The Helicobacter pylori single nucleotide polymorphisms SNPs associated with multiple therapy resistance in Colombia.

The eradication of Helicobacter pylori (H. pylori) using multiple therapies is used as a prevention strategy. However, its efficacy has been compromised by the emergence of single nucleotide polymorphisms in genes associated with H. pylori's resistance to multiple antibiotics. To estimate antibiotic resistance rates associated with mutations in H. pylori genes in the high-cancer-risk population in Colombia, we included 166 H. pylori whole genome sequences from a cohort of individuals with a high risk of gastric cancer. By using the reference strain ATCC 26695, we identified mutations in specific genes to evaluate resistance rates for different antibiotics: 23S rRNA for clarithromycin, 16S rRNA for tetracycline, pbp1A for amoxicillin, gyrA for levofloxacin, and rdxA for metronidazole. The phylogenomic analysis was conducted using the core genome consisting of 1,594 genes of H. pylori-ATCC 26695. Our findings revealed that the resistance rate of H. pylori to clarithromycin was 3.62%, primarily associated with mutations A2143G and A2142G in the 23S rRNA gene. For tetracycline, the resistance rate was 7.23%, with mutations A926G, A926T, and A928C observed in the 16S rRNA gene. Amoxicillin resistance was found in 25.9% of cases, with observed mutations in the pbp1A gene, including T556S, T593, R649K, R656P, and R656H. In the gyrA gene, mutations N87K, N87I, D91G, D91N, and D91Y were identified, resulting in a resistance rate of 12.04% to levofloxacin. The most common mutations in the rdxA gene associated with metronidazole resistance were a stop codon, and mutations at D59N and D59S, resulting in a resistance rate of 99.3%. The high resistance rate of H. pylori to metronidazole indicated that this drug should be excluded from the eradication therapy. However, the resistance rates for tetracycline and clarithromycin did not exceed the established resistance threshold in Colombia. The increased resistance rate of H. pylori to levofloxacin and amoxicillin may partially explain the observed therapeutic failures in Colombia. The phylogenomic tree showed that the H. pylori isolate belongs to its own lineage (hspColombia). These findings offer valuable insights to enhance the characterization of treatment protocols for the specific H. pylori lineage (hspColombia) at the local level.

Helicobacter pylori: Microorganismo patógeno o mutualista en poblaciones colombianas / Helicobacter pylori: Pathogenic or mutualistic microorganism in Colombian populations / Helicobacter pylori: microrganismo patógeno ou mutualista em populações Colombianas

Introducción: El riesgo de desarrollar cáncer gástrico varía entre continentes, países y regiones. A pesar de que existe una alta prevalencia de Helicobacter pylori su rol como patógeno o mutualista define el riesgo de cáncer gástrico en las regiones de Colombia. Objetivo: Discutir el rol de Helicobacter pylori en el riesgo de cáncer gástrico en Colombia. Materiales y métodos: Revisión de literatura mediante la búsqueda, en las bases de datos LILACS, SciELO, PubMed. Resultados: La coevolución del humano y de Helicobacter pylori; la virulencia de genes cagA, vacA; el tipo de respuesta inmune inflamatoria a Helicobacter pylori (Th1) o antinflamatoria (Th2) y la susceptibilidad humana a cáncer gástrico (IL1β, IL10), junto a la dieta y factores ambientales explican el papel de Helicobacter pylori como patógeno o mutualista asociado al riesgo de cáncer gástrico en Colombia. Conclusiones: Helicobacter pylori tiene un rol mutualista principalmente en poblaciones de bajo riesgo de cáncer gástrico (costas), no obstante, en poblaciones con alto riesgo de cáncer gástrico (andes), su papel como patógeno amerita la erradicación; única estrategia para mitigar la alta incidencia de este cáncer en Colombia.

Introduction: The risk to develop gastric cancer varies between continents, countries and regions. Although there is a high prevalence of Helicobater pylori, its role as either pathogen or mutualistic bacteria defines the risk of gastric cancer in Colombian regions. Objective: To discuss the role of Helicobacter pylori in the risk of gastric cancer in Colombia. Materials and methods: A literature review based on searching LILACS, SciELO, and PubMed databases. Results: Helicobacter pylori role as either a pathogen or mutualistic microorganism associated with gastric cancer risk in Colombia can be explained by analyzing elements such as: human and Helicobacter pylori coevolution; cagA and vacA gene virulence; inflammatory (Th1) or anti-inflammatory (Th2) responses induced by Helicobacter pylori; human susceptibility to gastric cancer (IL1β, IL10); diet; and environmental factors. Conclusions: Even though Helicobacter pylori has a mutualistic role in populations at low gastric cancer risk (coastal regions), its role as a pathogen in populations at higher risk (Andean regions) justifies its eradication as a key strategy to mitigate the incidence of this cancer in Colombia.

