The OLGA-OLGIM staging and the interobserver agreement for gastritis and preneoplastic lesion screening: a cross-sectional study.

Stomach cancer (SC) incidence and mortality are relevant public health issues worldwide. In Colombia, screening for preneoplastic lesions (PNL) and the presence of H. pylori is not routinely performed. Therefore, the aim of this study was to evaluate OLGA-OLGIM staging and the interobserver agreement in gastritis and preneoplastic lesions in patients with gastroduodenal symptoms from Colombia. A cross-sectional study was conducted in 272 patients with gastroduodenal symptoms. Gastric biopsies were taken following the Updated Sydney System with the OLGA-OLGIM classification, and the results were evaluated by two pathologists. Chronic gastritis and PNL were reported in 76% and 24% of the patients, respectively. Furthermore, 25% of the patients with PNL displayed gastric atrophy (GA) and 75% intestinal metaplasia (IM). Agreement in the histopathological reading for IM was good, whereas for OLGA was variable, and for the H. pylori quantity was poor. OLGA-OLGIM stages 0-II were the most frequent (96%), while stage III (4%) and SC (4%) were the least frequent. Age and coffee consumption were associated with a higher prevalence of PNL. This work determined that 4% of the population is at high risk of developing SC and would benefit from follow-up studies. Reinforcement of training programs to improve the agreement in histopathology readings is required.

Effect of two preservation methods on the viability and enzyme production of a recombinant Komagataella phaffii (Pichia pastoris) strain.

The methylotrophic yeast Komagataella phaffii, previously known as Pichia pastoris, has been reported as a host for producing human recombinant lysosomal enzymes intended for enzyme replacement therapy. K. phaffii has advantages such as easy genetic handling, rapid growth, cost-effective mediums, and the ability to develop mammalian-like post-translational modifications. To maintain cell viability and enzyme activity over time, it is important to consider the bioprocess optimization and the proper selection and preservation of clones. In this study, we evaluated the effect of glycerol and skim milk in cryopreservation at -80 °C, as well as the use of skim milk or its combination with NaCl, disaccharides or sorbitol in freeze-drying on the cell viability and activity of a recombinant lysosomal enzyme (i.e., human ß-hexosaminidase-A) produced in K. phaffii GS115 strain. The results showed that cryopreservation with glycerol and skim milk, as well as freeze-drying using disaccharides and sorbitol with skim milk, maintained the viability above 80%. Although variations in enzyme activity among treatments were found, the use of disaccharides had a positive effect on the enzymatic activity levels. This is the first report of the evaluation of two suitable methods to preserve a recombinant K. phaffii strain, preventing the loss of viability and maintaining the activity of the recombinant protein.

Draft Genome Sequences of 29 Helicobacter pylori Strains Isolated from Colombia.

Here, we present the draft genome sequences of 29 Colombian Helicobacter pylori strains. These strains were isolated in Bogotá, Colombia, from patients diagnosed with chronic gastritis. The genomic characterization of these strains will provide more information on the genetic composition of H. pylori strains from Colombia.

Prevalence of CYP2C19 polymorphism in Bogotá, Colombia: The first report of allele *17.

