Europe-wide expansion and eradication of multidrug-resistant Neisseria gonorrhoeae lineages: a genomic surveillance study

Centre for Genomic Pathogen Surveillance and the Euro-GASP study group: Sonja Pleininger, Alexander Indra, Irith De Baetselier, Wim Vanden Berghe, Blaženka Hunjak, Tatjana Nemeth Blažić, Panayiota Maikanti-Charalambous, Despo Pieridou, Hana Zákoucká, Helena Žemličková, Steen Hoffmann, Susan Cowan, Lasse Jessen Schwartz, Rita Peetso, Jevgenia Epstein, Jelena Viktorova, Ndeindo Ndeikoundam, Beatrice Bercot, Cécile Bébéar, Florence Lot, Susanne Buder, Klaus Jansen, Vivi Miriagou, Georgios Rigakos, Vasilios Raftopoulos, Eszter Balla, Mária Dudás, Lena Rós Ásmundsdóttir, Guðrún Sigmundsdóttir, Guðrún Svanborg Hauksdóttir, Thorolfur Gudnason, Aoife Colgan, Brendan Crowley, Sinéad Saab, Paola Stefanelli, Anna Carannante, Patrizia Parodi, Gatis Pakarna, Raina Nikiforova, Antra Bormane, Elina Dimina, Monique Perrin, Tamir Abdelrahman, Joël Mossong, Jean-Claude Schmit, Friedrich Mühlschlegel, Christopher Barbara, Francesca Mifsud, Alje Van Dam, Birgit Van Benthem, Maartje Visser, Ineke Linde, Hilde Kløvstad, Dominique Caugant, Beata Młynarczyk-Bonikowska, Jacinta Azevedo, Maria-José Borrego, Marina Lurdes Ramos Nascimento, Peter Pavlik, Irena Klavs, Andreja Murnik, Samo Jeverica, Tanja Kustec, Julio Vázquez Moreno, Asuncion Diaz, Raquel Abad, Inga Velicko, Magnus Unemo, Helen Fifer, Jill Shepherd, Lynsey PattersonBackground: Genomic surveillance using quality-assured whole-genome sequencing (WGS) together with epidemiological and antimicrobial resistance (AMR) data is essential to characterise the circulating Neisseria gonorrhoeae lineages and their association to patient groups (defined by demographic and epidemiological factors). In 2013, the European gonococcal population was characterised genomically for the first time. We describe the European gonococcal population in 2018 and identify emerging or vanishing lineages associated with AMR and epidemiological characteristics of patients, to elucidate recent changes in AMR and gonorrhoea epidemiology in Europe. Methods: We did WGS on 2375 gonococcal isolates from 2018 (mainly Sept 1-Nov 30) in 26 EU and EEA countries. Molecular typing and AMR determinants were extracted from quality-checked genomic data. Association analyses identified links between genomic lineages, AMR, and epidemiological data. Findings: Azithromycin-resistant N gonorrhoeae (8·0% [191/2375] in 2018) is rising in Europe due to the introduction or emergence and subsequent expansion of a novel N gonorrhoeae multi-antigen sequence typing (NG-MAST) genogroup, G12302 (132 [5·6%] of 2375; N gonorrhoeae sequence typing for antimicrobial resistance [NG-STAR] clonal complex [CC]168/63), carrying a mosaic mtrR promoter and mtrD sequence and found in 24 countries in 2018. CC63 was associated with pharyngeal infections in men who have sex with men. Susceptibility to ceftriaxone and cefixime is increasing, as the resistance-associated lineage, NG-MAST G1407 (51 [2·1%] of 2375), is progressively vanishing since 2009-10. Interpretation: Enhanced gonococcal AMR surveillance is imperative worldwide. WGS, linked to epidemiological and AMR data, is essential to elucidate the dynamics in gonorrhoea epidemiology and gonococcal populations as well as to predict AMR. When feasible, WGS should supplement the national and international AMR surveillance programmes to elucidate AMR changes over time. In the EU and EEA, increasing low-level azithromycin resistance could threaten the recommended ceftriaxone-azithromycin dual therapy, and an evidence-based clinical azithromycin resistance breakpoint is needed. Nevertheless, increasing ceftriaxone susceptibility, declining cefixime resistance, and absence of known resistance mutations for new treatments (zoliflodacin, gepotidacin) are promising.This study was supported by the European Centre for Disease Prevention and Control, the Centre for Genomic Pathogen Surveillance, the Li Ka Shing Foundation (Big Data Institute, University of Oxford), the Wellcome Genome Campus, the Foundation for Medical Research at Örebro University Hospital, and grants from Wellcome (098051 and 099202). LSB was funded by Conselleria de Sanitat Universal i Salut Pública, Generalitat Valenciana (Plan GenT CDEI-06/20-B), Valencia, Spain, and Ministry of Science, Innovation and Universities (PID2020–120113RA-I00), Spain, at the time of analysing and writing this manuscript.info:eu-repo/semantics/publishedVersio

