Maldi-Tof mass spectometry as a routine technique for identification of typical and atypical mycobacteria in the Laboratory of Clinical Microbiology

Introducción y Objetivo: Del género Mycobacterium se han descrito más de 120 especies de micobacterias diferentes de crecimiento lento y rápido. Estos microorganismos producen una importante morbilidad en humanos, incluyendo infecciones de tipo pulmonar, en la piel y tejidos blandos y enfermedad diseminada siendo el diagnóstico rápido y preciso es de gran importancia. Material y Métodos: La población de estudio de nuestro trabajo fueron 75 aislados de micobacterias procedentes de cultivo en medio sólido Lowenstein-Jensen. El diagnóstico fue realizado mediante técnicas moleculares de PCR e hibridación inversa: GenoType Mycobacterium CM y GenoType Mycobacterium AS. De forma paralela las cepas se identificaron mediante espectrometría de masas MALDITOF MS (Matrix-Assisted Laser Desorption Ionization– Time of Flight Mass Spectrometry). Resultados: La concordancia global de resultados entre la identificación realizada mediante PCR y la tecnología MALDI-TOF fue del 97%, con un coeficiente kappa de correlación de 0.929 (correlación excelente entre 0.081-1.0). Conclusiones: Nuestros resultados indican que es bastante factible incorporar MALDI-TOF MS para la identificación rutinaria de micobacterias en el flujo de trabajo del laboratorio de microbiología clínica.Introduction and aim: in the Mycobacterium genus have been described more than 120 species of Mycobacteria other than growth slow and fast. These microorganisms produce significant morbidity in humans, including type pulmonary infections, skin and soft tissues and disseminated disease being the rapid and precise is of great importance. Material and methods: the study population of our work were 75 isolated Mycobacteria from cultivation in solid Lowenstein-Jensen medium. The diagnosis was made by molecular techniques of PCR and reverse hybridization: GenoType Mycobacterium CM and GenoType Mycobacterium AS. Parallel strains were identified by mass spectrometry MALDITOF MS (Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry). Results: The overall agreement of results between the identification made by PCR and MALDI-TOF technology was 97, with a coefficient of correlation of 0.929 kappa (excellent correlation between 0.081-1.0). Conclusions: Our results indicate that it is quite feasible to incorporate MALDI-TOF MS for routine identification of Mycobacteria in the clinical microbiology laboratory workflow

Sweet cherry behaviour in the climatic conditions of the Region of Murcia

[SPA] En este trabajo se expone la influencia que ejercen los patrones Adara, Mariana 2624, Mayor, MaxMa 14, Santa Lucia 64, Gisela 5, Gisela 6, Pikú 1, Pikú 3 y Pikú 4 sobre la variedad de cerezo “Newstar”, y se han evaluado 69 variedades de cerezo injertadas sobre Mariana 2624 con intermediario de Adara. Ambos ensayos se han realizado en un suelo pesado, calcáreo y con alto contenido en arcilla ubicado en el término municipal de Jumilla. Se han encontrado diferencias significativas entre patrones para parámetros como el vigor, la producción, el tamaño del fruto, el contenido en solidos solubles y la firmeza. Mariana 2624 con intermediario de Adara es el patrón recomendado para la zona de cultivo. Los patrones Gisela 5, Gisela 6, SL 64, Mayor y Pikú 1 han presentado un mayor porcentaje de mortandad, lo que hace desaconsejable su uso. Por otro lado, se han determinado aquellas 20 variedades que mejor adaptadas están a la zona del ensayo, y que podrían ser más interesantes por su productividad y calidad de fruto. Sin embargo, no se han encontrado variedades extra-tempranas que puedan ser de interés. [ENG] The influence of Adara, Mariana 2624, Mayor, MaxMa 14, Saint Lucie GF 64 (SL 64), Gisela 5, Gisela 6, Pikú 1, Pikú 3 and Pikú 4 rootstocks onto vegetative growth, yield and fruit quality of “Newstar” sweet cherry cultivar was studied. Also, 69 sweet cherry cultivars grafted in Mariana 2624 with Adara, as interstock, was studied. Both trials were performed in Jumilla, on a heavy and calcareous soil. Significant differences in parameters such as vigour, yield, fruit size, soluble solids content (SSC) and fruit firmness were examined among rootstocks. Mariana 2624 with Adara, as interstock, was the rootstock with better agronomic performance. In general, Gisela 5, Gisela 6, SL 64, Mayor and Pikú 1 presented the highest mortality rate, that advice not to use in our conditions. On the other hand, the results of this investigation showed 20 cultivars that are better adapted and could be considered to introduce this crop in this area for their productivity and fruit quality. However, not early cultivars were found in our study.A los componentes del Grupo Cerezo I+D. Este trabajo forma parte del proyecto INIA RTA:2006-00057-00-00 y ha sido cofinanciado por el proyecto PO07-027. Este trabajo ha sido realizado en el marco de la Acción Cost FA 1104