INTRODUCTION: Proton pump inhibitors (PPIs) are a group of drugs that are essential for the treatment of acid-related disorders, such as gastroesophageal reflux (GERD), dyspepsia, gastric ulcers and Helicobacter pylori (H. pylori) infection. PPIs such as omeprazole, esomeprazole, pantoprazole and lansoprazole are metabolized by the CYP2C19 enzyme, which is encoded by a polymorphic gene. Four polymorphisms have an impact on the speed of PPI metabolism: CYP2C19*1/*1 (extensive metabolizers), CYP2C19*2/*2 (intermediate metabolizers), CYP2C19*3/*3 (poor metabolizers) and CYP2C19*17/*17 (ultrarapid metabolizers). Extensive and ultrarapid metabolizers inactivate PPIs quickly, which consequently causes low plasma concentrations of PPIs, while intermediate or poor metabolizers have higher plasma concentrations of PPIs and, therefore, PPIs have greater therapeutic efficacy in individuals with these polymorphisms. OBJECTIVE: To determine the frequency of genetic polymorphisms of the CPY2C19 enzyme in Bogotá, Colombia. METHODS: This observational study was conducted in Bogotá between 2012 and 2015 and was part of a clinical trial (ID: NCT03650543). It included 239 subjects with dyspepsia, H. pylori infection, or GERD symptoms. CYP2C19 genotyping was performed on gastric biopsy samples. Polymorphisms *1, *2, and *3 were analyzed by real-time PCR (Roche®), and PCR-RFLP was used to determine the presence of polymorphism *17. RESULTS: The distribution of different types of PPI metabolizers was as follows: extensive (70.7%), ultrarapid (12.9%), intermediate (8.8%) and poor (0.8%). CONCLUSION: The population studied consisted mainly of extensive and ultrarapid PPI metabolizers. These findings show that it is necessary to increase PPI doses in this group of subjects or to use PPIs that are not metabolized by CYP2C19 (rabeprazole). This is the first Colombian work to identify ultrarapid metabolizers.

An American lineage of Helicobacter pylori prophages found in Colombia.

BACKGROUND: Helicobacter pylori is a human gastric carcinogen that is highly prevalent in Latin American. The prophages of H. pylori show a structured population and contribute to the diversity of this bacterium. However, H. pylori prophages present in American strains have not been described to date. In this study, we identified, characterized, and present the phylogenetic analysis of the prophages present in Colombian H. pylori strains. METHODS: To characterize Colombian H. pylori strains and their prophages, a Multilocus Sequences Typing (MLST) and a Prophage Sequences Typing (PST), using the integrase and holin genes, were performed. Furthermore, five Colombian H. pylori had their full genome sequenced, and six Colombian H.pylori retrieved from databases, allowing to determine the prophage complete genome and insertion site. RESULTS: The integrase gene frequency was 12.6% (27/213), while both integrase and holin genes were present in 4.2% (9/213) of the samples analyzed. The PST analysis showed that Colombian prophages belong to different populations, including hpSWEurope, hpNEurope, hpAfrica1, and a new population, named hpColombia. The MLST analysis classified most of the Colombia strains in the hpEurope population. CONCLUSIONS: The new H. pylori prophage population revealed that Colombian prophages follow a unique evolutionary trajectory, contributing to bacterial diversity. The global H. pylori prophage phylogeny highlighted five phylogenetic groups, one more than previously reported. After the arrival of Europeans, the Colombian H. pylori bacteria and their prophages formed an independent evolutionary line to adapt to the new environment and new human hosts.

Correction: cagA gene EPIYA motif genetic characterization from Colombian Helicobacter pylori isolates: Standardization of a molecular test for rapid clinical laboratory detection.

[This corrects the article DOI: 10.1371/journal.pone.0227275.].

cagA gene EPIYA motif genetic characterization from Colombian Helicobacter pylori isolates: Standardization of a molecular test for rapid clinical laboratory detection.