Introdução: O risco de desenvolver câncer gástrico varia entre continentes, países e regiões. Embora haja uma alta prevalência de Helicobacter pylori, seu papel como patógeno ou mutualista define o risco de câncer gástrico nas regiões da Colômbia. Objetivo: Discutir o papel do Helicobacter pylori no risco de câncer gástrico na Colômbia. Materiais e métodos: Revisão da literatura por meio da busca, nas bases de dados LILACS, SciELO e PubMed. Resultados: A coevolução de humanos e Helicobacter pylori; a virulência dos genes cagA, vacA; o tipo de resposta imune inflamatória ao Helicobacter pylori (Th1) ou anti-inflamatório (Th2) e a suscetibilidade humana ao câncer gástrico (IL1β, IL10), juntamente com a dieta e fatores ambientais explicam o papel do Helicobacter pylori como patógeno ou mutualista associado ao risco de câncer gástrico na Colômbia. Conclusões: Helicobacter pylori tem um papel mutualista principalmente em populações de baixo risco de câncer gástrico (litoral), porém, em populações com alto risco de câncer gástrico (andes), seu papel como patógeno justifica a erradicação; única estratégia para mitigar a alta incidência deste câncer na Colômbia.

Efecto Inhibitorio de fracciones polifenolicas de la semilla de Persea americana var. Hass sobre el crecimiento de Helicobacter pylori / Inhibitory effect of seed polyphenolic fractions of Persea americana var. Hass on the Helicobacter pylori growth

ntroducción: El cáncer gástrico (CG) es la principal causa de muerte por cáncer en Colombia y de etiología multifactorial, asociada a factores genéticos del huésped, factores ambientales y el oncopatogeno Helicobacter pylori (H. pylori) como el principal factor de riesgo de la enfermedad. El aguacate (Persea americana var. Hass, (P. americana)) posee un alto contenido de polifenoles, con actividad bactericida, antioxidante, anti-ureasa, y antinflamatoria, que a su vez limitan los cambios en el ambiente gástrico que favorecen la colonización de la bacteria y posterior desencadenamiento de la cascada precancerosa. Objetivo: Evaluar la concentración mínima inhibitoria de fracciones polifenolicas de la semilla de P. americana sobre el crecimiento in vitro de H pylori. Resultados: La evaluación de la concentración mínima inhibitoria (CMI) de las tres fracciones obtenidas de la semilla de P. americana en cultivo de H. pylori in vitro, mostró que las fracciones uno y dos inhibieron el crecimiento bacteriano a 3000 ppm, mientras que la fracción 3 a 1500 ppm, P< 0,05. Conclusión: Se encontraron tres biofracciones polifenolicas de la semilla P. americana, principalmente constituidas por procianidinas, con actividad antibacterial in vitro de Helicobacter pylori, sin embargo, la fracción tres, de mayor peso molecular, inhibió el crecimiento de manera significativa a una CMI de 1500 ppm, comparada con las fracciones uno y dos.

Introduction: Gastric cancer (GC) is the main cause of cancer death in Colombia and of multifactorial etiology, associated with genetic factors of the host, environmental factors and the oncopathogen Helicobacter pylori (H. pylori) as the main risk factor of the disease. The avocado (Persea americana var. Hass, (P. americana)) has a high content of polyphenols, with bactericidal, antioxidant, anti-urease, and anti-inflammatory activity, which in turn limit changes in the gastric environment that favor colonization bacteria and subsequent triggering of the precancerous cascade. Objective: To evaluate the minimum inhibitory concentration of polyphenolic fractions of P. americana seed on the in vitro growth of H pylori. Results: The evaluation of the minimum inhibitory concentration (MIC) of the three fractions obtained from the P. americana seed in H. pylori culture in vitro, showed that fractions one and two inhibited bacterial growth at 3000 ppm, while fraction 3 at 1500 ppm, P <0.05. Conclusion: Three polyphenolic biofractions of the P. americana seed were found, mainly constituted by procyanidins, with in vitro antibacterial activity of Helicobacter pylori, however, fraction three, with a higher molecular weight, significantly inhibited growth at a MIC of 1500 ppm, compared to fractions one and two.

Microbiota according to gastric topography in patients with low or high risk of gastric cancer in Nariño, Colombia / La microbiota según la topografía gástrica en pacientes con bajo y con alto riesgo de cáncer gástrico en Nariño, Colombia

Introduction: Inflammation in the gastric antrum caused by Helicobacter pylori increases the risk of duodenal ulcer while inflammation in the body generates atrophic gastritis and increased risk of gastric cancer. These inflammatory responses according to gastric topography could be explained by the composition of the gastric microbiota associated with H. pylori. Objective: To identify and compare the microbiota of the gastric antrum and body of individuals from two populations, one with high risk and one with low risk of gastric cancer from Nariño, Colombia. Materials and methods: Biopsies of the gastric antrum and body of patients with non-atrophic gastritis or metaplastic atrophic gastritis were included. The microbiota was defined by sequencing the 16S rRNA gene, V3-V4 region, (illumina-MiSeq™). The operational taxonomic units were classified using the BLASTn and RDPII databases. The differences among microbial populations were evaluated with the PERMANOVA and multivariate analyses. Results: The Epsilonproteobacteria class represented by H. pylori was more abundant in the antrum and body biopsies of individuals with metaplastic atrophic gastritis (>50%) while in individuals with non-atrophic gastritis it was 20 % and had greater metagenomic diversity. Helicobacter pylori infection significantly decreases the metagenomic diversity of the gastric antrum (p=0.005) compared to that of the body. Conclusions: The bacterial groups involved in the dysbiosis can colonize both topographic regions of the stomach, regardless of the sectorized inflammation responses. Helicobacter pylori infection associated with the gastric microbiota is related to its localization in the stomach, the type of lesion, and the population at risk of gastric cancer, which suggests its importance in microbial dysbiosis and gastric disease.

