Innovation and sectoral linkages in the agri-food system in the Valencian Community

This paper aims to analyze the innovative effort of the agri-food system (AFS) in the Valencian Autonomous Community (VC), Spain, estimating the intensity of innovation in each subsector of the AFS. The analysis distinguishes between the direct and indirect (or induced) innovation intensities incorporated by the acquisition of inputs from other subsectors produced in the VC or in the rest of Spain. The methodology employed is based on the input-output framework combined with data of technological innovation in enterprises. This methodology provides the novelty of been applied to a region the VC and not to a country as it is usually done. The results show that the weight of intersectoral flows in the total innovation effort of the AFS is significant with marked differences between primary and food industry. In most activities, embodied knowledge in inputs purchased from Spain is greater than embodied knowledge of inputs produced inside the region.Authors would like to thank the Ministry of Science and innovation for its support for this paper (Project AGRINNOVA; reference: AGL2009-13303-C02-02).García Alvarez-Coque, JM.; Alba ., MF.; López-García Usach, T. (2012). Innovation and sectoral linkages in the agri-food system in the Valencian Community. SPANISH JOURNAL OF AGRICULTURAL RESEARCH. REVISTA DE INVESTIGACION AGRARIA. 10(1):18-28. https://doi.org/10.5424/sjar/2012101-207-11S1828101McKENZIE, D., & O’NIONS, R. K. (1991). Partial Melt Distributions from Inversion of Rare Earth Element Concentrations. Journal of Petrology, 32(5), 1021-1091. doi:10.1093/petrology/32.5.102

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

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

Altered Ecology of the Respiratory Tract Microbiome and Nosocomial Pneumonia

10 p.Nosocomial pneumonia is one of the most frequent infections in critical patients. It is primarily associated with mechanical ventilation leading to severe illness, high mortality, and prolonged hospitalization. The risk of mortality has increased over time due to the rise in multidrug-resistant (MDR) bacterial infections, which represent a global public health threat. Respiratory tract microbiome (RTM) research is growing, and recent studies suggest that a healthy RTM positively stimulates the immune system and, like the gut microbiome, can protect against pathogen infection through colonization resistance (CR). Physiological conditions of critical patients and interventions as antibiotics administration and mechanical ventilation dramatically alter the RTM, leading to dysbiosis. The dysbiosis of the RTM of ICU patients favors the colonization by opportunistic and resistant pathogens that can be part of the microbiota or acquired from the hospital environments (biotic or built ones). Despite recent evidence demonstrating the significance of RTM in nosocomial infections, most of the host-RTM interactions remain unknown. In this context, we present our perspective regarding research in RTM altered ecology in the clinical environment, particularly as a risk for acquisition of nosocomial pneumonia. We also reflect on the gaps in the field and suggest future research directions. Moreover, expected microbiome-based interventions together with the tools to study the RTM highlighting the "omics" approaches are discussed.Comunidad de MadridFundación Ramón ArecesInstituto de Salud Carlos IIIFondo Europeo de Desarrollo RegionalCIBERON