The aim of this work was to determine current cagA gene EPIYA motifs present in Colombian Helicobacter pylori isolates using a fast and reliable molecular test. DNA from eighty-five Helicobacter pylori-cagA positive strains were analyzed. Strains were obtained from patients diagnosed with functional dyspepsia at Clínica Fundadores in Bogotá. The 3' region of the cagA gene was amplified through conventional Polymerase Chain Reaction (PCR). Obtained amplicons were sequenced using the Sanger method and analyzed with bioinformatics tools. Additionally, a significant Spearman correlation coefficient was determined between the patients' age and the number of EPIYA-C repeats; with p values < 0.05 considered significant. Estimates were obtained using a 95% CI. The 3´ variable region of the cagA gene was amplified and PCR products of the following sizes corresponded to the following EPIYA motifs: 400 bp: EPIYA AB, 500 bp: EPIYA ABC, 600 bp: EPIYA ABCC and 700 bp: ABCCC. A single PCR band was observed for 58 out of 85 Helicobacter pylori isolates, with an EPIYA distribution motif as follows: 7/85 AB (8.2%), 34/85 ABC (40%), 26/85 ABCC (30.6%) and 18/85 ABCCC (21.2%). However, in 27 out of 85 Helicobacter pylori isolates, two or more bands were observed, where the most predominant cagA genotype were ABC-ABCC (26%, 7/27) and ABCC-ABCCC (22.2%, 6/27). A direct proportionality between the number of EPIYA-C repeats and an increase in the patients' age was observed, finding a greater number of EPIYA ABCC and ABCCC repeats in the population over 50 years old. All isolates were of the Western cagA type and 51.8% of them were found to have multiple EPIYA-C repeats. These standardized molecular test allowed to identify the number of EPIYA C motifs based on band size.

Personalized therapy for Helicobacter pylori: CYP2C19 genotype effect on first-line triple therapy.

BACKGROUND: Triple therapy efficacy against Helicobacter pylori is low worldwide, and thus, alternatives must be sought to improve eradication. The aim of the present study was to determine CYP2C19 genetic polymorphism effect on H pylori eradication. METHODS: A randomized, single-blinded clinical trial including 133 participants was carried out. H pylori infection was confirmed by histologic and microbiologic test. Antibiotic susceptibility to amoxicillin and clarithromycin was performed. CYP2C19 polymorphisms *1, *2, and *3 were analyzed by real-time PCR (Roche ®), and nested PCR for CYP2C19*17 polymorphisms. Participants were randomized into two groups for different H pylori therapies, one with standard omeprazole doses and another with omeprazole doses depending on CYP2C19 polymorphism. H pylori eradication was verified by stool antigen tests (Meridian ®). RESULTS: The most common CYP2C19 polymorphism was *1/*1 in 54.9% of the participants followed by *17/*17 in 21.1%. Triple therapy efficacy with standard omeprazole doses versus personalized therapy based on CYP2C19 polymorphism by ITT analysis was 84% (95% CI: 0.73-0.91) vs 92.2% (95% CI: 0.82-0.97) (P = 0. 14), respectively. The efficacy by PP analysis was 92.1% (95% CI: 0.82-0.97) vs 100% (95% CI: 0.92-0.01) (P = 0.027), respectively. CONCLUSIONS: The most frequent polymorphism was extensive PPI metabolizers (62.4%). Effectiveness of guided therapies by susceptibility test was good, yet they can be further improved by customized therapy based on CYP genotype. Therefore, high PPI (80 mg/d) doses are recommended for H pylori eradication therapies in Colombia. ClinicalTrials.gov ID: NCT03650543.

Surveillance of Levofloxacin Resistance in Helicobacter pylori Isolates in Bogotá-Colombia (2009-2014).

Increased resistance of Helicobacter pylori to clarithromycin and metronidazole has resulted in recommendation to substitute fluoroquinolones for eradication therapy. The aims of the study were to determine the prevalence and changes in primary levofloxacin resistance related to H. pylori gyrA sequences. The study utilized H. pylori strains isolated from patients undergoing gastroscopy in Bogotá, Colombia from 2009 to 2014. Levofloxacin susceptibility was assessed by agar dilution. Mutations in gyrA sequences affecting the quinolone resistance-determining region (QRDR) were evaluated by direct sequencing. Overall, the mean prevalence of primary levofloxacin resistance was 18.2% (80 of 439 samples). Resistance increased from 11.8% (12/102) in 2009 to 27.3% (21/77) in 2014 (p = 0.001). gyrA mutations in levofloxacin resistant strains were present in QRDR positions 87 and 91. The most common mutation was N87I (43.8%, 35/80) followed by D91N (28.8%, 23/80) and N87K (11.3%, 9/80). Levofloxacin resistance increased markedly in Colombia during the six-year study period. Primary levofloxacin resistance was most often mediated by point mutations in gyrA, with N87I being the most common QRDR mutation related to levofloxacin resistance.

