rifabutin, amoxicillin-levofloxacin or amoxicillin-furazolidone. Resistance to any of these drugs means their use must be avoided. In some instances, it may also be advisable to prescribe amoxicillin as the sole antibacterial, or to use a quadruple therapy with furazolidone instead of metronidazole. Although it is theoretically possible to cure a drug-resistant H. pylori infection, a practical limitation is the availability of the drugs in certain countries. Furthermore, the progressive increase in drug resistance warrants the need for new antibacterials in the near future.

Application of 3'-mismatched reverse primer PCR compared with real-time PCR and PCR-RFLP for the rapid detection of 23S rDNA mutations associated with clarithromycin resistance in Helicobacter pylori

Helicobacter pylori clarithromycin (Cla) resistance dramatically reduces efficacy of eradication therapy. In this study, 3'-mismatched reverse primer PCR (3M-PCR), real-time PCR (LightCycler), and PCR-RFLP assays were investigated to determine their sensitivity for detecting clarithromycin resistance associated with 23S rDNA mutations (A2142G, A2142C, and A2143G). For 84.8% (123/145) of isolates, the same allelic type was detected by each method although methods differed in efficiency of detecting mutations in cultures either containing mixtures of two alleles (24 isolates), or that were dual allelic variants (two isolates). The novel 3M-PCR assay format was the most sensitive, detecting all alleles at > or =0.02 ng/microl in DNA mixtures, and thus provides more precise information to guide clinical management of patients at risk of treatment failure.

Eradication of Helicobacter pylori by 7-day triple-therapy regimens combining pantoprazole with clarithromycin, metronidazole, or amoxicillin in patients with peptic ulcer disease: results of two double-blind, randomized studies

AIM

To compare the short-term (7-day) safety and efficacy of two triple-therapy regimens using pantoprazole with those of two dual-therapy regimens (one with pantoprazole and one without), for Helicobacter pylori eradication in patients with peptic ulcer disease.

METHODS

H. pylori infection was identified by rapid urease (CLOtest), and confirmed by histology and culture. Patients were enrolled into one of two randomized, double-blind, multicenter, parallel-group studies. In study A, patients received oral pantoprazole 40 mg, clarithromycin 500 mg, and metronidazole 500 mg (PCM); pantoprazole, clarithromycin and amoxicillin 1000 mg (PCA); or pantoprazole and clarithromycin (PC). In study B, patients received PCM, PCA, PC, or clarithromycin and metronidazole without pantoprazole (CM). Treatments were given twice daily for 7 days. H. pylori status after therapy was assessed by histology and culture at 4 weeks after completing the course of study treatment. Modified intent-to-treat (MITT; each study: n = 424, n = 512) and per-protocol (PP; each study: n = 371, n = 454) populations were analyzed. The MITT population comprised all patients whose positive H. pylori status was confirmed by culture and histology; the PP population comprised patients who also complied with > or = 85% of study medication doses.

RESULTS

A total of 1016 patients were enrolled. Cure rates among patients with clarithromycin-susceptible H. pylori strains were 82 and 86% for PCM, and 72 and 71% for PCA, in studies A and B, respectively. Cure rates among patients with metronidazole-susceptible H. pylori strains were 82 and 87% for PCM, and 71 and 69% for PCA, in studies A and B, respectively. The combined eradication rates observed with the PCM regimen were superior to those of all other regimens tested. Side-effects were infrequent and mild.

CONCLUSIONS

PCM had the highest overall eradication rate in these two studies examining 7-day treatment regimens. All regimens were safe and well tolerated.

Molecular mechanism of the resistance of Helicobacter pylori to clarithromycin

AIM

To investigate the resistance mechanism of Hp to clarithromycin.

METHODS

With E-test method, we examined the minimal inhibitory concentration (MIC) to clarithromycin of 35 Hp clinical isolates. Resistance strains were defined when MIC≥8 mg/L. Extract the DNA from the bacteria with the phenol-chloroform extraction method. Then amplify the fragments from 2 047 to 2 347 of 23 S rRNA gene. Gene sequence of the PCR products was analyzed to observe the mutation in the resistant Hp strains.

RESULTS

Compared with susceptible strains, No13 strain contained one point mutation (T2289C), No17 had two point mutations (G2224A, T2289C) and No22 strain had 3 point mutations (G2224A, C2245T, T2289C).The MICs of the 3 resistant Hp isolates were as follows: No13 of 8.0 mg/L, No17 of 64 mg/L, No22 of >256 mg/L. With increase of the resistance of Hp strains, the number of point mutations increased.

CONCLUSION

The point-mutations at 23 S rRNA gene responsible for Hp resistance to clarithromycin have not been reported in literature either at home or abroad, demonstrating that different mechanism of Hp resistance to clarithromycin exists in different regions.