Comportamiento de patrones de cerezo en las condiciones edafoclimáticas de la Región de Murcia

En este trabajo se expone la influencia que ejercen los patrones Adara, Mariana 2624, Mayor, MaxMa 14, Santa Lucia GF 64, Gisela 5, Gisela 6, Piku 1, Piku 3 y Piku4 en el crecimiento vegetativo, producción y calidad del fruto de la variedad de cerezo NewStar. Este ensayo se ha realizado en un suelo pesado, calcáreo y con alto contenido en arcilla ubicado en el término municipal de Jumilla. Se han encontrado diferencias significativas para parámetros como el vigor, producción, tamaño del fruto, contenido en solidos solubles y firmeza. Las mayores producciones acumuladas fueron para patrones vigorosos como son Mariana 2624, Mayor y Adara. Los patrones de menor vigor como Gisela 5 y Piku 1, presentaron una tendencia excesiva al enanismo. Aquellos patrones peor adaptados a las condiciones edafoclimáticas del ensayo como Gisela 5, Gisela 6, SL 64, Mayor y Piku 1 presentaron mayor porcentaje de mortandad.A los componentes del Grupo Cerezo I+D. Este trabajo forma parte del proyecto INIA RTA:2006‐ 00057‐00‐00 y ha sido cofinanciado por el proyecto PO07‐027. Este trabajo ha sido realizado en el marco de la Acción Cost FA 1104

Frutales de hueso y pepita

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GEHEP 010 study: Prevalence and distribution of hepatitis B virus genotypes in Spain (2000–2016)

[Objective] To study the prevalence and distribution of HBV genotypes in Spain for the period 2000–2016.[Methods] Retrospective study recruiting 2559 patients from 17 hospitals. Distribution of HBV genotypes, as well as sex, age, geographical origin, mode of transmission, HDV-, HIV- and/or HCV-coinfection, and treatment were recorded.[Results] 1924 chronically HBV native Spanish patients have been recruited. Median age was 54 years (IQR: 41–62), 69.6% male, 6.3% HIV-coinfected, 3.1% were HCV-coinfected, 1.7% HDV-co/superinfected. Genotype distribution was: 55.9% D, 33.5% A, 5.6% F, 0.8% G, and 1.9% other genotypes (E, B, H and C). HBV genotype A was closely associated with male sex, sexual transmission, and HIV-coinfection. In contrast, HBV genotype D was associated with female sex and vertical transmission. Different patterns of genotype distribution and diversity were found between different geographical regions. In addition, HBV epidemiological patterns are evolving in Spain, mainly because of immigration. Finally, similar overall rates of treatment success across all HBV genotypes were found.[Conclusions] We present here the most recent data on molecular epidemiology of HBV in Spain (GEHEP010 Study). This study confirms that the HBV genotype distribution in Spain varies based on age, sex, origin, HIV-coinfection, geographical regions and epidemiological groups.This study has been funded in part by the funds of the research project GEHEP-2018-010, granted by the Hepatitis Group of the Spanish Society of Infectious Diseases and Clinical Microbiology (Grupo de Hepatitis de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica, GEHEP/SEIMC)