Implications of smallholder livelihoods for scaling oil palm agroforestry in Brazilian Eastern Amazon

Despite its economic potential, oil palm has earned a bad reputation for its negative environmental and mixed social impacts. In the Eastern Brazilian Amazon, oil palm production has expanded rapidly over the past decade. Meanwhile, in the same landscape, Agroforestry Systems (AFS) have been widely promoted as a solution to achieve economic growth coupled with socio-environmental benefits for smallholders. Our study seeks to shed light on pathways for reconciling oil palm production with farmer livelihoods. We randomly sampled 198 smallholders in the municipality of Tomé-Açu, Pará, Brazil. Our findings point to diverse livelihoods and widely varying yearly income, averaging USD 13,100. Different types of AFS were adopted by 85 % of farmers in our sample, in contrast to just 11 % adopting monocrop oil palm. Almost one third of on-farm income and produced food came from AFS, which mostly contributed to achieving life aspirations. Key indicators on financial and physical capitals (technology level, housing, total income and land size) indicate economic success as most households achieved intermediate levels of living standard. We conclude that family farmers can successfully adopt AFS and that oil palm producers overall are less likely to have low economic success. An overwhelming majority of farmers would like to expand their AFS, but very few would choose to include oil palm. We argue that the expansion of oil palm-based AFS hinges on the extent to which the prevailing business model and technological package can provide sufficient resources to reduce family farmer risks, including: credit conditions, plantation size, species selection and systems suited to farmer livelihood objectives and constraints

The Use of DRIS for Nutritional Diagnosis in Oil Palm in the State of Pará

ABSTRACT: The oil palm crop has expanded significantly in the state of Pará, which has not been followed in a proportional manner by studies aiming at increasing yield through plant nutrition. The objective of this study was to evaluate general and specific norms of the Diagnosis and Recommendation Integrated System (DRIS) for genetic materials of oil palm (African and interspecific hybrid) at two ages (young and adult plants) and evaluate possible deficiencies in fertilization and soil correction practices. The DRIS norms were composed of means, standard deviations, and coefficients of variation of bivariate, specific, and general relationships among nutrients of 144 leaf samples. The DRIS norms specific for genetic material did not differ from the general norms; however, a large number of differences were found between specific bivariate relationships for age groups, among themselves, and in relation to the general norms. The regression analysis between the nutritional balance index and yield were better explained when age groups were discriminated. In the young plants, the number of cases of stands with deficiencies followed the order Ca > Fe > B > S > Mn > K > Mg = Cu > Zn > N > P; and for adults, this order was Ca > Mn > Zn > Fe > S = B > N = Cu > K > Mg > P. The DRIS norms can be utilized in diagnostics regardless of genetic material; however, they must be specified for the age of the plant. Most of the stands showed deficiency in Ca and micronutrients, coinciding with the least used nutrients in oil palm crops in the state of Pará, as well as emphasizing the need for soil liming

Soil potentially toxic element contents in an area under different land uses in the Brazilian Amazon