The use of the resonant mirror biosensor to detect point mutations, as demonstrated with synthetic oligonucleotides

The possibility of using the resonant mirror biosensor to detect point substitutions in oligonucleotides was demonstrated with a fragment of the Helicobacter pylori 23S rRNA gene, point mutations in which are responsible for clarythromycin resistance. Conditions were optimized for the interaction of a probe immobilized on the sensing surface with targets containing various nucleotide substitutions. A probe allowing reliable discrimination of mutant targets was selected. The mismatch position in the probe was shown to affect the kinetic parameters (response) of hybridization with mutant targets, reporting not only the position, but also the character (G or C) of a substitution.

Validation of diffusion methods for macrolide susceptibility testing of Helicobacter pylori

Helicobacter pylori resistance to macrolides is increasing, and the need for susceptibility testing has become crucial. The only standardized method is agar dilution, which is not adapted to clinical practice. The present work aimed: (1) to optimize the technical conditions and to assess the reproducibility of the E-test and disk diffusion method for macrolides susceptibility testing of H. pylori, and (2) to assess the performances of these two phenotypic methods in detecting strains harboring a resistance mechanism to macrolides. We used 191 isolates collected in nine centers of France and Belgium. Phenotypic tests were performed on Mueller-Hinton agar supplemented with 10% horse blood, inoculated with a 2-day-old H. pylori suspension (10(8) CFU/ml), and incubated for 72 hr at 37 degrees C under microaerophilic conditions. The reproducibility studied on two randomly selected strains was better for disk diffusion than for the E-test for both clarithromycin and erythromycin. For a subset of 10 strains, the MICs of erythromycin and clarithromycin did not differ from more than one two-fold dilution when determined by E-test or agar dilution method. The breakpoints were for MICs: 1 mg/L for both clarithromycin and erythromycin and for inhibition diameters, 22 mm for clarithromycin and 17 mm for erythromycin. There was a 100% concordance between susceptibility to erythromycin and clarithromycin. However, the susceptible and resistant populations were better separated by testing erythromycin. Of 34 resistant strains, two lacked the A2142G and A2143G point mutations in 23S rRNA by PCR-RFLP. None of 15 tested sensitive strains were positive for one of these two point mutations. For clinical practice, we recommend to assess macrolide susceptibility of H. pylori by using one of these two phenotypic methods under the described technical conditions.

Rapid and accurate determination of genotypic clarithromycin resistance in cultured Helicobacter pylori by fluorescent in situ hybridization

Phenotypic susceptibility testing for clarithromycin by E-test and disk diffusion of 109 cultured Helicobacter pylori isolates was compared with the genotypic susceptibility determination by fluorescent in situ hybridization (FISH). No discrepancies were found between these three methods. However, FISH has the advantage of providing results after 3 h.

Rapid and accurate determination of genotypic clarithromycin resistance in cultured Helicobacter pylori by fluorescent in situ hybridization

Phenotypic susceptibility testing for clarithromycin by E-test and disk diffusion of 109 cultured Helicobacter pylori isolates was compared with the genotypic susceptibility determination by fluorescent in situ hybridization (FISH). No discrepancies were found between these three methods. However, FISH has the advantage of providing results after 3 h.

Resistance of Helicobacter pylori to antibiotics and its impact on treatment options

The treatment of Helicobacter pylori infection is jeopardized by resistance to the antibiotics used, which turns out to be the main risk factor for failure. Resistance is due to point mutations. For clarithromycin only two sites in the 23S rRNA sequence are concerned and can be easily detected by molecular methods, while for metronidazole several mutations on rdxA and other genes can be responsible and so do not allow such detection. The situation for the rare cases of amoxicillin resistance is not fully determined. The impact of resistance on the clinical outcome is dramatic for clarithromycin while it only decreases the success by 20% for metronidazole.

Accurate diagnosis of Helicobacter pylori. Polymerase chain reaction tests

Although PCR has improved considerably the sensitivity of the diagnosis of H. pylori infection, many studies have not shown conclusively the full potential of PCR in clinical diagnosis. In daily clinical practice, PCR does not have to be performed to establish H. pylori infection. PCR is still classified primarily as a research technique in the Helicobacter field. PCR or similar technology will expand in the future when automation and commercialized kits are available to most laboratories. The development of a noninvasive PCR test may prove useful because it may lead ultimately to the determination of the source and route of transmission of this important pathogen.

Clarithromycin-resistance and point mutations in the 23S rRNA gene in Helicobacter pylori isolates from Japan

BACKGROUND

Resistance of Helicobacter pylori to clarithromycin is mostly due to the point mutations in the 23S rRNA. In Japan, however, the frequency of these mutations has not been fully investigated. Furthermore, no study has used gastric biopsy specimens to detect these point mutations.