Introducción. La inflamación del antro gástrico por Helicobacter pylori aumenta el riesgo de úlcera duodenal, y la del cuerpo gástrico puede producir gastritis atrófica e incrementar la probabilidad de cáncer gástrico. Estas reacciones inflamatorias diferenciadas según su localización, podrían explicarse por la composición de la microbiota gástrica asociada con H. pylori. Objetivo. Identificar y comparar la microbiota del antro y del cuerpo del estómago en individuos de dos poblaciones: una con alto riesgo y otra con bajo riesgo de cáncer gástrico en Nariño, Colombia. Materiales y métodos. Se incluyeron biopsias del cuerpo y el antro gástrico de pacientes con gastritis no atrófica o con gastritis atrófica y metaplasia. La microbiota se definió por secuenciación de la región V3-V4 del gen 16S del ARNr de H. pylori (illumina-MiSeq™). Las unidades taxonómicas operativas se clasificaron utilizando las bases de datos BLASTn y RDPII. Las diferencias entre las poblaciones microbianas del antro y del cuerpo gástrico se evaluaron mediante el análisis de varianza multivariado con base en permutaciones (Permutational Multivariate Analysis of Variance, PERMANOVA) y análisis multivariados. Resultados. La clase Epsilonproteobacteria representada por H. pylori fue más abundante en las biopsias del antro y del cuerpo de los individuos con gastritis no atrófica (>50 %), en tanto que, en los individuos con gastritis no atrófica, esta clase correspondió al 20 % con una mayor diversidad metagenómica. La infección por H. pylori disminuyó significativamente la diversidad metagenómica del antro (p=0,005), en comparación con la del cuerpo gástrico. Conclusiones. Los grupos bacterianos involucrados en la disbacteriosis pueden colonizar ambas regiones topográficas del estómago, independientemente de las reacciones sectorizadas de inflamación. La infección por H. pylori asociada con la microbiota gástrica está relacionada con su localización en el estómago, el tipo de lesión y el mayor o menor riesgo de cáncer gástrico, lo que sugiere su importancia en la disbacteriosis y la de esta en la enfermedad gástrica.

La microbiota según la topografía gástrica en pacientes con bajo y con alto riesgo de cáncer gástrico en Nariño, Colombia / Microbiota according to gastric topography in patients with low or high risk of gastric cancer in Nariño, Colombia

Resumen Introducción. La inflamación del antro gástrico por Helicobacter pylori aumenta el riesgo de úlcera duodenal, y la del cuerpo gástrico puede producir gastritis atrófica e incrementar la probabilidad de cáncer gástrico. Estas reacciones inflamatorias diferenciadas según su localización, podrían explicarse por la composición de la microbiota gástrica asociada con H. pylori. Objetivo. Identificar y comparar la microbiota del antro y del cuerpo del estómago en individuos de dos poblaciones: una con alto riesgo y otra con bajo riesgo de cáncer gástrico en Nariño, Colombia. Materiales y métodos. Se incluyeron biopsias del cuerpo y el antro gástrico de pacientes con gastritis no atrófica o con gastritis atrófica y metaplasia. La microbiota se definió por secuenciación de la región V3-V4 del gen 16S del ARNr de H. pylori (illumina-MiSeq™). Las unidades taxonómicas operativas se clasificaron utilizando las bases de datos BLASTn y RDPII. Las diferencias entre las poblaciones microbianas del antro y del cuerpo gástrico se evaluaron mediante el análisis de varianza multivariado con base en permutaciones (Permutational Multivariate Analysis of Variance, PERMANOVA) y análisis multivariados. Resultados. La clase Epsilonproteobacteria representada por H. pylori fue más abundante en las biopsias del antro y del cuerpo de los individuos con gastritis no atrófica (>50 %), en tanto que, en los individuos con gastritis no atrófica, esta clase correspondió al 20 % con una mayor diversidad metagenómica. La infección por H. pylori disminuyó significativamente la diversidad metagenómica del antro (p=0,005), en comparación con la del cuerpo gástrico. Conclusiones. Los grupos bacterianos involucrados en la disbacteriosis pueden colonizar ambas regiones topográficas del estómago, independientemente de las reacciones sectorizadas de inflamación. La infección por H. pylori asociada con la microbiota gástrica está relacionada con su localización en el estómago, el tipo de lesión y el mayor o menor riesgo de cáncer gástrico, lo que sugiere su importancia en la disbacteriosis y la de esta en la enfermedad gástrica.

