Efectos de la diversificación ganadera de las explotaciones agrícolas en la adopción de innovaciones

publishedTomo I . Sección: Sistemas Ganaderos-Economía y Gestión. Sesión: Sostenibilidad. Ponencia nº 3

High submicellar liquid chromatography

Surfactant addition above the critical micellar concentration (CMC), in reversed-phase liquid chromatography (RPLC), was proposed as a way to modify the selectivity and analysis time, giving rise to a chromatographic mode called micellar liquid chromatography (MLC). However, solutions containing only surfactant are too weak and yield poor peak shape. This was remediated by the addition of a small amount of organic solvent. To preserve the existence of micelles, in MLC high contents of organic solvent are avoided. Nevertheless, there is no reason to neglect the potentiality of mobile phases containing a surfactant above its CMC in water and a high organic solvent content (without micelles). This chromatographic mode has been called high submicellar liquid chromatography (HSLC). Several reported procedures show that the combination of stronger elution strength, larger selectivity and improved peak shape, with respect to MLC and conventional RPLC, makes HSLC a promising chromatographic mode to achieve in practical times separations of compounds unresolved or highly retained with other RPLC modes. Some insights on the interactions that occur inside the chromatographic column, the modification of the stationary and mobile phases, retention modeling, and chromatographic performance in HSLC are here offered, in comparison to MLC and conventional RPLC

Spread of blaCTX-M-14 is driven mainly by IncK plasmids disseminated among Escherichia coli phylogroups A, B1, and D in Spain

et al.Since its first description in 2000, CTX-M-14 has become one of the most widespread extended-spectrum β-lactamases in Spain. In the present Escherichia coli multilevel population genetic study involving the characterization of phylogroups, clones, plasmids, and genetic platforms, 61 isolates from 16 hospitalized patients and 40 outpatients and healthy volunteers recovered from 2000 to 2005 were analyzed. Clonal relatedness (XbaI pulsed-field gel electrophoresis [PFGE] type, phylogenetic group, multilocus sequence type [MLST]) was established by standard methods. Analysis of transferred plasmids (I-CeuI; S1 nuclease; restriction fragment length polymorphism analysis; and analysis of RNA interference, replicase, and relaxase) was performed by PCR, sequencing, and hybridization. The genetic environment of blaCTX-M-14 was characterized by PCR on the basis of known associated structures (ISEcp1, IS903, ISCR1). The isolates were mainly recovered from patients in the community (73.8%; 45/61) with urinary tract infections (62.2%; 28/45). They were clonally unrelated by PFGE and corresponded to phylogenetic groups A (36.1%), D (34.4%), and B1 (29.5%). MLST revealed a high degree of sequence type (ST) diversity among phylogroup D isolates and the overrepresentation of the ST10 complex among phylogroup A isolates and ST359/ST155 among phylogroup B1 isolates. Two variants of blaCTX-M-14 previously designated blaCTX-M-14a (n = 59/61) and bla CTX-M-14b (n = 2/61) were detected. blaCTX-M-14a was associated with either ISEcp1 within IncK plasmids (n = 27), ISCR1 linked to an IncHI2 plasmid (n = 1), or ISCR1 linked to IncI-like plasmids (n = 3). The blaCTX-M-14b identified was associated with an ISCR1 element located in an IncHI2 plasmid (n = 1) or with ISEcp1 located in IncK (n = 1). The CTX-M-14-producing E. coli isolates in our geographic area are frequent causes of community-acquired urinary tract infections. The increase in the incidence of such isolates is mostly due to the dissemination of IncK plasmids among E. coli isolates of phylogroups A, B1, and D. Copyright © 2009, American Society for Microbiology. All Rights Reserved.A.V. is supported by CIBERESP Network for Biomedical Research in Epidemiology and Public Health (Instituto Carlos III, Spanish Ministry of Science and Innovation). Work by the HRYC group was funded by research grants from the European Commission (grants LSHM-CT-2005-018705, LSHM-CT-2009-223031, and KBBE-2008-2B-227258) and the Spanish Ministry of Health and Innovation (CB06/ 02/0053 and FIS 08/624). Work in the FdlC laboratory was supported by grants from the European Commission (grant LSHM-CT-2005_019023); the Spanish Ministry of Education (grant BFU2008- 00995/BMC); and the RETICS Research Network, Instituto de Salud Carlos III, Spanish Ministry of Health (grant RD06/0008/1012).Peer Reviewe

Plasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET), a new method for plasmid reconstruction from whole genome sequences

This is an open-access article distributed under the terms of the Creative Commons Attribution License.Bacterial whole genome sequence (WGS) methods are rapidly overtaking classical sequence analysis. Many bacterial sequencing projects focus on mobilome changes, since macroevolutionary events, such as the acquisition or loss of mobile genetic elements, mainly plasmids, play essential roles in adaptive evolution. Existing WGS analysis protocols do not assort contigs between plasmids and the main chromosome, thus hampering full analysis of plasmid sequences. We developed a method (called plasmid constellation networks or PLACNET) that identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets. The workflow of the method is based on three types of data: assembly information (including scaffold links and coverage), comparison to reference sequences and plasmid-diagnostic sequence features. The resulting network is pruned by expert analysis, to eliminate confounding data, and implemented in a Cytoscape-based graphic representation. To demonstrate PLACNET sensitivity and efficacy, the plasmidome of the Escherichia coli lineage ST131 was analyzed. ST131 is a globally spread clonal group of extraintestinal pathogenic E. coli (ExPEC), comprising different sublineages with ability to acquire and spread antibiotic resistance and virulence genes via plasmids. Results show that plasmids flux in the evolution of this lineage, which is wide open for plasmid exchange. MOBF12/IncF plasmids were pervasive, adding just by themselves more than 350 protein families to the ST131 pangenome. Nearly 50% of the most frequent γ–proteobacterial plasmid groups were found to be present in our limited sample of ten analyzed ST131 genomes, which represent the main ST131 sublineages.Work was financed by the Spanish Ministry of Economy and Competitivity (BFU2011-26608 to FdlC, FIS-PI09/01273 and AGL2013-47852-R to JB and FIS-PI12-01581 and CB06/02/0053 to TMC), by the European Seventh Framework Program (612146/FP7-ICT-2013-10 to FdlC and 282004/FP7-HEALTH-2011-2.3.1-2 to FdlC and TMC); by Red Española de Investigación en Patología­ Infecciosa (REIPI RD06/0008/1018-1016) to JB, by Consellería de Cultura, Educación e Ordenación Universitaria, Xunta de Galicia and European Regional Development Fund, ERDF (CN2012/303 and EM2014/001) to JB and by the regional government of Madrid (PROMPT-S2010/BMD2414) to TMC. We are also grateful to the Spanish Network for the Study of Plasmids and Extrachromosomal Elements (REDEEX) for funding cooperation among Spanish microbiologists working on the biology of MGEs (Spanish Ministry of Science and Innovation BFU2011-14145-E).Peer Reviewe

Co-diversification of Enterococcus faecium Core Genomes and PBP5: Evidences of pbp5 Horizontal Transfer

