Mechanism and clinical significance of metronidazole resistance in Helicobacter pylori

Functional insights of antibiotic resistance mechanism in Helicobacter pylori: Driven by gene interaction network and centrality-based nodes essentiality analysis

Increased antibiotic resistance in Helicobacter pylori (H. pylori), a major human pathogen, constitutes a substantial threat to human health. Understanding the pathophysiology and development of antibiotic resistance can aid our battle with the infections caused by H. pylori. The aim of this study is to discover the high-impact key regulatory mechanisms and genes involved in antimicrobial drug resistance (AMR). In this study, we constructed a functional gene interaction network by integrating multiple sources of data related to antibiotic resistant genes (number-77) from H. pylori. The gene interaction network was assortative, with a hierarchical, scale-free topology enriched in a variety of gene ontology (GO) categories and KEGG pathways. Using an iterative clustering methodology, we identified a number of communities in the AMR gene network that comprised nine genes (sodB, groEL, gyrA, recA, polA, tuf, infB, rpsJ, and gyrB) that were present at the deepest level and hence were key regulators of AMR. Further, an antibiotic-resistant gene network-based centrality analysis revealed superoxide dismutase (sodB) as a bottleneck node in the network. Our findings suggested that sodB is critically enriched in the cellular response to oxidative stress, removal of superoxide radicals, cellular oxidant detoxification processes, cellular component biogenesis, response to reactive oxygen species, urea metabolic process, nitrogen cycle metabolic process and reactive oxygen species metabolic process. We demonstrated how the sodB, which are involved in the response to reactive oxygen species, urea metabolic process, nitrogen cycle metabolic process, reactive oxygen species metabolic process, regulated by Fur gene/proteins, claim a major authority over regulation and signal propagation in the AMR.

Comparison of Culture With Antibiogram to Next-Generation Sequencing Using Bacterial Isolates and Formalin-Fixed, Paraffin-Embedded Gastric Biopsies

BACKGROUND & AIMS

The decline in Helicobacter pylori cure rates emphasizes the need for readily available methods to determine antimicrobial susceptibility. Our aim was to compare targeted next-generation sequencing (NGS) and culture-based H pylori susceptibility testing using clinical isolates and paired formalin-fixed, paraffin-embedded (FFPE) gastric biopsies.

METHODS

H pylori isolates and FFPE tissues were tested for susceptibility to amoxicillin, clarithromycin, metronidazole, levofloxacin, tetracycline, and rifabutin using agar dilution and NGS targeted to 23S rRNA, gyrA, 16S rRNA, pbp1, rpoB and rdxA. Agreement was quantified using κ statistics.

RESULTS

Paired comparisons included 170 isolates and FFPE tissue for amoxicillin, clarithromycin, metronidazole, and rifabutin and 57 isolates and FFPE tissue for levofloxacin and tetracycline. Agreement between agar dilution and NGS from culture isolates was very good for clarithromycin (κ = 0.90012), good for levofloxacin (κ = 0.78161) and fair for metronidazole (κ = 0.55880), and amoxicillin (κ = 0.21400). Only 1 isolate was resistant to tetracycline (culture) and 1 to rifabutin (NGS). Comparison of NGS from tissue blocks and agar dilution from isolates from the same stomachs demonstrated good accuracy to predict resistance for clarithromycin (94.1%), amoxicillin (95.9%), metronidazole (77%), levofloxacin (87.7%), and tetracycline (98.2%). Lack of resistance precluded comparisons for tetracycline and rifabutin.

CONCLUSIONS

Compared with agar dilution, NGS reliably determined resistance to clarithromycin, levofloxacin, rifabutin, and tetracycline from clinical isolates and formalin-fixed gastric tissue. Consistency was fair for metronidazole and amoxicillin. Culture-based testing can predict treatment outcomes with clarithromycin and levofloxacin. Studies are needed to compare the relative ability of both methods to predict treatment outcomes for other antibiotics.

