Phenotypic, molecular characterization, antimicrobial susceptibility and draft genome sequence of Corynebacterium argentoratense strains isolated from clinical samples

During a 12-year period we isolated five Corynebacterium argentoratense strains identified by phenotypic methods, including the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) and 16S rRNA gene sequencing. In addition, antimicrobial susceptibility was determined, and genome sequencing for the detection of antibiotic resistance genes was performed. The organisms were isolated from blood and throat cultures and could be identified by all methods used. All strains were resistant to cotrimoxazole, and resistance to β-lactams was partly present. Two strains were resistant to erythromycin and clindamycin. The draft genome sequences of theses isolates revealed the presence of the erm(X) resistance gene that is embedded in the genetic structure of the transposable element Tn5423. Although rarely reported as a human pathogen, C. argentoratense can be involved in bacteraemia and probably in other infections. Our results also show that horizontal transfer of genes responsible for antibiotic resistance is occurring in this species.Supported in part by the Gerencia Regional de Salud, Junta de Castilla y León, Spain (research project GRS 698/A/2011

Isolation of Neisseria meningitidis strains with increase of penicillin minimal inhibitory concentrations

We report the isolation and characterization of ten strains showing an increase in the minimal inhibitory concentrations to penicillin (MICs > 0·1 μg/ml), and describe the epidemiological, clinical and microbiological features. The susceptibility of 3432 meningococcal strains isolated from patients in the recent epidemic wave (1978–86) in Spain, to several antimicrobial agents used in the treatment and chemoprophylaxis of meningococcal infection has been tested. Most were resistant to sulphadiazine but sensitive to other antibiotics. The possible existence of a new pattern of behaviour of meningococcal to penicillin is discussed

Dynamics of a Sporadic Nosocomial Acinetobacter calcoaceticus – Acinetobacter baumannii Complex Population

Our objective was to improve current knowledge of sporadic (Spo) nosocomial Acinetobactercalcoaceticus-Acinetobacter baumannii (Acb) complex populations, and thus better understand the epidemiology of Spo and endemoepidemic (EE) strains. Between 1999 and 2010, 133 isolates of Spo Acb complex were obtained from a single hospital. Species were identified by gyrB-PCR, and via gyrB- and rpoB-sequencing. Clonal analysis was undertaken using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. Susceptibility to antimicrobial agents was determined by microdilution and E-tests. Carbapenemase genes were detected by PCR. One hundred and one PFGE types were detected. A. baumannii was the most common (67/101 PFGE types), followed by Acinetobacter pittii (22/101), Acinetobacter lactucae (6/101), and Acinetobacter calcoaceticus (2/101). gyrB, rpoB1, and rpoB2 sequencing returned 49, 13, and 16 novel sequences, respectively. Sixty-three sequence types (STs) (38 new STs and 66 new alleles) were detected; the most common were ST2 (29/133 isolates) and ST132 (14/133). Twenty-six OXA-51 allelic variants were detected, nine of which were novel. The PFGE types were generally susceptible (88/101) to all the tested antimicrobials; 3/101 were carbapenem-resistant due to the presence of the genetic structure ISAba2-blaOXA-58-like-ISAba3, and 2/101 were multidrug-resistant. It can be concluded that the examined Spo Acb complex population was mainly composed of A. baumannii. Many different clones were detected (with ST2 clearly dominant), all largely susceptible to antimicrobials; multidrug resistance was rare. In contrast, a previously examined EE Acb population was composed of just four expanding, multidrug-resistant A. baumannii clones -ST2, ST3, ST15, and ST80-

Capsule Switching among C:2b:P1.2,5 Meningococcal Epidemic Strains after Mass Immunization Campaign, Spain

A mass immunization campaign for 18-month to 19-year-olds was undertaken in Spain in 1996–1997 because of an epidemic of serogroup C meningococcal disease associated with a C:2b:P1.2,5 strain belonging to the A4 lineage. Surveillance for the “capsule-switching” phenomenon producing B:2b:P1.2,5 isolates was undertaken. Of 2,975 meningococci characterized, B:2b:P1.2,5 and B:2b:P1.2 antigenic combinations were found in 18 isolates; 15 meningococci were defined as serogroup B belonging to the A4 lineage

La estructura sísmica de la corteza de la Zona de Ossa Morena y su interpretación geológica

El experimento de sísmica de reflexión profunda IBERSEIS ha proporcionado una imagen de la corteza del Orógeno Varisco en el sudoeste de Iberia. Este artículo se centra en la descripción de la corteza de la Zona de Ossa Morena (OMZ), que está claramente dividida en una corteza superior, con reflectividad de buzamiento al NE, y una corteza inferior de pobre reflectividad. Las estructuras geológicas cartografiadas en superficie se correlacionan bien con la reflectividad de la corteza superior, y en la imagen sísmica se ven enraizar en la corteza media. Ésta está constituida por un cuerpo muy reflectivo, interpretado como una gran intrusión de rocas básicas. La imagen de las suturas que limitan la OMZ muestra el carácter fuertemente transpresivo de la colisión orogénica varisca registrada en el sudoeste de Iberia. La Moho actual es plana y, en consecuencia, no se observa la raíz del orógeno

Biochar versus hydrochar as growth media constituents for ornamental plant cultivation