Tasa de reinfección por Helicobacter pylori en una cohorte de pacientes colombianos tratados exitosamente con seguimiento superior a 2 años / Helicobacter Pylori Reinfection Rate after More Than Two Years of Follow-up in a Cohort of Successfully Treated Colombian Patients

El Helicobacter pylori (H. pylori) infecta por lo menos a la mitad de la población mundial, aunque la prevalencia es más alta en países subdesarrollados. La tasa de reinfección es variable en las diferentes regiones y puede incluir recrudescencia de la infección o verdadera recurrencia. Hasta el momento hay pocos estudios en Colombia que hayan investigado la recurrencia de la infección y ninguno se ha realizado en Bogotá, Colombia. Objetivo: determinar la tasa de recurrencia de H. pylori en pacientes tratados eficazmente con 3 terapias triples diferentes. Materiales y métodos: estudio observacional analítico anidado en una cohorte de 180 pacientes a la que se le erradicó exitosamente H. pylori durante 2008-2009. La erradicación se verificó con test respiratorio con urea marcada y el tiempo promedio de seguimiento fue 43,7 meses (rango 31-56 meses). La recurrencia se investigó con la prueba de antígenos fecales monoclonales ImmunoCard STAT® HpSA (Meridian Bioscience Inc.). Resultados: se siguieron 86 pacientes y el porcentaje total de reinfección por H. pylori fue de 5,8% (5/86) y la tasa anual de reinfección fue de 1,59% (5/313,4 pacientes año x 100). El primer caso de reinfección se presentó a los 32 meses y los demás ocurrieron a los 37, 42, 44 y 56 meses de seguimiento. La tasa de reinfección calculada fue 1,8%/año después de 2 años de seguimiento. Conclusiones: la tasa de reinfección de H. pylori en Bogotá es baja e inferior a la previamente informada para otras regiones de Colombia.

Helicobacter pylori (H. pylori) infects at least half the world’s population although its prevalence is higher in developing countries. The reinfection rate varies from region to region and may include recrudescence of infection or true recurrence. So far there are few studies that have investigated recurrence of infections in Colombia, and none had been done in Bogota, Colombia. Objective: The objective of this study was to determine the rate of recurrence of H. pylori in patients who had been treated effectively with three different triple therapies. Materials and Methods: This was an observational study nested in a cohort of 180 patients in whom H. pylori had been successfully eradicated during 2008 and 2009. Eradication was verified with the labeled urea breath test. The average follow-up time was 43.7 months (range: 31-56 months). Recurrence was investigated with monoclonal stool antigen tests (ImmunoCard STAT®, HpSA (Meridian Bioscience Inc.)). Results: A total of 86 patients were monitored during the follow-up period. Out of this group the reinfection rate was 5.8% (5/86). The annual reinfection rate was 1.59% (5/313.4 patient-years x 100). The first case of reinfection was presented at 32 months, and the other cases occurred at 37, 42, 44 and 56 month of follow-up. The reinfection rate was 1.8%/year calculated after two years of monitoring. Conclusions: The H. pylori reinfection rate in Bogotá is low and is less than that previously reported for other regions of Colombia.