Using Interpretable Machine Learning to Identify Baseline Predictive Factors of Remission and Drug Durability in Crohn’s Disease Patients on Ustekinumab

Ustekinumab has shown efficacy in Crohn's Disease (CD) patients. To identify patient profiles of those who benefit the most from this treatment would help to position this drug in the therapeutic paradigm of CD and generate hypotheses for future trials. The objective of this analysis was to determine whether baseline patient characteristics are predictive of remission and the drug durability of ustekinumab, and whether its positioning with respect to prior use of biologics has a significant effect after correcting for disease severity and phenotype at baseline using interpretable machine learning. Patients' data from SUSTAIN, a retrospective multicenter single-arm cohort study, were used. Disease phenotype, baseline laboratory data, and prior treatment characteristics were documented. Clinical remission was defined as the Harvey Bradshaw Index <= 4 and was tracked longitudinally. Drug durability was defined as the time until a patient discontinued treatment. A total of 439 participants from 60 centers were included and a total of 20 baseline covariates considered. Less exposure to previous biologics had a positive effect on remission, even after controlling for baseline disease severity using a non-linear, additive, multivariable model. Additionally, age, body mass index, and fecal calprotectin at baseline were found to be statistically significant as independent negative risk factors for both remission and drug survival, with further risk factors identified for remission

Effectiveness and Safety of the Sequential Use of a Second and Third Anti-TNF Agent in Patients With Inflammatory Bowel Disease: Results From the Eneida Registry

Background: The effectiveness of the switch to another anti-tumor necrosis factor (anti-TNF) agent is not known. The aim of this study was to analyze the effectiveness and safety of treatment with a second and third anti-TNF drug after intolerance to or failure of a previous anti-TNF agent in inflammatory bowel disease (IBD) patients. Methods: We included patients diagnosed with IBD from the ENEIDA registry who received another anti-TNF after intolerance to or failure of a prior anti-TNF agent. Results: A total of 1122 patients were included. In the short term, remission was achieved in 55% of the patients with the second anti-TNF. The incidence of loss of response was 19% per patient-year with the second anti-TNF. Combination therapy (hazard ratio [HR], 2.4; 95% confidence interval [CI], 1.8-3; P < 0.0001) and ulcerative colitis vs Crohn's disease (HR, 1.6; 95% CI, 1.1-2.1; P = 0.005) were associated with a higher probability of loss of response. Fifteen percent of the patients had adverse events, and 10% had to discontinue the second anti-TNF. Of the 71 patients who received a third anti-TNF, 55% achieved remission. The incidence of loss of response was 22% per patient-year with a third anti-TNF. Adverse events occurred in 7 patients (11%), but only 1 stopped the drug. Conclusions: Approximately half of the patients who received a second anti-TNF achieved remission; nevertheless, a significant proportion of them subsequently lost response. Combination therapy and type of IBD were associated with loss of response. Remission was achieved in almost 50% of patients who received a third anti-TNF; nevertheless, a significant proportion of them subsequently lost response

Long-Term Real-World Effectiveness and Safety of Ustekinumab in Crohn’s Disease Patients: The SUSTAIN Study

Background Large real-world-evidence studies are required to confirm the durability of response, effectiveness, and safety of ustekinumab in Crohn’s disease (CD) patients in real-world clinical practice. Methods A retrospective, multicentre study was conducted in Spain in patients with active CD who had received ≥1 intravenous dose of ustekinumab for ≥6 months. Primary outcome was ustekinumab retention rate; secondary outcomes were to identify predictive factors for drug retention, short-term remission (week 16), loss of response and predictive factors for short-term efficacy and loss of response, and ustekinumab safety. Results A total of 463 patients were included. Mean baseline Harvey-Bradshaw Index was 8.4. A total of 447 (96.5%) patients had received prior biologic therapy, 141 (30.5%) of whom had received ≥3 agents. In addition, 35.2% received concomitant immunosuppressants, and 47.1% had ≥1 abdominal surgery. At week 16, 56% had remission, 70% had response, and 26.1% required dose escalation or intensification; of these, 24.8% did not subsequently reduce dose. After a median follow-up of 15 months, 356 (77%) patients continued treatment. The incidence rate of ustekinumab discontinuation was 18% per patient-year of follow-up. Previous intestinal surgery and concomitant steroid treatment were associated with higher risk of ustekinumab discontinuation, while a maintenance schedule every 12 weeks had a lower risk; neither concomitant immunosuppressants nor the number of previous biologics were associated with ustekinumab discontinuation risk. Fifty adverse events were reported in 39 (8.4%) patients; 4 of them were severe (2 infections, 1 malignancy, and 1 fever). Conclusions Ustekinumab is effective and safe as short- and long-term treatment in a refractory cohort of CD patients in real-world clinical practice