Abstract Introduction: Inflammation in the gastric antrum caused by Helicobacter pylori increases the risk of duodenal ulcer while inflammation in the body generates atrophic gastritis and increased risk of gastric cancer. These inflammatory responses according to gastric topography could be explained by the composition of the gastric microbiota associated with H. pylori. Objective: To identify and compare the microbiota of the gastric antrum and body of individuals from two populations, one with high risk and one with low risk of gastric cancer from Nariño, Colombia. Materials and methods: Biopsies of the gastric antrum and body of patients with non-atrophic gastritis or metaplastic atrophic gastritis were included. The microbiota was defined by sequencing the 16S rRNA gene, V3-V4 region, (illumina-MiSeq™). The operational taxonomic units were classified using the BLASTn and RDPII databases. The differences among microbial populations were evaluated with the PERMANOVA and multivariate analyses. Results: The Epsilonproteobacteria class represented by H. pylori was more abundant in the antrum and body biopsies of individuals with metaplastic atrophic gastritis (>50%) while in individuals with non-atrophic gastritis it was 20 % and had greater metagenomic diversity. Helicobacter pylori infection significantly decreases the metagenomic diversity of the gastric antrum (p=0.005) compared to that of the body. Conclusions: The bacterial groups involved in the dysbiosis can colonize both topographic regions of the stomach, regardless of the sectorized inflammation responses. Helicobacter pylori infection associated with the gastric microbiota is related to its localization in the stomach, the type of lesion, and the population at risk of gastric cancer, which suggests its importance in microbial dysbiosis and gastric disease.

Punctual mutations in 23S rRNA gene of clarithromycin-resistant Helicobacter pylori in Colombian populations.

AIM: To characterize punctual mutations in 23S rRNA gene of clarithromycin-resistant Helicobacter pylori (H. pylori) and determine their association with therapeutic failure. METHODS: PCR products of 23S rRNA gene V domain of 74 H. pylori isolates; 34 resistant to clarithromycin (29 from a low-risk gastric cancer (GC) population: Tumaco-Colombia, and 5 from a high-risk population: Tuquerres-Colombia) and 40 from a susceptible population (28 from Tumaco and 12 from Túquerres) were sequenced using capillary electrophoresis. The concordance between mutations of V domain 23S rRNA gene of H. pylori and therapeutic failure was determined using the Kappa coefficient and McNemar's test was performed to determine the relationship between H. pylori mutations and clarithromycin resistance. RESULTS: 23S rRNA gene from H. pylori was amplified in 56/74 isolates, of which 25 were resistant to clarithromycin (20 from Tumaco and 5 from Túquerres, respectively). In 17 resistant isolates (13 from Tumaco and 4 from Túquerres) the following mutations were found: A1593T1, A1653G2, C1770T, C1954T1, and G1827C in isolates from Tumaco, and A2144G from Túquerres. The mutations T2183C, A2144G and C2196T in H. pylori isolates resistant to clarithromycin from Colombia are reported for the first time. No association between the H. pylori mutations and in vitro clarithromycin resistance was found. However, therapeutic failure of eradication treatment was associated with mutations of 23S rRNA gene in clarithromycin-resistant H. pylori (κ = 0.71). CONCLUSION: The therapeutic failure of eradication treatment in the two populations from Colombia was associated with mutations of the 23S rRNA gene in clarithromycin-resistant H. pylori.

Draft Genome Sequences of 13 Colombian Helicobacter pylori Strains Isolated from Pacific Coast and Andean Residents.

We present here the draft genomes of 13 Helicobacter pylori strains isolated from Colombian residents on the Pacific coast (n = 6) and in the Andes mountains (n = 7), locations that differ in gastric cancer risk. These 13 strains were obtained from individuals with diagnosed gastric lesions.

Effect of treatment failure on the CagA EPIYA motif in Helicobacter pylori strains from Colombian subjects.

AIM: To evaluate effect of treatment failure on cagA and vacA genotypes in Helicobacter pylori (H. pylori) isolates from Colombia. METHODS: One hundred and seventy-six participants infected with H. pylori from Colombia were treated during 14 d with the triple-standard therapy. Six weeks later, eradication was evaluated by 13C-Urea breath test. Patients with treatment failure were subjected to endoscopy control; biopsies obtained were used for histopathology and culture. DNA from H. pylori isolates was amplified using primers specific for cagA and vacA genes. The phylogenetic relationships among isolates obtained before and after treatment were established by conglomerate analysis based on random amplified polymorphic DNA (RAPD) fingerprinting. RESULTS: Treatment effectiveness was at 74.6%. Of the participants with treatment failure, 25 accepted subjected to a second endoscopy. Prevalence of post-treatment infection was 64% (16/25) and 40% (10/25) by histology and culture, respectively. Upon comparing the cagA and vacA genotypes found before and after therapy, multiple cagA genotypes (cagA-positive and cagA-negative) were found before treatment; in contrast, cagA-negative genotypes decreased after treatment. vacA s1m1 genotype was highly prevalent in patients before and after therapy. The 3'cagA region was successfully amplified in 95.5% (21/22) of the isolates obtained before and in 81.8% (18/22) of the isolates obtained after treatment. In the isolates obtained from patients with treatment failure, it was found that 72.7% (16/22) presented alterations in the number of EPIYA motifs, compared to isolates found before treatment. CONCLUSION: Unsuccessful treatment limits colonization by low-virulence strains resulting in partial and selective eradication in mixed infections, and acts on the cagA-positive strains inducing genetic rearrangements in cagA variable region that produces a loss or gain of EPIYA repetitions.

Genomic variability of Helicobacter pylori isolates of gastric regions from two Colombian populations.