Effect of Temperature on Metronidazole Resistance in Helicobacter pylori

Efficacy of Helicobacter pylori (H. pylori) eradication therapy has declined due to rapid rises in antibiotic resistance. We investigated how increased temperature affected H. pylori (NCTC 11637) growth and its sensitivity to metronidazole in vitro. We performed transcriptomic profiling using RNA-sequencing to identify differentially expressed genes (DEGs) associated with increased temperature. Transcriptional pathways involved in temperature-driven metronidazole resistance changes were analyzed through bioinformatic and literature curation approaches. We showed that H. pylori growth was inhibited at 41°C and inhibition was more apparent with prolonged incubation. Resistance to metronidazole was also reduced—minimum inhibitory concentration for metronidazole decreased from > 256 μg/ml at 37°C to 8 μg/ml at 41°C after culturing for 3 days. RNA-sequencing results, which were highly concordant within treatment conditions, revealed more than one third of genes (583/1,552) to be differentially expressed at increased temperatures with similar proportions up and down-regulated. Quantitative real-time PCR validation for 8 out of 10 DEGs tested gave consistent direction in gene expression changes. We found enrichment for redox and oxygen radical pathways, highlighting a mechanistic pathway driving temperature-related metronidazole resistance. Independent literature review of published genes associated with metronidazole resistance revealed 46 gene candidates, 21 of which showed differential expression and 7 out of 9 DEGs associated with “redox” resistance pathways. Sanger sequencing did not detect any changes in genetic sequences for known resistance genes rdxA, frxA nor fdxB. Our findings suggest that temperature increase can inhibit the growth and reduce H. pylori resistance to metronidazole. Redox pathways are possible potential drivers in metronidazole resistance change induced by temperature. Our study provides insight into potential novel approaches in treating antibiotic resistant H. pylori.

Helicobacter pylori and Its Antibiotic Heteroresistance: A Neglected Issue in Published Guidelines

"Heteroresistance" is a widely applied term that characterizes most of the multidrug-resistant microorganisms. In microbiological practice, the word "heteroresistance" indicates diverse responses to specific antibiotics by bacterial subpopulations in the same patient. These resistant subpopulations of heteroresistant strains do not respond to antibiotic therapy in vitro or in vivo. Presently, there is no standard protocol available for the treatment of infections caused by heteroresistant Helicobacter pylori in clinical settings, at least according to recent guidelines. Thus, there is a definite need to open a new discussion on how to recognize, how to screen, and how to eliminate those problematic strains in clinical and environmental samples. Since there is great interest in developing new strategies to improve the eradication rate of anti-H. pylori treatments, the presence of heteroresistant strains/clones among clinical isolates of the bacteria should be taken into account. Indeed, increased knowledge of gastroenterologists about the existence of heteroresistance phenomena is highly required. Moreover, the accurate breakpoints should be examined/determined in order to have a solid statement of heteroresistance among the H. pylori isolates. The primary definition of heteroresistance was about coexistence of both resistant and susceptible isolates at the similar gastric microniche at once, while we think that it can be happened subsequently as well. The new guidelines should include a personalized aspect in the standard protocol to select a precise, effective antibiotic therapy for infected patients and also address the problems of regional antibiotic susceptibility profiles.

Analysis of core protein clusters identifies candidate variable sites conferring metronidazole resistance in Helicobacter pylori

Background

Metronidazole is one of the first-line drugs of choice in the standard triple therapy used to eradicate Helicobacter pylori infection. Hence, the global emergence of metronidazole resistance in Hp poses a major challenge to health professionals. Inactivation of RdxA is known to be a major mechanism of conferring metronidazole resistance in H. pylori. However, metronidazole resistance can also arise in H. pylori strains expressing functional RdxA protein, suggesting that there are other mechanisms that may confer resistance to this drug.

Methods

We performed whole-genome sequencing on 121 H. pylori clinical strains, among which 73 were metronidazole-resistant. Sequence-alignment analysis of core protein clusters derived from clinical strains containing full-length RdxA was performed. Variable sites in each alignment were statistically compared between the resistant and susceptible groups to determine candidate genes along with their respective amino-acid changes that may account for the development of metronidazole resistance in H. pylori.

Results

Resistance due to RdxA truncation was identified in 34% of metronidazole-resistant strains. Analysis of core protein clusters derived from the remaining 48 metronidazole-resistant strains and 48 metronidazole-susceptible identified four variable sites significantly associated with metronidazole resistance. These sites included R16H/C in RdxA, D85N in the inner-membrane protein RclC (HP0565), V265I in a biotin carboxylase protein (HP0370) and A51V/T in a putative threonylcarbamoyl–AMP synthase (HP0918).

Conclusions

Our approach identified new potential mechanisms for metronidazole resistance in H. pylori that merit further investigation.

The Toronto Consensus for the Treatment of Helicobacter pylori Infection in Adults

BACKGROUND & AIMS

Helicobacter pylori infection is increasingly difficult to treat. The purpose of these consensus statements is to provide a review of the literature and specific, updated recommendations for eradication therapy in adults.

METHODS

A systematic literature search identified studies on H pylori treatment. The quality of evidence and strength of recommendations were rated according to the Grading of Recommendation Assessment, Development and Evaluation (GRADE) approach. Statements were developed through an online platform, finalized, and voted on by an international working group of specialists chosen by the Canadian Association of Gastroenterology.

