Genotypic determination of resistance and heteroresistance to clarithromycin in Helicobacter pylori isolates from antrum and corpus of Colombian symptomatic patients.

BACKGROUND: The effectiveness of Helicobacter pylori first-line treatment has decreased drastically with the rise of strains resistant to clarithromycin. Therapy failure has also been described in patients with infections by strains with dissimilar antimicrobial susceptibilities. The present study aims to estimate the prevalence of resistance and heteroresistance to clarithromycin in H. pylori isolates from antrum and corpus of Colombian patients. METHODS: The study material included 126 isolates from antrum and corpus biopsies from 63 symptomatic patients over 18 years old who had a gastric endoscopy performed on them between June 2014 to August 2016. PCR amplification and sequencing of the H. pylori 23S rDNA gene was performed to determine the presence of mutations associated with clarithromycin resistance. Random amplified polymorphic DNA analysis was implemented in cases of resistance and heteroresistance. RESULTS: The overall frequency of resistance to clarithromycin was 38.1% (24/63 patients), of which 19 patients had resistant isolates in both stomach segments (14 with A2143G mutation and 5 with A2142G mutation), and 5 patients had a heteroresistant status. The remaining 61.9% (39/63 patients) presented only susceptible isolates. DNA fingerprinting analysis showed different patterns in 4/22 paired isolates. CONCLUSIONS: The high prevalence of H. pylori clarithromycin-resistance obtained (> 15%) constitutes an alert for gastroenterologists and suggests the need for reconsideration of the current eradication regimen for H. pylori in the studied population. The data show that heteroresistance status is an additional factor to be considered in the assessment of resistance. In consequence, it is advisable to examine at least two biopsies from different gastric segments.

Tryptophan usage by Helicobacter pylori differs among strains.

Because of its association with severe gastric pathologies, including gastric cancer, Helicobacter pylori has been subject of research for more than 30 years. Its capacity to adapt and survive in the human stomach can be attributed to its genetic flexibility. Its natural competence and its capacity to turn genes on and off allows H. pylori to adapt rapidly to the changing conditions of its host. Because of its genetic variability, it is difficult to establish the uniqueness of each strain obtained from a human host. The methods considered to-date to deliver the best result for differentiation of strains are Rapid Amplification of Polymorphic DNA (RAPD), Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) analysis. While RAPD analysis is cost-effective, it requires a stable genome for its reliability. MLST and WGS are optimal for strain identification, however, they require analysis of data at the bioinformatics level. Using the StainFree method, which modifies tryptophan residues on proteins using 2, 2, 2, - trichloroethanol (TCE), we observed a strain specific pattern of tryptophan in 1D acrylamide gels. In order to establish the effectiveness of tryptophan fingerprinting for strain identification, we compared the graphic analysis of tryptophan-labelled bands in the gel images with MLST results. Based on this, we find that tryptophan banding patterns can be used as an alternative method for the differentiation of H. pylori strains. Furthermore, investigating the origin for these differences, we found that H. pylori strains alters the number and/or position of tryptophan present in several proteins at the genetic code level, with most exchanges taking place in membrane- and cation-binding proteins, which could be part of a novel response of H. pylori to host adaptation.

Helicobacter pylori culture as a key tool for diagnosis in Colombia.

INTRODUCTION: The presence of H. pylori in the stomach is associated with gastric pathologies. However, its diagnosis through culture methods is challenging because of its complex nutritional requirements and microaerophilic conditions for optimal growth. The preferred method for rapid diagnosis of H. pylori is the Rapid Urease Test (RUT) from human biopsies, which relies on the high activity of the urease enzyme present in H. pylori. However, RUT cannot say much more information about H. pylori. This makes evident the need for bacterial culture to know essential information such as the strain type, the kind of infection present and the bacteria's antibiotic susceptibility. METHODOLOGY: Gastric biopsies from 347 patients were used for H. pylori isolation. We correlated the culture results with the RUT and histological grading used at Hospital Universitario Fundación SantaFe de Bogotá (HU-FSFB), Colombia. The concordance between techniques was determined by the Cohen's Kappa coefficient (K). The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were also calculated. RESULTS: The culture standardization was successful, and it could be applied for diagnosis in the clinical practice. H. pylori was positive by culture in 88 (26.34%) patients. The concordance of RUT and culture was strong (K= 0.805), and between histology and culture was moderate (K= 0.763) as well as for the gold standard defined and culture (K= 0.80). CONCLUSIONS: We present evidence that RUT and histological methods will be better interpreted for diagnosis of H. pylori if combined with bacterial isolation in cholesterol enriched culture.

Intramolecular energies of the cytotoxic protein CagA of Helicobacter pylori as a possible descriptor of strains' pathogenicity level.