Soil pollution with potentially toxic elements (PTE) from incipient basic sanitation, dumps and industrial activities developed in the Amazon has been of international interest due to health and environmental issues. This study aimed to evaluate the concentration of PTE in five adjacent land occupations (a dump, a alumina refinery area and three residential centers) in the municipality of Barcarena, Amazon Region, Brazil. In a total area of 912 ha, 274 soil samples were collected at a depth of 0–0.2 m. Afterwards, the concentrations of As, Ba, Pb, Co, Cu, Cr, Hg, Ni and Zn were determined. The results were explored using descriptive and multivariate statistics, as well as geostatistical. Considering the data by location, maximum concentrations exceeding the prevention values of Brazilian soils were found for Cu, Ni and Zn in Dump (148; 42.8 and 356 mg kg−1), for Cu and Hg in Bom Futuro (333 and 1.99 mg kg−1) and for Cu in Itupanema (91.2 mg kg−1). Cu, Hg, Pb and Zn were grouped in the same principal component and showed the highest similarity measure in the cluster analysis. The interpolation point maps of the two principal components and of the individual concentrations of the PTEs showed the area of influence of the dump as the main reason for the increase in soil contamination. These results show the need for public policies aimed at the proper disposal of solid waste, in order to promote the reduction of pollutants in the soil, health and well-being for the local population, and also the environmental quality of the study area

The Use of DRIS for Nutritional Diagnosis in Oil Palm in the State of Pará

ABSTRACT The oil palm crop has expanded significantly in the state of Pará, which has not been followed in a proportional manner by studies aiming at increasing yield through plant nutrition. The objective of this study was to evaluate general and specific norms of the Diagnosis and Recommendation Integrated System (DRIS) for genetic materials of oil palm (African and interspecific hybrid) at two ages (young and adult plants) and evaluate possible deficiencies in fertilization and soil correction practices. The DRIS norms were composed of means, standard deviations, and coefficients of variation of bivariate, specific, and general relationships among nutrients of 144 leaf samples. The DRIS norms specific for genetic material did not differ from the general norms; however, a large number of differences were found between specific bivariate relationships for age groups, among themselves, and in relation to the general norms. The regression analysis between the nutritional balance index and yield were better explained when age groups were discriminated. In the young plants, the number of cases of stands with deficiencies followed the order Ca > Fe > B > S > Mn > K > Mg = Cu > Zn > N > P; and for adults, this order was Ca > Mn > Zn > Fe > S = B > N = Cu > K > Mg > P. The DRIS norms can be utilized in diagnostics regardless of genetic material; however, they must be specified for the age of the plant. Most of the stands showed deficiency in Ca and micronutrients, coinciding with the least used nutrients in oil palm crops in the state of Pará, as well as emphasizing the need for soil liming

Implementation of a Brazilian Cardioprotective Nutritional (BALANCE) Program for improvement on quality of diet and secondary prevention of cardiovascular events: A randomized, multicenter trial

Background: Appropriate dietary recommendations represent a key part of secondary prevention in cardiovascular disease (CVD). We evaluated the effectiveness of the implementation of a nutritional program on quality of diet, cardiovascular events, and death in patients with established CVD. Methods: In this open-label, multicenter trial conducted in 35 sites in Brazil, we randomly assigned (1:1) patients aged 45 years or older to receive either the BALANCE Program (experimental group) or conventional nutrition advice (control group). The BALANCE Program included a unique nutritional education strategy to implement recommendations from guidelines, adapted to the use of affordable and regional foods. Adherence to diet was evaluated by the modified Alternative Healthy Eating Index. The primary end point was a composite of all-cause mortality, cardiovascular death, cardiac arrest, myocardial infarction, stroke, myocardial revascularization, amputation, or hospitalization for unstable angina. Secondary end points included biochemical and anthropometric data, and blood pressure levels. Results: From March 5, 2013, to Abril 7, 2015, a total of 2534 eligible patients were randomly assigned to either the BALANCE Program group (n = 1,266) or the control group (n = 1,268) and were followed up for a median of 3.5 years. In total, 235 (9.3%) participants had been lost to follow-up. After 3 years of follow-up, mean modified Alternative Healthy Eating Index (scale 0-70) was only slightly higher in the BALANCE group versus the control group (26.2 ± 8.4 vs 24.7 ± 8.6, P <.01), mainly due to a 0.5-serving/d greater intake of fruits and of vegetables in the BALANCE group. Primary end point events occurred in 236 participants (18.8%) in the BALANCE group and in 207 participants (16.4%) in the control group (hazard ratio, 1.15; 95% CI 0.95-1.38; P =.15). Secondary end points did not differ between groups after follow-up. Conclusions: The BALANCE Program only slightly improved adherence to a healthy diet in patients with established CVD and had no significant effect on the incidence of cardiovascular events or death. © 2019 The Author