RESULTS

Because of increasing failure of therapy, the consensus group strongly recommends that all H pylori eradication regimens now be given for 14 days. Recommended first-line strategies include concomitant nonbismuth quadruple therapy (proton pump inhibitor [PPI] + amoxicillin + metronidazole + clarithromycin [PAMC]) and traditional bismuth quadruple therapy (PPI + bismuth + metronidazole + tetracycline [PBMT]). PPI triple therapy (PPI + clarithromycin + either amoxicillin or metronidazole) is restricted to areas with known low clarithromycin resistance or high eradication success with these regimens. Recommended rescue therapies include PBMT and levofloxacin-containing therapy (PPI + amoxicillin + levofloxacin). Rifabutin regimens should be restricted to patients who have failed to respond to at least 3 prior options.

CONCLUSIONS

Optimal treatment of H pylori infection requires careful attention to local antibiotic resistance and eradication patterns. The quadruple therapies PAMC or PBMT should play a more prominent role in eradication of H pylori infection, and all treatments should be given for 14 days.

The effect of metronidazole on the cell cycle and DNA in metronidazole-susceptible and -resistant Giardia cell lines

Metronidazole (MTZ) is used as the drug of choice to treat Giardia infections. It is believed that the prodrug is transformed intracellularly into toxic intermediates that interact with cellular components, leading to cell death. The present study aimed to describe the effects of MTZ treatment on DNA and cell cycle progression in MTZ-sensitive and in vitro-derived MTZ-resistant cell lines. Detection of the phosphorylated form of histone H2A in cell nuclei together with electrophoresis of genomic DNA, flow cytometry analysis and incubation of cells with other drugs (albendazole or neomycin) demonstrated that DNA damage in MTZ-treated cells is clearly conditioned by the presence of this drug. The flow cytometry analysis and a BrdU labeling assay showed that the sublethal drug concentration affects the replication phase of the cell cycle. Cells incubated with lethal drug concentration exhibit unchanged DNA profile, only about 50% of cells are positive for γH2A and lose an ability to attach to a surface after few hours of incubation. It is likely that the early reaction of cells to lethal concentration of MTZ is not primarily initiated by the reaction to DNA damage but rather by the immediate interaction of MTZ with biomolecules where activated MTZ is generated. Interestingly, in MTZ-resistant lines incubated in the presence of the drug, about 40% of cells remain permanently positive for γH2A without any effects on the cell cycle progression suggesting that DNA damage caused by MTZ treatment persists in these cells. Accelerated mutagenesis caused by MTZ-induced DNA damage may therefore be a new factor contributing to the development of natural resistance.

Bi-functionalization of a calcium phosphate-coated titanium surface with slow-release simvastatin and metronidazole to provide antibacterial activities and pro-osteodifferentiation capabilities

Coating the surface of titanium implants or other bone graft substitute materials with calcium phosphate (Ca-P) crystals is an effective way to enhance the osteoconduction of the implants. Ca-P coating alone cannot confer pro-osteodifferentiation and antibacterial capabilities on implants; however, it can serve as a carrier for biological agents which could improve the performance of implants and bone substitutes. Here, we constructed a novel, bi-functional Ca-P coating with combined pro-osteodifferentiation and antibacterial capabilities. Different concentrations of metronidazole (MNZ) and simvastatin (SIM) were integrated into biomimetic Ca-P coatings on the surface of titanium disks. The biological effects of this bi-functional biomimetic coating on human bone marrow mesenchymal stem cells (hBMMSCs), human adipose derived stromal cells (hASCs), and Porphyromonas gingivalis were assessed in vitro. We observed that Ca-P coatings loaded with both SIM and MNZ display favorable release kinetics without affecting cell proliferation or attachment. In the inhibition zone test, we found that the bi-functional coating showed lasting antibacterial effects when incubated with Porphyromonas gingivalis for 2 and 4 days. Moreover, the osteodifferentiation of hBMMSCs and hASCs were increased when cultured on this bi-functional coating for 7 and 14 days. Both drugs were loaded onto the Ca-P coating at specific concentrations (10⁻⁵ M SIM; 10⁻² M MNZ) to achieve optimal release kinetics. Considering the safety, stability and low cost of SIM and MNZ, this novel bi-functional Ca-P coating technique represents a promising method to improve the performance of metal implants or other bone substitute materials, and can theoretically be easily translated to clinical applications.

Pyruvate:ferredoxin oxidoreductase and thioredoxin reductase are involved in 5-nitroimidazole activation while flavin metabolism is linked to 5-nitroimidazole resistance in Giardia lamblia

OBJECTIVES

The mechanism of action of, and resistance to, metronidazole in the anaerobic (or micro-aerotolerant) protozoan parasite Giardia lamblia has long been associated with the reduction of ferredoxin (Fd) by the enzyme pyruvate:ferredoxin oxidoreductase (PFOR) and the subsequent activation of metronidazole by Fd to toxic radical species. Resistance to metronidazole has been associated with down-regulation of PFOR and Fd. The aim of this study was to determine whether the PFOR/Fd couple is the only pathway involved in metronidazole activation in Giardia.