Estado actual de la resistencia de Helicobacter pylori a tetraciclina:revisión sistemática de la literatura / Current status of Helicobacter pylori resistance to tetracycline: a systematic review of the literature / Estado atual da resistência do Helicobacter pylori à tetraciclina: uma revisão sistemática da literatura

Determinar la prevalencia de resistencia de Helicobacter pylori a tetraciclina y las posibles mutaciones que generan estaresistencia mundialmente. Materiales y método. Se realizó una búsqueda sistemática de literatura en las bases de datos: Medline,Science Direct (Elsevier), Ovid, Pubmed, Lilacs y MEDICLATINA, con el uso de palabras clave relevantes. La extracción de losdatos fue independiente y se realizaron listas de verificación para evaluar la calidad metodológica de los estudios. El análisis de lainformación fue realizado en el programa RevMan 5®. Resultados. Se evidenció resistencia a tetraciclina por Helicobacter pyloricon prevalencias de 1% para Norte América, 8% para Centro y Sur América; 5% para Asia y 2% para Europa . La alta resistencia sedebe a la triple mutación AGA(926-928)-->TTC, en el gen 16S rDNA. Conclusiones. La resistencia antibiótica es una de las causasque más se asocia a falla terapéutica en la erradicación de Helicobacter pylori, así como la poca adherencia al tratamiento y el usoindiscriminado de antibióticos. Se evidenció que la tasa de resistencia a tetraciclina aumenta después de un primer tratamiento con esteantibiótico, sin embargo la prevalencia de la resistencia global a tetraciclina es baja sin aún alcanzar límites que impidan su utilizaciónen los esquemas de tratamiento...

To determinethe prevalence of Helicobacter pylori resistance to and the possible mutations that generate this worldwide resistance. Materials andmethods. A systematic search for literature was performed in the databases Medline, Science Direct (Elsevier), Ovid, PubMed, Lilacsand MedicLatina using relevant key words. Data extraction was independent and checklists were prepared to assess the methodologicalquality of the studies. Analysis of information was done with RevMan 5®. Results. We found Helicobacter pylori resistance prevalencerates of 1% for North America, 8% for Central and South America, 5% for Asia, and 2% for Europe. The mutation associated to thisresistance is in the 16S rDNA gene at nucleotide position 967TTC to AGA965 responsible of high resistance to tetracycline. Conclusions.Antibiotic resistance is one of the causes most associated to treatment failure in the eradication of Helicobacter pylori, as well as pooradherence to treatment and indiscriminate use of antibiotics. We also evidenced that the rate of tetracycline resistance is higher whenit is used in a second treatment scheme. The distribution of resistance is variable in different areas and it is important to know theseresistances to avoid treatment failures...

Determinara prevalência da resistência do Helicobacter pylori à tetraciclina e possíveis mutações que geram esta resistência a nível mundial.Materiais e métodos. Foi realizada uma procura sistemática da literatura nas bases de dados Medline, Science Direct (Elsevier), Ovid,Pubmed, Lilacs e MEDICLATINA, usando palavras-chave relevantes. A extração dos dados foi independente e realizaram-se listas deverificação para avaliar a qualidade metodológica dos estudos. A análise dos dados foi realizada em REVMAN 5®. Resultados. Foievidenciada a resistência de Helicobacter pylori com taxas de prevalência de 1% para a América do Norte, 8% para América Central eAmérica do Sul; 5% para Ásia e 2% para Europa. A mutação associada a estas resistências no gen 16S rDNA nos nucleótidos da posiçãoAGA965 a 967TTC é responsável da alta resistência à tetraciclina. Conclusões. A resistência aos antibióticos é uma das razões maisassociadas à falha do tratamento na erradicação de Helicobacter pylori, assim como a pouca adesão ao tratamento e uso indiscriminadode antibióticos; também foi evidente que a taxa de resistência à tetraciclina é maior quando utilizado em regime de segundo tratamento;a distribuição da resistência varia em diferentes áreas e é importante saber estas resistências a fim de evitar falhas terapêuticas...