METHODS

The frequency of primary clarithromycin-resistant H. pylori was examined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Eighty-two strains (42 isolated from patients with gastric cancer and 40 isolated from patients with chronic gastritis) were examined. Two biopsy specimens obtained from patients in whom eradication therapy including clarithromycin had failed were also studied.

RESULTS

Either A2143G or A2144G point mutation was detected in 90% of clarithromycin-resistant H. pylori strains. Eight out of 82 strains (9.8%) had either A2143G or A2144G point mutation. Only one out of 42 strains in patients with gastric cancer had A2143G mutation, whereas five strains had A2144G and two had A2143G mutations in 40 strains isolated from control subjects. The proportion was significantly lower in patients with early gastric cancer (P < 0.05). This PCR-RFLP was also applicable for DNA samples extracted from biopsy specimens and infection of clarithromycin-resistant H. pylori was observed.

CONCLUSION

The results suggest that the point mutation in the 23S rRNA gene is commonly seen in clarithromycin-resistant H. pylori and it contributes to the treatment failure in Japan. The PCR-RFLP system is a sensitive method by which to diagnose H. pylori infection as well as a simple method for detecting clarithromycin resistance without bacterial culture.

PCR using 3'-mismatched primers to detect A2142C mutation in 23S rRNA conferring resistance to clarithromycin in Helicobacter pylori clinical isolates

Twenty-five clarithromycin-resistant Helicobacter pylori strains (selected by agar dilution) were studied to detect A2142G and A2143G mutations in the 23S rRNA gene by a PCR-restriction fragment length polymorphism method and an A2142C mutation by PCR using a 3'-mismatched specific primer. A 700-bp amplified fragment was obtained by the mismatched PCR only in strains without an A2142G or A2143G mutation, indicating that those strains had the A2142C mutation.

Metronidazole and clarithromycin resistance amongst Helicobacter pylori isolates from a large metropolitan hospital in the United States

BACKGROUND

Metronidazole and clarithromycin-based therapies are among the most efficacious treatment regimens for H. pylori infection. Resistance to metronidazole or clarithromycin is associated with impaired therapy with these agents. We conducted a retrospective review of susceptibility data to determine the frequency of primary metronidazole and clarithromycin resistance among H. pylori isolates from a single metropolitan hospital in the United States. The database comprised 933 patients who presented at the Digestive Diseases Clinic at the Veterans Affairs Medical Center in Houston between September 1988 and January 1997 with complaints of dyspepsia, abdominal pain and peptic ulcer disease. One hundred and seventy-nine of these patients had both pharmaceutical records available for evaluation and culture and antimicrobial susceptibility data for analysis. The MICs were determined by both E-test and broth microdilution tests. The frequency of primary metronidazole resistance was 37.4% (67/179). The level of primary clarithromycin resistance was 6.1%. Dual metronidazole and clarithromycin resistance was present in approx. 3%. The high level of primary metronidazole and clarithromycin resistance in H. pylori isolates from this metropolitan hospital is such that antimicrobial susceptibility data should be available so that informed choice can be made for specific eradication therapies, especially in patients who fail treatment.

Regulation of the transcription of genes encoding different virulence factors in Helicobacter pylori by free iron

Since free iron possesses a poor solubility under physiologic conditions and thus becomes a limiting nutrient for growth, a shift from high- to low-iron environmental conditions is an important signal for bacteria to coordinate the regulation of gene expression. Here, we studied and compared the level of transcripts corresponding to the vacA (cytotoxin), ureA (urease), cagA (cytotoxin-associated antigen) and fur (ferric uptake regulator) genes of Helicobacter pylori, grown under iron-sufficient and iron-restricted conditions. A significant increase in the accumulation of vacA and fur transcripts was observed under iron-restricted conditions. This up-regulation by low levels of iron seems to be not directly regulated by Fur, and certainly requires other regulatory factors. No statistical difference was defined in the accumulation of cagA and ureA.

Mutations in 23S rRNA in Helicobacter pylori conferring resistance to erythromycin do not always confer resistance to clarithromycin

Mutations conferring resistance to erythromycin or clarithromycin in Helicobacter pylori were studied. Mutation A2142G was consistently associated with clarithromycin MIC of > 256 micrograms/ml, whereas mutants carrying A2143G had MICs ranging from < or = 0.016 to > 256 micrograms/ml, suggesting that additional factors account for the observed multiple levels of resistance to clarithromycin.