AIM: To compare the genomic variability and the multiple colonization of Helicobacter pylori (H. pylori) in patients with chronic gastritis from two Colombian populations with contrast in the risk of developing gastric cancer (GC): Túquerres-Nariño (High risk) and Tumaco-Nariño (Low risk). METHODS: Four hundred and nine patients from both genders with dyspeptic symptoms were studied. Seventy-two patients were included in whom H. pylori was isolated from three anatomic regions of the gastric mucosa, (31/206) of the high risk population of GC (Túquerres) and (41/203) of the low risk population of GC (Tumaco). The isolates were genotyped by PCR-RAPD. Genetic diversity between the isolates was evaluated by conglomerates analysis and multiple correspondence analyses. RESULTS: The proportion of virulent genotypes of H. pylori was 99% in Túquerres and 94% in Tumaco. The coefficient of similarity of Nei-Li showed greater genetic diversity among isolates of Túquerres (0.13) than those of Tumaco (0.07). After adjusting by age, gender and type of gastritis, the multiple colonization was 1.7 times more frequent in Túquerres than in Tumaco (P = 0.05). CONCLUSION: In Túquerres, high risk of GC there was a greater probability of multiple colonization by H. pylori. From the analysis of the results of the PCR-RAPD, it was found higher genetic variability in the isolates of H. pylori in the population of high risk for the development of GC.

Epigenetic and genetic variation in GATA5 is associated with gastric disease risk.

Gastric cancer incidence varies considerably among populations, even those with comparable rates of Helicobacter pylori infection. To test the hypothesis that genetic variation plays a role in gastric disease, we assessed the relationship between genotypes and gastric histopathology in a Colombian study population, using a genotyping array of immune-related single nucleotide polymorphisms (SNPs). Two synonymous SNPs (rs6061243 and rs6587239) were associated with progression of premalignant gastric lesions in a dominant-effects model after correction for multiple comparisons (p = 2.63E-07 and p = 7.97E-07, respectively); effect sizes were ß = -0.863 and ß = -0.815, respectively, where ß is an estimate of effect on histopathology scores, which ranged from 1 (normal) to 5 (dysplasia). In our replication cohort, a second Colombian population, both SNPs were associated with histopathology when additively modeled (ß = -0.256, 95 % CI = -0.47, -0.039; and ß = -0.239, 95 % CI = -0.45, -0.024), and rs6587239 was significantly associated in a dominant-effects model (ß = -0.330, 95 % CI = -0.66, 0.00). Because promoter methylation of GATA5 has previously been associated with gastric cancer, we also tested for the association of methylation status with more advanced histopathology scores in our samples and found a significant relationship (p = 0.001). A multivariate regression model revealed that the effects of both the promoter methylation and the exonic SNPs in GATA5 were independent. A SNP-by-methylation interaction term was also significant. This interaction between GATA5 variants and GATA5 promoter methylation indicates that the association of either factor with gastric disease progression is modified by the other.

Human and Helicobacter pylori coevolution shapes the risk of gastric disease.

Helicobacter pylori is the principal cause of gastric cancer, the second leading cause of cancer mortality worldwide. However, H. pylori prevalence generally does not predict cancer incidence. To determine whether coevolution between host and pathogen influences disease risk, we examined the association between the severity of gastric lesions and patterns of genomic variation in matched human and H. pylori samples. Patients were recruited from two geographically distinct Colombian populations with significantly different incidences of gastric cancer, but virtually identical prevalence of H. pylori infection. All H. pylori isolates contained the genetic signatures of multiple ancestries, with an ancestral African cluster predominating in a low-risk, coastal population and a European cluster in a high-risk, mountain population. The human ancestry of the biopsied individuals also varied with geography, with mostly African ancestry in the coastal region (58%), and mostly Amerindian ancestry in the mountain region (67%). The interaction between the host and pathogen ancestries completely accounted for the difference in the severity of gastric lesions in the two regions of Colombia. In particular, African H. pylori ancestry was relatively benign in humans of African ancestry but was deleterious in individuals with substantial Amerindian ancestry. Thus, coevolution likely modulated disease risk, and the disruption of coevolved human and H. pylori genomes can explain the high incidence of gastric disease in the mountain population.

In vitro effect of amoxicillin and clarithromycin on the 3' region of cagA gene in Helicobacter pylori isolates.

AIM: To evaluate the in vitro effect of amoxicillin and clarithromycin on the cag pathogenicity island (cag PAI). METHODS: One hundred and forty-nine clinical isolates of Helicobacter pylori (H. pylori) cultured from gastric biopsies from 206 Colombian patients with dyspeptic symptoms from a high-risk area for gastric cancer were included as study material. Antimicrobial susceptibility was determined by the agar dilution method. Resistant isolates at baseline and in amoxicillin and clarithromycin serial dilutions were subjected to genotyping (cagA, vacA alleles s and m), Glu-Pro-Ile-Tyr-Ala (EPIYA) polymerase chain reaction and random amplified polymorphic DNA (RAPD). Images of the RAPD amplicons were analyzed by Gel-Pro Analyzer 4.5 program. Cluster analyses was done using SPSS 15.0 statistical package, where each of the fingerprint bands were denoted as variables. Dendrograms were designed by following Ward's clustering method and the estimation of distances between each pair of H. pylori isolates was calculated with the squared Euclidean distance. RESULTS: Resistance rates were 4% for amoxicillin and 2.7% for clarithromycin with 2% double resistances. Genotyping evidenced a high prevalence of the genotype cagA-positive/vacA s1m1. The 3' region of cagA gene was successfully amplified in 92.3% (12/13) of the baseline resistant isolates and in 60% (36/60) of the resistant isolates growing in antibiotic dilutions. Upon observing the distribution of the number of EPIYA repetitions in each dilution with respect to baseline isolates, it was found that in 61.5% (8/13) of the baseline isolates, a change in the number of EPIYA repetitions lowered antibiotic pressure. The gain and loss of EPIYA motifs resulted in a diversity of H. pylori subclones after bacterial adjustment to changing conditions product of antibiotic pressure. RAPD PCR evidenced the close clonal relationship between baseline isolates and isolates growing in antibiotic dilutions. CONCLUSION: Antibiotic pressure does not induce loss of the cag pathogenicity island, but it can lead--in most cases--to genetic rearrangements within the 3' region cagA of the founding bacteria that can affect the level of tyrosine phosphorylation impacting on its cellular effects and lead to divergence of cagA-positive subclones.