Risk Factors for COVID-19 in Inflammatory Bowel Disease: A National, ENEIDA-Based Case–Control Study (COVID-19-EII)

(1) Scant information is available concerning the characteristics that may favour the acquisition of COVID-19 in patients with inflammatory bowel disease (IBD). Therefore, the aim of this study was to assess these differences between infected and noninfected patients with IBD. (2) This nationwide case-control study evaluated patients with inflammatory bowel disease with COVID-19 (cases) and without COVID-19 (controls) during the period March-July 2020 included in the ENEIDA of GETECCU. (3) A total of 496 cases and 964 controls from 73 Spanish centres were included. No differences were found in the basal characteristics between cases and controls. Cases had higher comorbidity Charlson scores (24% vs. 19%; p = 0.02) and occupational risk (28% vs. 10.5%; p < 0.0001) more frequently than did controls. Lockdown was the only protective measure against COVID-19 (50% vs. 70%; p < 0.0001). No differences were found in the use of systemic steroids, immunosuppressants or biologics between cases and controls. Cases were more often treated with 5-aminosalicylates (42% vs. 34%; p = 0.003). Having a moderate Charlson score (OR: 2.7; 95%CI: 1.3-5.9), occupational risk (OR: 2.9; 95%CI: 1.8-4.4) and the use of 5-aminosalicylates (OR: 1.7; 95%CI: 1.2-2.5) were factors for COVID-19. The strict lockdown was the only protective factor (OR: 0.1; 95%CI: 0.09-0.2). (4) Comorbidities and occupational exposure are the most relevant factors for COVID-19 in patients with IBD. The risk of COVID-19 seems not to be increased by immunosuppressants or biologics, with a potential effect of 5-aminosalicylates, which should be investigated further and interpreted with caution

All-cause mortality in the cohorts of the Spanish AIDS Research Network (RIS) compared with the general population: 1997Ł2010

Abstract Background: Combination antiretroviral therapy (cART) has produced significant changes in mortality of HIVinfected persons. Our objective was to estimate mortality rates, standardized mortality ratios and excess mortality rates of cohorts of the AIDS Research Network (RIS) (CoRIS-MD and CoRIS) compared to the general population. Methods: We analysed data of CoRIS-MD and CoRIS cohorts from 1997 to 2010. We calculated: (i) all-cause mortality rates, (ii) standardized mortality ratio (SMR) and (iii) excess mortality rates for both cohort for 100 personyears (py) of follow-up, comparing all-cause mortality with that of the general population of similar age and gender. Results: Between 1997 and 2010, 8,214 HIV positive subjects were included, 2,453 (29.9%) in CoRIS-MD and 5,761 (70.1%) in CoRIS and 294 deaths were registered. All-cause mortality rate was 1.02 (95% CI 0.91-1.15) per 100 py, SMR was 6.8 (95% CI 5.9-7.9) and excess mortality rate was 0.8 (95% CI 0.7-0.9) per 100 py. Mortality was higher in patients with AIDS, hepatitis C virus (HCV) co-infection, and those from CoRIS-MD cohort (1997. Conclusion: Mortality among HIV-positive persons remains higher than that of the general population of similar age and sex, with significant differences depending on the history of AIDS or HCV coinfection