Rapid PCR detection of Helicobacter pylori-associated virulence and resistance genes directly from gastric biopsy material

We have developed a PCR-based method to detect macrolide resistance and the virulence gene cagA in Helicobacter pylori within 24 h, thereby improving the lengthy process of culture-based approaches. Total DNA was prepared directly from stomach biopsy specimens. The procedure proved to be rapid and reliable and could be utilized for diagnostic purposes.

Detection of point mutations associated with resistance of Helicobacter pylori to clarithromycin by hybridization in liquid phase

When the standard procedure for determining antibiotic susceptibility of bacteria is used, the results are delayed, especially for bacteria that grow slowly, such as Helicobacter pylori. Treatment for this bacterium may involve clarithromycin, a compound for which resistance has been associated with point mutations on the 23S rRNA gene. This resistance is currently found in organisms isolated from 0 to 15% of patients and jeopardizes the success of the treatment. We have designed a test involving amplification and colorimetric hybridization in the liquid phase to detect the mutation at the molecular level. First, four reference strains, including the wild type and three strains with the mutations A2143C, A2143G, and A2144G, were used to optimize the method. Amplification was carried out with primers previously published. The amplified products were added to probe-coated microtiter wells. A DNA enzyme immunoassay was used to detect the hybrids. The optimal conditions of the hybridization were defined for each probe. Nineteen H. pylori strains resistant to clarithromycin and 22 susceptible according to phenotypic data were submitted to restriction with BsaI and BbsI, and part of the 23S rRNA gene was sequenced in order to determine the mutation involved for the resistant strains. The new assay showed a complete correlation with the reference methods, except for one strain. Cross-hybridizations as well as application of the reaction to other bacteria did not lead to optical densities higher than the cutoff values chosen with the receiving operating characteristic curve. This method can be easily standardized and gives a result within a day. Its application directly to the biopsy specimens or infected gastric juice is planned in the future.

Co-detection of Helicobacter pylori and of its resistance to clarithromycin by PCR

Our aim was to develop a rapid molecular test based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and making it possible to detect Helicobacter pylori directly from gastric biopsy samples, and to test its susceptibility to clarithromycin. A 629-bp fragment of the 23S rRNA gene of H. pylori was amplified by PCR and the mutations responsible for clarithromycin resistance were detected with Bsa1 and Bbs1 restriction endonucleases. Thirty-five gastric samples were tested in parallel by standard microbiologic methods (culture and clarithromycin susceptibility testing with E-test strips) and by PCR-RFLP. The 10 culture-negative samples were also PCR-negative. Sixteen out of the 25 culture-positive samples (64%) were PCR-positive. RFLP analysis could be done in 12 cases and the results were in agreement with those of the E-test: susceptibility in five cases, resistance in seven (six A2144G mutations and one A2143G mutation).

Antimicrobial resistance in Helicobacter pylori: a global overview

Helicobacter pylori resistance to antimicrobial agents is of particular concern because it is a major determinant in the failure of eradication regimens. Antimicrobial drug resistance has been reported to occur for nitroimidazoles, macrolides, fluoroquinolones, rifampin and tetracyclines. Resistance to nitroimidazoles is the most common, in the range of 30-40% on the average in Europe while the overall prevalence rate of resistance to macrolides is lower, probably ranging between 2-10% in most countries. Development of secondary (acquired) resistance to nitroimidazoles and to the macrolides usually occurs as a rule (> 70-100%) in case of failed eradication therapy. Data available from several centres seems however to indicate that a significant shift towards increasing resistance to metronidazole and to the macrolides might have possibly occurred in many countries over the last years. Resistances to both metronidazole and to clarithromycin are the most significant ones because they influence the success of the treatments although this seems to be less marked and more dependent on the treatment regimens considered in the case of metronidazole resistance than in the setting of clarithromycin resistance. These differences may in part relate to methodological variations and to the inherent difficulties in assessing the susceptibility of H. pylori to metronidazole. It is possible that different resistance cut-off might also have to be considered for metronidazole depending on the treatment regimens administered. The mechanisms of resistance have been well defined for the macrolides and are beginning to be unraveled for the nitroimidazoles. In all cases, resistance of H. pylori to antimicrobial agent seems to be due to the development of single mutational events in chromosomal genes rather than to the acquisition of exogenous resistance genes. Owing to the restricted ability of microbiology laboratories with expertise in H. pylori culture and the lack of standardised methodology for susceptibility testing, H. pylori culture is not often performed routinely. It should however be considered after documented treatment failure or in patients from a geographic area or of an ethnic origin with higher likelihood of antimicrobial drug resistance. Likewise it is deemed very important to institute national and regional surveillance programs to follow the evolution of H. pylori resistance and to better adapt treatment regimens to changes in resistance patterns.