METHODS

PFOR and Fd activities were measured in extracts of highly metronidazole-resistant (MTR(r)) lines and activities of recombinant G. lamblia thioredoxin reductase (GlTrxR) and NADPH oxidase were assessed for their involvement in metronidazole activation and resistance.

RESULTS

We demonstrated that several lines of highly MTR(r) G. lamblia have fully functional PFOR and Fd indicating that PFOR/Fd-independent mechanisms are involved in metronidazole activation and resistance in these cells. Flavin-dependent GlTrxR, like TrxR of other anaerobic protozoa, reduces 5-nitroimidazole compounds including metronidazole, although expression of TrxR is not decreased in MTR(r) Giardia. However, reduction of flavins is suppressed in highly MTR(r) cells, as evidenced by as much as an 80% decrease in NADPH oxidase flavin mononucleotide reduction activity. This suppression is consistent with generalized impaired flavin metabolism in highly MTR(r) Trichomonas vaginalis.

CONCLUSIONS

These data add to the mounting evidence against the dogma that PFOR/Fd is the only couple with a low enough redox potential to reduce metronidazole in anaerobes and point to the multi-factorial nature of metronidazole resistance.

Mutational analysis of metronidazole resistance in Helicobacter pylori

Metronidazole is one of a few antibiotics effective in eliminating Helicobacter pylori infection of the human stomach. Several chromosomal loci have been implicated in resistance to this drug. Saturation transposon mutagenesis of the H. pylori genome revealed inactivation of the rdxA gene as uniquely able to confer metronidazole resistance.

Stability of metronidazole, tetracycline HCl and famotidine alone and in combination

Metronidazole, tetracycline HCl and famotidine are commonly used for the treatment of Helicobacter pylori-associated peptic ulcer. In this paper, stabilities of these drugs and their combinations in solid and liquid states were studied as part of preformulation in the development of a combination drug delivery system. Solubility studies of metronidazole and tetracycline HCl were investigated, which indicated that both metronidazole and tetracycline HCl have high solubilities at and around pH 2.0. Metronidazole is relatively stable with little degradation in liquid phase. Tetracycline HCl in the dry state is stable when stored at room temperature regardless of exposure to light or humidity in the range of 20-65%. Enhanced temperature associated humidity effect was responsible for the instabilities of tetracycline HCl and famotidine to different extents. Elevated temperature accelerated the degradation of all the drugs in liquid phase but light exposure was not a factor for the degradation. The degradation processes of tetracycline HCl and famotidine were highly dependent on the pH of the solution, and relatively stable profiles were achieved at pH 4.0. No potential incompatibility between the drugs under storage conditions was observed in the development of a new multi-drug delivery tablet.

Infection à Helicobacter pylori et résistance aux antibiotiques

PURPOSE

Seven days triple therapies combining a proton pump inhibitor (PPI) and 2 antimicrobial agents (clarithromycin [C], amoxicillin [A], metronidazole [M]), are recommended for the treatment of Helicobacter pylori infection. The eradication failures have increased these last years, particularly in France (about 30%). They are essentially related to the development of antimicrobial agents resistance, mainly concerning macrolides and nitro-imidazoles.

CURRENT KNOWLEDGE AND KEY POINTS

Primary resistance to clarithromycin is variable, but reaching now about 10% throughout the world and about 20% in France. It reduces the eradication success rate at 25%. The secondary resistance is very high, contra-indicating the use of clarithromycin in second line regimens. Primary resistance to amoxicillin has recently appeared, but remains very low until now, less than 2%, as the tetracyclin (T) resistance. Primary resistance to metronidazole is 3 times higher than macrolides resistance, but its determination is less accurate. Metronidazole resistance reduces eradication rate of about 25%, leading to the use of metronidazole in second line therapy, in increasing the triple therapy duration at 14 days (PPI-A-M), or in combination with quadruple therapy (Bismuth-PPI-T-M). Other rescue-treatments are efficacious, based on ranitidine bismuth citrate combined regimens or on rifabutine (R) based regimens (PPI-A-R).

FUTURE PROSPECTS AND PROJECTS

The recent knowledge of the mutations mainly responsible for H. pylori resistance to antimicrobial agents now allows the development of detection methods based on the study of bacterial DNA. These methods have been validated for clarithromycin and should favour in the near future the determination of resistance by the use of biopsy culture or directly on the gastric biopsy.