[Antimicrobial susceptibility of Helicobacter pylori with chronic gastritis]. / Sensibilidad in vitro a amoxicilina y claritromicina de Helicobacter pylori obtenido de biopsias gástricas de pacientes en zona de bajo riesgo para cáncer gástrico.

INTRODUCTION: Infection by Helicobacter pylori is prevalent in approximately half the world´s population.However, the susceptibility of H. pylori to antimicrobial agents must be evaluated by in vitro methods in order to determine the susceptibility levels and to guide treatment regimes. OBJECTIVE: The prevalence of infection and antibiotic susceptibility was evaluated in gastric biopsies containing H. pylori. MATERIALS AND METHODS: The prevalence of infection and antibiotic susceptibility was investigated in 203 patients with chronic gastritis from Tumaco, Colombia. Diagnosis was confirmed by histopathological evidence (Dixon scale) and microbiological (culture on blood agar supplemented with antibiotics).The antibiotic resistance of H. pylori was measured by its response toantimicrobial amoxicillin and clarithromycin using the agar dilution method. RESULTS: The prevalence of infection for H. pylori with histopathological and microbiological tests was88.7% and 84.7% respectively. The prevalence of resistance of H. pylori to antimicrobial amoxicillin was 20.5%, to clarithromycin 19.8%, and to both antibiotics concurrently, 10.9%. CONCLUSIONS: A high incidence of clarithromycin-resistant and amoxicillin-resistant H. pylori was discovered in patients from Tumaco with chronic gastritis. Dual drug-resistant strains of H. pylori to clarithromycin and amoxicillin were also present.

Sensibilidad in vitro a amoxicilina y claritromicina de Helicobacter pylori obtenido de biopsias gástricas de pacientes en zona de bajo riesgo para cáncer gástrico / Antimicrobial susceptibility of Helicobacter pylori with chronic gastritis

Introducción. La infección por Helicobacter pylori prevalece en más de la mitad de la población mundial. Es prioritario evaluar la sensibilidad actual in vitro de H. pylori a los antimicrobianos usados en los protocolos de erradicación, fundamentalmente para determinar los patrones y resolver la infección. Objetivo. Determinar la prevalencia de la infección y la sensibilidad antibiótica de H. pylori en biopsias gástricas. Materiales y métodos. Se investigan la prevalencia de la infección y la sensibilidad antibiótica de H. pylori de 203 pacientes con gastritis crónica procedentes de Tumaco (Nariño), mediante pruebas histopatológicas (escala Dixon) y microbiológicas (cultivo en agar sangre con suplemento de antibióticos) y, además, su resistencia a amoxicilina y claritromicina mediante el método de dilución en agar. Resultados. La prevalencia de la infección para H. pylori con pruebas histopatológicas y microbiológicas es de 88,7 % y 84,7 % respectivamente; la prevalencia de resistencia de H. pylori a amoxicilina y claritromicina y a ambos antibióticos, fue de 20,5 %, 19,8 % y 10,96 %, respectivamente. Conclusiones. Los resultados de este estudio indican que es alta la incidencia de H. pylori resistente a claritromicina y amoxicilina en pacientes de Tumaco con gastritis crónica. También, se encontraron cepas multirresistentes a claritromicina y amoxicilina.

Introduction. Infection by Helicobacter pylori is prevalent in approximately half the world´s population.However, the susceptibility of H. pylori to antimicrobial agents must be evaluated by in vitro methods in order to determine the susceptibility levels and to guide treatment regimes. Objective. The prevalence of infection and antibiotic susceptibility was evaluated in gastric biopsies containing H. pylori. Materials and methods. The prevalence of infection and antibiotic susceptibility was investigated in 203 patients with chronic gastritis from Tumaco, Colombia. Diagnosis was confirmed by histopathological evidence (Dixon scale) and microbiological (culture on blood agar supplemented with antibiotics).The antibiotic resistance of H. pylori was measured by its response toantimicrobial amoxicillin and clarithromycin using the agar dilution method. Results. The prevalence of infection for H. pylori with histopathological and microbiological tests was88.7% and 84.7% respectively. The prevalence of resistance of H. pylori to antimicrobial amoxicillin was 20.5%, to clarithromycin 19.8%, and to both antibiotics concurrently, 10.9%. Conclusions. A high incidence of clarithromycin-resistant and amoxicillin-resistant H. pylori was discovered in patients from Tumaco with chronic gastritis. Dual drug-resistant strains of H. pylori to clarithromycin and amoxicillin were also present.