Innovative firms and the urban/rural divide: the case of agro-food system

Purpose - This paper aims to analyse the capacity of rural and urban spaces to promote innovation in the agro-food firms. The purpose is to determine if the rural/urban division affects the innovative behaviour of agriculture, food processing and food distribution firms. Design/methodology/approach - Business data have been obtained for over 2,000 firms based in the Valencia region, Spain. Out of them, over 200 declared to have taken part in R&D&i activities, mainly in partnership with public support institutions. The database supplies data of micro and small enterprises, which have been typically underestimated in the Spanish Survey on Technological Innovation in Enterprises. The database also makes it possible to identify the main location of agro-food business, and the territory is divided in Local Labour Systems (LLS). LIS were in turn classified as rural or urban according to alternative criteria (OECD, national legislation). A logit model has been used in the analyses. Findings - The location of enterprises according to the rural/urban divide does not appear relevant concerning innovation, although businesses orientated to the primary sector seem less innovative. Co-op businesses appear to be more innovative. Originality/value - The paper offers an approach of innovation in the agro-food traditionally considered as a non-innovative system. It explores how territory affects innovation using data from firms.Fearne, A.; García Alvarez-Coque, JM.; Usach Mercedes, TL.; Garcia, S. (2013). Innovative firms and the urban/rural divide: the case of agro-food system. Management Decision. 51(6):1293-1310. doi:10.1108/MD-12-2011-0482S12931310516Acosta, M., Coronado, D., & Toribio, M. R. (2011). The use of scientific knowledge by Spanish agrifood firms. Food Policy, 36(4), 507-516. doi:10.1016/j.foodpol.2011.04.003Alba, M., Mas, F. and García‐Alvarez‐Coque, J.M. (2011), “New firm creation and innovation: industrial patterns and inter‐sectoral linkages”,International Entrepreneurship and Management Journal, DOI 10.1007/s11365‐011‐0210‐3.Alfranca, O., Rama, R., & von Tunzelmann, N. (2004). Innovation spells in the multinational agri-food sector. Technovation, 24(8), 599-614. doi:10.1016/s0166-4972(02)00129-3Atance, I., Martínez Jávega, M. T., Pujol, R., & Urruela, J. (2011). La población rural en España: un enfoque a escala municipal. Economía Agraria y Recursos Naturales, 10(1), 35. doi:10.7201/earn.2010.01.03Audretsch, D. B. (2003). Innovation And Spatial Externalities. International Regional Science Review, 26(2), 167-174. doi:10.1177/0160017602250973Boix, R. and Galletto, V. (2008), “Marshallian Industrial districts in Spain”,Scienze Regionali, Vol. 7 No. 3, pp. 29‐52.Capitanio, F., Coppola, A., & Pascucci, S. (2009). Indications for drivers of innovation in the food sector. British Food Journal, 111(8), 820-838. doi:10.1108/00070700910980946Dahlander, L., & Gann, D. M. (2010). How open is innovation? Research Policy, 39(6), 699-709. doi:10.1016/j.respol.2010.01.013Garcia Martinez, M. (2000). Innovation in the Spanish food & drink industry. The International Food and Agribusiness Management Review, 3(2), 155-176. doi:10.1016/s1096-7508(00)00033-1Martinez, M. G., & Burns, J. (1999). Sources of technological development in the spanish food and drink industry. A ?supplier-dominated? industry? Agribusiness, 15(4), 431-448. doi:10.1002/(sici)1520-6297(199923)15:43.0.co;2-0Giannakas, K., & Fulton, M. (2005). Process Innovation Activity in a Mixed Oligopoly: The Role of Cooperatives. American Journal of Agricultural Economics, 87(2), 406-422. doi:10.1111/j.1467-8276.2005.00731.xGiusti, A., & Grassini, L. (2007). Local Labor Systems and Agricultural Activities: The Case of Tuscany. International Advances in Economic Research, 13(4), 475-487. doi:10.1007/s11294-007-9112-0Hansen, M. and Birkinshaw, J.M. (2007), “The innovation value chain”,Harvard Business Review, Vol. 85 No. 6, pp. 121‐131.Hauknes, J., & Knell, M. (2009). Embodied knowledge and sectoral linkages: An input–output approach to the interaction of high- and low-tech industries. Research Policy, 38(3), 459-469. doi:10.1016/j.respol.2008.10.012Henderson, J. (2002), “Building rural economy with high‐growth entrepreneurs”,Economic Review, December, pp. 45‐70.Kalantaridis, C., & Bika, Z. (2006). Local Embeddedness and Rural Entrepreneurship: Case-Study Evidence from Cumbria, England. Environment and Planning A: Economy and Space, 38(8), 1561-1579. doi:10.1068/a3834Kühne, B., Vanhonacker, F., Gellynck, X., & Verbeke, W. (2010). Innovation in traditional food products in Europe: Do sector innovation activities match consumers’ acceptance? Food Quality and Preference, 21(6), 629-638. doi:10.1016/j.foodqual.2010.03.013Mas-Verdú, F., Wensley, A., Alba, M., & García Álvarez-Coque, J. M. (2011). How much does KIBS contribute to the generation and diffusion of innovation? Service Business, 5(3), 195-212. doi:10.1007/s11628-011-0110-1Mohnen, P., Mairesse, J. and Dagenais, M. (2007), “Innovativity: a comparison across seven European countries”,Economics of Innovation and New Technologies, Vol. 15 Nos 4/5, pp. 391‐413.Papaconstantinou, G., Sakurai, N., & Wyckoff, A. (1998). Domestic and international product-embodied R&D diffusion. Research Policy, 27(3), 301-314. doi:10.1016/s0048-7333(98)00044-4Pezzini, M. (2001). Rural Policy Lessons from OECD Countries. International Regional Science Review, 24(1), 134-145. doi:10.1177/016001701761013024Pischke, J.-S., & Velling, J. (1997). Employment Effects of Immigration to Germany: An Analysis Based on Local Labor Markets. Review of Economics and Statistics, 79(4), 594-604. doi:10.1162/003465397557178Porter, M. (2003). The Economic Performance of Regions. Regional Studies, 37(6-7), 549-578. doi:10.1080/0034340032000108688Salavou, H., & Avlonitis, G. (2008). Product innovativeness and performance: a focus on SMEs. Management Decision, 46(7), 969-985. doi:10.1108/00251740810890168Topel, R. H. (1986). Local Labor Markets. Journal of Political Economy, 94(3, Part 2), S111-S143. doi:10.1086/261401Verhees, F. J. H. M., & Meulenberg, M. T. G. (2004). Market Orientation, Innovativeness, Product Innovation, and Performance in Small Firms. Journal of Small Business Management, 42(2), 134-154. doi:10.1111/j.1540-627x.2004.00102.xWeaver, R. D. (2008). Collaborative pull innovation: origins and adoption in the new economy. Agribusiness, 24(3), 388-402. doi:10.1002/agr.20165Webber, D., Curry, N., & Plumridge, A. (2009). Business Productivity and Area Productivity in Rural England. Regional Studies, 43(5), 661-675. doi:10.1080/0034340070187415

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