Ampicillin resistance has greatly contributed to the recent dramatic increase of a cluster of human adapted Enterococcus faecium lineages (ST17, ST18, and ST78) in hospital-based infections. Changes in the chromosomal pbp5 gene have been associated with different levels of ampicillin susceptibility, leading to protein variants (designated as PBP5 C-types to keep the nomenclature used in previous works) with diverse degrees of reduction in penicillin affinity. Our goal was to use a comparative genomics approach to evaluate the relationship between the diversity of PBP5 among E. faecium isolates of different phylogenomic groups as well as to assess the pbp5 transferability among isolates of disparate clonal lineages. The analyses of 78 selected E. faecium strains as well as published E. faecium genomes, suggested that the diversity of pbp5 mirrors the phylogenomic diversification of E. faecium. The presence of identical PBP5 C-types as well as similar pbp5 genetic environments in different E. faecium lineages and clones from quite different geographical and environmental origin was also documented and would indicate their horizontal gene transfer among E. faecium populations. This was supported by experimental assays showing transfer of large (≈180–280 kb) chromosomal genetic platforms containing pbp5 alleles, ponA (transglycosilase) and other metabolic and adaptive features, from E. faecium donor isolates to suitable E. faecium recipient strains. Mutation profile analysis of PBP5 from available genomes and strains from this study suggests that the spread of PBP5 C-types might have occurred even in the absence of a significant ampicillin resistance phenotype. In summary, genetic platforms containing pbp5 sequences were stably maintained in particular E. faecium lineages, but were also able to be transferred among E. faecium clones of different origins, emphasizing the growing risk of further spread of ampicillin resistance in this nosocomial pathogen.This work was supported by Fundação para a Ciência e a Tecnologia (FCT)/Ministério da Educacão e Ciência (MEC) through national funds and co-financed by Fundo Europeu de Desenvolvimento Regional (FEDER) under the Partnership Agreement PT2020 with the reference UID/ MULTI/04378/2013–POCI/01/0145/FERDER/007728 to CN and LP, Instituto de Salud Carlos III (Plan Estatal de I+D+i 2013-2016), Grant PI12-01581 and PI15-01307 to TMC and CIBERESP (CB06/02/0053) to FB, European Commission, Seventh Framework Program (EVOTARFP7-HEALTH-282004) to TMC and FB and the Regional Government of Madrid in Spain (PROMPT- S2010/BMD2414) to FB and TMC.Peer reviewedPeer Reviewe

Public Health Risks of Enterobacterial Isolates Producing Extended-Spectrum β-Lactamases or AmpC β-Lactamases in Food and Food-Producing Animals: An EU Perspective of Epidemiology, Analytical Methods, Risk Factors, and Control Options

The blaESBL and blaAmpC genes are spread by plasmid-mediated integrons, insertion sequences, and transposons, some of which are homologous in food animals and humans. Cephalosporin usage in animal production is an important risk factor; restricting such use would be an effective control optio

The impact of host metapopulation structure on the population genetics of colonizing bacteria

Many key bacterial pathogens are frequently carried asymptomatically, and the emergence and spread of these opportunistic pathogens can be driven, or mitigated, via demographic changes within the host population. These inter-host transmission dynamics combine with basic evolutionary parameters such as rates of mutation and recombination, population size and selection, to shape the genetic diversity within bacterial populations. Whilst many studies have focused on how molecular processes underpin bacterial population structure, the impact of host migration and the connectivity of the local populations has received far less attention. A stochastic neutral model incorporating heightened local transmission has been previously shown to fit closely with genetic data for several bacterial species. However, this model did not incorporate transmission limiting population stratification, nor the possibility of migration of strains between subpopulations, which we address here by presenting an extended model. We study the consequences of migration in terms of shared genetic variation and show by simulation that the previously used summary statistic, the allelic mismatch distribution, can be insensitive to even large changes in microepidemic and migration rates. Using likelihood-free inference with genotype network topological summaries we fit a simpler model to commensal and hospital samples from the common nosocomial pathogens Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis and Enterococcus faecium. Only the hospital data for E. faecium display clearly marked deviations from the model predictions which may be attributable to its adaptation to the hospital environment

Global dissemination of a multidrug resistant Escherichia coli clone.