Caracterización de la microbiota láctica gástrica asociada a gastritis crónica / Characterization of the gastric microbiota lactic associated with chronic gastritis

ntroducción: El papel de las bacterias ácido lácticas (BAL) en el ambiente gástrico humano es importante, así como la interacción con Helicobacter pylori, microorganismo asociado con gastritis y cáncer gástrico, influye en la colonización y en el tipo de respuesta inflamatoria del hospedero. Las BAL son microbiota del estómago humano y como probiótico podrían modular la infección por H. pylori. Objetivo: Determinar la distribución de BAL según el tipo de gastritis en sujetos procedentes de regiones con contraste de riesgo de cáncer gástrico: La Florida-Nariño (alto riesgo) y Tumaco-Nariño (bajo riesgo). Metodología: Se incluyeron 113 pacientes adultos con diagnóstico de gastritis, 65 de La Florida y 48 de Tumaco. Se obtuvieron biopsias de mucosa gástrica por endoscopia, para análisis histológicos y aislamiento de H. pylori y BAL. Resultados: La prevalencia de la colonización por bacterias lácticas gástricas fue mayor en los pacientes de La Florida (35%) que en los de Tumaco (25%). El 68% de las BAL se encontraron en individuos con gastritis no atrófica. Conclusiones: La distribución de la microbiota láctica gástrica varió según la procedencia y el tipo de gastritis. La especie más frecuente aislada de pacientes de ambas regiones fue L. paracasei ssp paracasei 1. La prevalencia de H. pylori fue similar en los pacientes de La Florida (88%) y Tumaco (85%). Sin embargo, la proporción de pacientes con gastritis atrófica fue significativamente mucho mayor en la Florida (43%). Sin embargo, la proporción de pacientes con gastritis atrófica fue significativamente mucho más alta en La Florida (43%) que en Tumaco (25%), p <0,05. Probablemente, otros factores como la variabilidad genética de H. pylori la dieta, y los polimorfismos humanos de acogida podrían explicar estas diferencias geográficas.

Introduction: The role of lactic acid bacteria (LAB) in the human gastric environment is important, as well as the interaction with Helicobacter pylori, a microorganism associated with gastritis and gastric cancer, influences the colonization and the type of host inflammatory response. The LAB are part of the microbiota of human stomach, and used as probiotic, it could modulate H. pylori infection. Objetive: To determine the distribution of LAB according to the type of gastritis in patients from two regions with contrasting risk for gastric cancer: La Florida-Nariño (high risk) and Tumaco-Nariño (low risk). Methods: 113 adult patients diagnosed for gastritis were enrolled: 65 from La Florida and 48 from Tumaco. Mucous biopsies and gastric juices were obtained by endoscopies and were used for histology, isolation of H. pylory and LAB. Results: The prevalence of LAB colonization was higher in patients from La Florida (35%) than in those from Tumaco (25%). 68% of the LAB were found in patients with non-atrophic gastritis. Conclusions: Lactic gastric microbiota varied with the region of origin and the type of gastritis. Lactobacillus paracasei ssp paracasei 1 was the most frequently isolated species in both regions. The prevalence of H. pylori infection was similar both in the patients from La Florida (88%) as in those from Tumaco (85%). However, the proportion of patients with atrophic gastritis was significatively much higher in La Florida (43%) than in Tumaco (25%), p<0.05. Probably, other factors such as H. pylori genetic variability, diet and human host polymorphisms could explain these geographical differences.

Evaluación de dss métodos de extracción de adn partir de biopsias fijadas en forMalina y embebidas en parafina en condiciones no pttimas / Evaluation of Two Methods DNA Extraction from Formalin-Fixed, Paraffin-Embedded Tissues on Non-Optimal Conditions

Los tejidos de archivo son material de incalculable valor para estudios retrospectivos que requieran la aplicación de análisis moleculares. Existen múltiples métodos de extracción de ADN a partir de este tipo de muestras. No obstante, la mayoría de métodos toman mucho tiempo y los reactivos empleados contribuyen a la fragmentación del ADN. Con el objetivo de optimizar dos métodos de extracción de ADN a partir de tejidos embebidos en parafina en condiciones no óptimas, se seleccionaron 47 bloques en parafina que contenían biopsias de pleura, pulmón y pericardio correspondientes a 24 pacientes (66,6% hombres) mayores de 18 años, con inflamación granulomatosa crónica, remitidos al Departamento de Patología, Hospital Universitario del Valle entre 2002 y 2007. Se realizaron 10 cortes a cada muestra y se sometieron a dos métodos de extracción de ADN: 1. convencional y 2. QIAamp-DNA mini kit®. La eficiencia del ADN fue valorada por espectrofotometría y amplificación del gen GAPDH. La concentración de ADN de las muestras extraídas por el método convencional fue de 65,52 ng/µL ±11,47 (promedio ± EE) y la relación 260/280 varió entre 0,52 y 2,30. De las muestras extraídas por el método comercial, la concentración media de ADN fue 60,89 ng/µL ± 6,02, con una absorbancia que osciló entre 0 y 2,64. El ADN obtenido fue sometido a PCR, de 47 muestras extraídas por ambos métodos, 25 y 23 respectivamente amplificaron exitosamente el gen GAPDH. Los métodos usados para la obtención de ADN presentaron un desempeño similar, revelando así su potencial utilidad en estudios retrospectivos a partir de biopsias embebidas en parafina en condiciones inadecuadas.