Experiencias colombianas en la utilización de medios de cultivo y extractos experimentales a partir de macroalgas marinas del caribe: estado actual de su conocimiento / Colombian experiences in the use of culture media and experimental extracts from marine macroalgae of the caribbean sea: current state of knowledge

Después de desarrollarse una amplia y ambiciosa serie de investigaciones, se ha avanzado en aislamiento, purificación y caracterización química de las sustancias responsables de la actividad especialmente antibacterial y antifungicida, pero también antimitótica, citotóxica e ictiotóxica de los extractos orgánicos crudos, liofilizados y especificos (metanólicos) de algunas macroalgas marinas colombianas. Igualmente se ha determinado la cantidad y calidad del agar, agaroides y mucílagos obtenidos de algas rodofíceas en la región noroeste de Colombia. Tres grupos de investigación en diferentes ciudades del país, pero utilizando el material biológico recolectado en las regiones de Cartagena (Bolívar), Santa Marta (Magdalena) y Riohacha (Guajira), trabajan en los proyectos “Estudio preliminar para la obtención de agar bacteriológico a partir de algas nativas del Caribe colombiano” (Pontificia Universidad Javeriana, Bogotá), “Estudio de la actividad antimicrobiana de los extractos alcohólicos de algunas macroalgas del Caribe colombiano” (Universidad de Antioquia - Universidad Nacional de Colombia, Medellín), “Ensayos de actividad biológica y ecología química de extractos orgánicos crudos de algunas macroalgas del Caribe colombiano” (Universidad de Bogotá Jorge Tadeo Lozano, Santa Marta). Si se tiene en cuenta que en Colombia el consumo de agar bacteriológico asciende aproximadamente a una tonelada anual, es evidente que a partir de los resultados obtenidos en dichos proyectos sería posible disminuir los costos al producirse agar a partir de algas rojas, además de los avances biológicos, ecológicos, químicos y médicos previstos.

After developing a wide and ambitious series of investigations, advancements have been made regarding the isolation, purification and chemical characterization of the substances responsible for the antibacterial and antifungal activity, but also in the antimitotic, cytotoxic and ictiotoxic activity of the raw, liofilized and specific (metanolics) organic extracts of some Colombian marine macroalgae. In the same manner, the quantity and quality of the agar, agaroids and mucilages obtained from rodophyties algae in the northwest region of Colombia have been determined. Three research groups in different cities of the country, but using the biological material gathered in Cartagena (Bolívar), Santa Marta (Magdalena) and Riohacha (Guajira) regions work on the following projects: “Preliminary study on the obtainment of bacteriological agar from native algae of the Colombian Caribbean" (Pontificia Universidad Javeriana, Bogotá), “Study on the antibacterial activity of the alcoholic extracts of some macroalgae of the Colombian Caribbean” (Universidad de Antioquia - National University of Colombia, Medellín), “Tests on the biological activity and chemical ecology of raw organic extracts of some macroalgae of the Colombian Caribbean” (University of Bogotá Jorge Tadeo Lozano, Santa Marta). Keeping in mind that in Colombia, the consumption of bacteriological agar rises to approximately one annual ton, it is evident that based on the results obtained in these projects, it would be possible to diminish the costs when producing agar from red algae, as well as the expected biological, ecological, chemical, and medical advances.

Evaluación y utilización potencial de las macroalgas marinas del Caribe y el Pacífico de Colombia: estado actual de su conocimiento / Evaluation and potential uses of the marine macroalgae from Colombian Caribean and Pacific seas: actual state of knowledgement

Con el fin de rescatar y aplicar en un futuro los avances en el conocimiento adquirido sobre las macro-algas marinas del Caribe y el Pacífico de Colombia, se realizó una revisión de las publicaciones y trabajos de grado que se han realizado acerca de la composición química y utilización de las algas marinas colombianas. A partir de dicha revisión se obtuvo una cantidad apreciable de información que se presenta y analiza en el presente artículo. Esta información confirma que las macro-algas marinas poseen todo un potencial que hasta ahora no ha sido aprovechado y que las condiciones ecológicas y bioquímicas de las especies evaluadas permiten tener la certeza de una utilización futura bastante promisoria.