Escherichia coli sequence type 131 (ST131) is a globally disseminated, multidrug resistant (MDR) clone responsible for a high proportion of urinary tract and bloodstream infections. The rapid emergence and successful spread of E. coli ST131 is strongly associated with several factors, including resistance to fluoroquinolones, high virulence gene content, the possession of the type 1 fimbriae FimH30 allele, and the production of the CTX-M-15 extended spectrum β-lactamase (ESBL). Here, we used genome sequencing to examine the molecular epidemiology of a collection of E. coli ST131 strains isolated from six distinct geographical locations across the world spanning 2000-2011. The global phylogeny of E. coli ST131, determined from whole-genome sequence data, revealed a single lineage of E. coli ST131 distinct from other extraintestinal E. coli strains within the B2 phylogroup. Three closely related E. coli ST131 sublineages were identified, with little association to geographic origin. The majority of single-nucleotide variants associated with each of the sublineages were due to recombination in regions adjacent to mobile genetic elements (MGEs). The most prevalent sublineage of ST131 strains was characterized by fluoroquinolone resistance, and a distinct virulence factor and MGE profile. Four different variants of the CTX-M ESBL-resistance gene were identified in our ST131 strains, with acquisition of CTX-M-15 representing a defining feature of a discrete but geographically dispersed ST131 sublineage. This study confirms the global dispersal of a single E. coli ST131 clone and demonstrates the role of MGEs and recombination in the evolution of this important MDR pathogen

Collaboration for social innovation in the agri-food system in Latin America and the Caribbean

Aim of study: This study reviews the state of the art of collaboration for social innovation in food and rural systems. The analysis focuses on cooperation by farms and agro-industry companies. The purpose is to identify not only the state of the art of this research topic but also the main authors, the countries where these studies are conducted and the dynamics of research networks in relation to these topics. Area of study: Latin America and the Caribbean (LAC). Material and methods: The Web of Science database was used to search for articles containing the terms ‘cooperation’, ‘networks’, ‘innovation’, ‘social’, ‘rural’ and ‘LAC’. Using VOSviewer network creation and analysis software, maps of citations, co-authorship, co-citations and co-occurrence of key-words were created and analysed. Content analysis was then performed. Finally, the research areas that the authors of the analysed articles consider to be of interest for future research were identified. Main results: The results reveal that researchers from Latin America and other regions, especially Europe and the English-speaking world, are showing a growing interest in collaborative systems for development and social innovation in LAC. Research highlights: The analysis enables further progress to be made in identifying the main drivers of collaboration in the LAC rural sector. These main drivers include social innovation, knowledge, sustainable management and social capital

The Complete Genome Sequence of Escherichia coli EC958: A High Quality Reference Sequence for the Globally Disseminated Multidrug Resistant E. coli O25b:H4-ST131 Clone

Escherichia coli ST131 is now recognised as a leading contributor to urinary tract and bloodstream infections in both community and clinical settings. Here we present the complete, annotated genome of E. coli EC958, which was isolated from the urine of a patient presenting with a urinary tract infection in the Northwest region of England and represents the most well characterised ST131 strain. Sequencing was carried out using the Pacific Biosciences platform, which provided sufficient depth and read-length to produce a complete genome without the need for other technologies. The discovery of spurious contigs within the assembly that correspond to site-specific inversions in the tail fibre regions of prophages demonstrates the potential for this technology to reveal dynamic evolutionary mechanisms. E. coli EC958 belongs to the major subgroup of ST131 strains that produce the CTX-M-15 extended spectrum β-lactamase, are fluoroquinolone resistant and encode the fimH30 type 1 fimbrial adhesin. This subgroup includes the Indian strain NA114 and the North American strain JJ1886. A comparison of the genomes of EC958, JJ1886 and NA114 revealed that differences in the arrangement of genomic islands, prophages and other repetitive elements in the NA114 genome are not biologically relevant and are due to misassembly. The availability of a high quality uropathogenic E. coli ST131 genome provides a reference for understanding this multidrug resistant pathogen and will facilitate novel functional, comparative and clinical studies of the E. coli ST131 clonal lineage