Paraffin wax embedded tissues are an invaluable material for retrospective studies requiring the application of molecular analysis. Multiple methods are available to extract DNA from these kind of samples. However, the most common methods are slow and the reagents often contribute to the fragmentation of genetic material. In order to optimize the procedure, two methods for DNA extraction from paraffin embedded tissue non-optimal conditions were used. 47 blocks containing paraffin-embedded biopsies of pleura, lung and pericardium from 24 patients (66.6% males) older than 18 years, with biopsy proven chronic granulomatous inflammation referred to the Department of Pathology at University hospital of Valle between 2002 and 2007 were selected. Each sample was subjected to 10 cuts and was to two methods of DNA extraction: 1. conventional and 2. QIAamp-DNA mini kit®. The efficiency of the extracted DNA, was assessed by spectrophotometry and PCR amplification of a fragment of the housekeeping gene GAPDH. The concentration of DNA samples extracted by the conventional method was of 65.52 ng/µL ± 11.47 (mean ± SE) and the 260/280 absorbance ratio ranged between 0.52 and 2.30 the average concentration of DNA of the samples extracted by the commercial method was 60.89 ng/µL ± 6.02 (mean ± SE), with an absorbance that fluctuated between 0 and 2.64. The DNA obtained was amplified by PCR, of 47 samples extracted by both methods, 25 and 23 respectively the GAPDH gene amplified successfully. The methods used to obtain DNA showed similar performance, highlighting the potential utility of both extraction methods for the retrospective studies from paraffin embedded tissues in unsuitable conditions.

Bacilos ácido accoholresistentes en biopsias emebidasen parafina en casos de iinflamacióngranulomatosa crónica. / Detection of Acid-Fast Bacilli in Formalin-Fixed,Paraffin-Embedded Tissues of Patientswith Chronic Granulomatous Inflammation.

La detección de bacilos ácido alcohol resistentes (BAAR) en frotis resulta un aporte significativo al diagnóstico y tratamiento de individuos con inflamación granulomatosa crónica (IGC). Con el objetivo de evaluar la presencia de BAAR en diferentes tejidos de pa-cientes con IGC demostrada y comparar la frecuencia de los extendidos positivos para BAAR con el grado de formación de granulomas y necrosis, se diseño un estudio retrospectivo, en el que se seleccionaron 57 bloques embebidos en parafina que contenían biopsias de pleura, pulmón, pericardio, ganglio linfático y lóbulo cerebral, correspon-dientes a 30 pacientes (63,3% hombres), mayores de 18 años, con IGC demostrada y remitidos al departamento de patología del Hospital Universitario del Valle entre el 2002-2008. A cada muestra se le realizaron tres cortes y se sometieron a tinciones de H/E, Zielh Neelsen y Auramina. La detección de BAAR en frotis fue similar para ambas tinciones especiales en pacientes con IGC necrotizante, reflejando una excelente concordancia en el diagnóstico (kappa=0,89, IC95%(0,68-1,0)). Sin embargo, la tinción con Auramina fue superior a la tinción Ziehl Neelsen para la detección de BAAR en pacientes con IGC no necrotizante (kappa=0,65, IC95%(0,23-1,0)). No se encontraron diferencias signi-ficativas entre la presencia de BAAR y el tipo de inflamacion, sexo y localización anatómica comprometida. En general, fue buena la concordancia entre los métodos histológicos empleados. Además, se hizo evidente la importancia de implementar el uso de técnicas moleculares mínimamente afectadas por el escaso número de bacilos presentes en las muestras, que finalmente ayudan en el reconocimiento del microorganismo.

Detection of acid fast bacilli (AFB) in smears is a significant aid in diagnosis and treatment of individuals with chronic granulomatous inflammation (CGI). This study was designed in order to detect the presence of AFB in several tissues of patients with histologically proven CGI and to compare the frequency of AFB positive smears with the degree of granuloma formation and necrosis. We selected 57 formalin-fixed, paraffin embedded blocks containing specimens of pleura, lung, pericardium, lymph nodes and cerebral lobe, from 30 patients (63.3% males) older than 18 years, with biopsy proven CGI referred to the Pathology department at University Hospital of Valle del Cauca (Colombia),between 2002 and 2008.Each sample was cut into 3 sections, and stained using the H/E, Ziehl-Neelsen and Auramine staining. AFB smear detection was similar in both special staining procedures in individuals with necrotizing CGI, reflecting an excellent diagnostic agreement (kappa=0.89, IC 95% (0.68-1.0)). However, Auramine was superior to Ziehl-Neelsen staining for AFB detection among subjects with nonnecrotizing CGI (kappa=0.65, IC95% (0.23-1.00)). Non-significant differences were found between the presence of AFB and the degree of granuloma necrosis, gender, and specific anatomic location. In general, there was a good agreement between both histological methods employed. Additionally it is clear that implementation of molecular tests that are minimally influenced by scant numbers of bacilli in samples is necessary for a definite diagnosis.