The Helicobacter pylori cytotoxin-associated gene A (CagA) is known for causing gastroduodenal diseases, such as atrophic gastritis and peptic ulcerations. Furthermore Helicobacter pylori CagA positive strains has been reported as one of the main risk factors for gastric cancer (Parsonnet et al., 1997). Structural variations in the CagA structure can alter its affinity with the host proteins, inducing differences in the pathogenicity of H. pylori. CagA N-terminal region is characterized for be conserved among all H. pylori strains since the C-terminal region is characterized by an intrinsically disorder behavior. We generated complete structural models of CagA using different conformations of the C-terminal region for two H. pylori strains. These models contain the same EPIYA (ABC1C2) motifs but different level of pathogenicity: gastric cancer and duodenal ulcer. Using these structural models we evaluated the pathogenicity level of the H. pylori strain, based on the affinity of the interaction with SHP-2 and Grb2 receptors and on the number of interactions with the EPIYA motif. We found that the main differences in the interaction was due to the contributions of certain types of energies from each strain and not from the total energy of the molecule. Specifically, the electrostatic energy, helix dipole energy, Wander Waals clashes, torsional clash, backbone clash and cis bond energy allowed a separation between severe and mild pathology for the interaction of only CagA with SHP2.

Genotipificación de cagA y de la región intermedia de vacA en cepas de Helicobacter pylori aisladas de pacientes adultos colombianos y su asociación con enfermedades gástricas / Genotyping of cagA and the intermediate region of vacA in strains of Helicobacter pylori isolated from Colombian adult patients and associations with gastric diseases

Resumen Objetivo: este estudio caracteriza la diversidad de los genes de virulencia cagA (gen asociado con la citotoxina A) y vacA (citotoxina vacuolizante) en pacientes colombianos para determinar posibles asociaciones entre estos 2 genes y la severidad de los hallazgos endoscópicos teniendo en cuenta todos los genotipos reportados para el gen vacA (s, m e i). Materiales y métodos: Helicobacter pylori fue detectado por cultivo y por métodos moleculares en biopsias de 62 pacientes. Los genotipos de cagA y vacA (m/i/s) se determinaron por reacción en cadena de la polimerasa (PCR) y secuenciación. Resultados: se aislaron 124 cepas de 62 pacientes; de estas, el 48,5% (n = 48) fueron vacA s2/m2/i2-cagA (-) presente en su mayoría en pacientes con gastritis folicular; mientras el 32,3% (n = 32) fueron vacA s1/m1/i1-cagA (+) presentes mayormente en pacientes con gastritis folicular, gastritis crónica y posible metaplasia. Se encontró una asociación significativa entre la presencia de cagA y el genotipo vacA s1/m1/i1 y la ausencia de cagA y el genotipo vacA s2/m2/i2 (p <0,001). No se encontró una asociación significativa entre la severidad de los hallazgos endoscópicos y el estatus cagA-vacA de las cepas. Conclusión: se encontró una baja prevalencia de cepas cagA (+), el estatus cagA-vacA no es un predictor de riesgo en la población estudiada y la presencia de infecciones heterogéneas sin tropismo sugieren la necesidad de tomar biopsias tanto del cuerpo como del antro del estómago en la práctica clínica rutinaria.

Abstract Objective: This study characterizes the diversity of cagA and vacA virulence genes in Colombian patients to determine possible associations between them and the severity of endoscopic findings. It considers all four genotypes reported for the vacA gene (s, m and i). Materials and methods: Helicobacter pylori was detected in biopsies of 62 patients through culturing and by molecular methods. Genotypes of cagA and vacA (m/i/s) were determined by PCR and sequencing. Results: One hundred twenty four strains from 62 patients were isolated. Of these, 48.5% (n = 48) were vacA s2/m2/i2 - cagA (-) which were mostly found in patients with follicular gastritis; 32.3% (n = 32) were vacA s1/m1/i1-cagA (+) which were mostly found in patients with follicular gastritis, chronic gastritis and possible metaplasia. Significant associations were found between the presence of cagA and the vacA s1/m1/i1 genotype and the absence of cagA and the vacA s2/m2/i2 genotype (p <0.001). No significant association was found between the severity of endoscopic findings and the cagA-vacA status of the strains. Conclusion: We found a low prevalence of cagA (+) strains, the cagA-vacA status is not a predictor of risk in this population. Moreover, the presence of heterogenous infections without tropism suggests a need for biopsies from both the corpus and the antrum of the stomach in routine clinical practice.

Detection of cytoplasmic proteins from Helicobacter pylori in Colony Lift Immunoassay.

Use of the Colony Lift Immunoassay has been described for several Gram negative bacteria of medical interest. In all cases detection was limited to the use of antibodies against outer membrane proteins. Here we describe the adaptation of this method for detection of the cytoplasmic CagA toxin from Helicobacter pylori.