[EN] Biochar and hydrochar have been proposed as novel materials for providing soilless growth media. However, much more knowledge is required before reliable advice can be given on the use of these materials for this purpose. Depending on the material and the technology applied (pyrolysis or hydrothermal carbonization), phytotoxicity and greenhouse gas emissions have been found for certain chars. In this study, our aim was to assess the feasibility of three chars as substrate constituents. We compared two biochars, one from forest waste and the other from olive mill waste, and a hydrochar from forest waste. We studied how chars affected substrate characteristics, plant performance, water economy and respiratory CO2 emission. Substrates containing biochar from forest waste showed the best characteristics, with good air/water relationships and adequate electrical conductivity. Those with biochar from olive mill waste were highly saline and, consequently, low quality. The substrates with hydrochar retained too much water and were poorly aerated, presenting high CO2 concentrations due to high respiratory activity. Plants performed well only when grown in substrates containing a maximum of 25 % biochar from forest waste or hydrochar. After analyzing the char characteristics, we concluded that biochar from forest waste could be safely used as a substrate constituent and is environmentally friendly when applied due to its low salinity and low CO2 emission. However, biochar from olive mill waste and hydrochar need to be improved before they can be used as substrate constituents.This study was funded by the Polytechnic University of Valencia (Projects on New Multidisciplinary Research; PAID-05-12). We thank Molly Marcus-McBride for supervising the English.Fornes Sebastiá, F.; Belda Navarro, RM. (2018). Biochar versus hydrochar as growth media constituents for ornamental plant cultivation. Scientia Agricola (Online). 75(4):304-312. https://doi.org/10.1590/1678-992X-2017-0062S304312754Abad, M., Noguera, P., & Burés, S. (2001). National inventory of organic wastes for use as growing media for ornamental potted plant production: case study in Spain. Bioresource Technology, 77(2), 197-200. doi:10.1016/s0960-8524(00)00152-8Bargmann, I., Martens, R., Rillig, M. C., Kruse, A., & Kücke, M. (2013). Hydrochar amendment promotes microbial immobilization of mineral nitrogen. Journal of Plant Nutrition and Soil Science, 177(1), 59-67. doi:10.1002/jpln.201300154Bargmann, I., Rillig, M. C., Buss, W., Kruse, A., & Kuecke, M. (2013). Hydrochar and Biochar Effects on Germination of Spring Barley. Journal of Agronomy and Crop Science, 199(5), 360-373. doi:10.1111/jac.12024Bedussi, F., Zaccheo, P., & Crippa, L. (2015). Pattern of pore water nutrients in planted and non-planted soilless substrates as affected by the addition of biochars from wood gasification. Biology and Fertility of Soils, 51(5), 625-635. doi:10.1007/s00374-015-1011-6Belda, R. M., Lidón, A., & Fornes, F. (2016). Biochars and hydrochars as substrate constituents for soilless growth of myrtle and mastic. Industrial Crops and Products, 94, 132-142. doi:10.1016/j.indcrop.2016.08.024Costello, R. C., & Sullivan, D. M. (2013). Determining the pH Buffering Capacity of Compost Via Titration with Dilute Sulfuric Acid. Waste and Biomass Valorization, 5(3), 505-513. doi:10.1007/s12649-013-9279-yFernandes, C., & Corá, J. E. (2004). Bulk density and relationship air/water of horticultural substrate. Scientia Agricola, 61(4), 446-450. doi:10.1590/s0103-90162004000400015Fornes, F., Belda, R. M., Carrión, C., Noguera, V., García-Agustín, P., & Abad, M. (2007). Pre-conditioning ornamental plants to drought by means of saline water irrigation as related to salinity tolerance. Scientia Horticulturae, 113(1), 52-59. doi:10.1016/j.scienta.2007.01.008Fornes, F., Belda, R. M., & Lidón, A. (2015). Analysis of two biochars and one hydrochar from different feedstock: focus set on environmental, nutritional and horticultural considerations. Journal of Cleaner Production, 86, 40-48. doi:10.1016/j.jclepro.2014.08.057Fornes, F., & Belda, R. M. (2017). Acidification with nitric acid improves chemical characteristics and reduces phytotoxicity of alkaline chars. Journal of Environmental Management, 191, 237-243. doi:10.1016/j.jenvman.2017.01.026Fornes, F., Belda, R. M., Fernández de Córdova, P., & Cebolla-Cornejo, J. (2017). Assessment of biochar and hydrochar as minor to major constituents of growing media for containerized tomato production. Journal of the Science of Food and Agriculture, 97(11), 3675-3684. doi:10.1002/jsfa.8227Fornes, F., Carrión, C., García-de-la-Fuente, R., Puchades, R., & Abad, M. (2010). Leaching composted lignocellulosic wastes to prepare container media: Feasibility and environmental concerns. Journal of Environmental Management, 91(8), 1747-1755. doi:10.1016/j.jenvman.2010.03.017GARCIADELAFUENTE, R., CARRION, C., BOTELLA, S., FORNES, F., NOGUERA, V., & ABAD, M. (2007). Biological oxidation of elemental sulphur added to three composts from different feedstocks to reduce their pH for horticultural purposes. Bioresource Technology, 98(18), 3561-3569. doi:10.1016/j.biortech.2006.11.008Genty, B., Briantais, J.-M., & Baker, N. R. (1989). The relationship between the quantum yield of photosynthetic electron transport and quenching of chlorophyll fluorescence. Biochimica et Biophysica Acta (BBA) - General Subjects, 990(1), 87-92. doi:10.1016/s0304-4165(89)80016-9Hoitink, H. A. J., Stone, A. G., & Han, D. Y. (1997). Suppression of Plant Diseases by Composts. HortScience, 32(2), 184-187. doi:10.21273/hortsci.32.2.184Libra, J. A., Ro, K. S., Kammann, C., Funke, A., Berge, N. D., Neubauer, Y., … Emmerich, K.-H. (2011). Hydrothermal carbonization of biomass residuals: a comparative review of the chemistry, processes and applications of wet and dry pyrolysis. Biofuels, 2(1), 71-106. doi:10.4155/bfs.10.81Mazuela, P., Salas, M. del C., & Urrestarazu, M. (2005). Vegetable Waste Compost as Substrate for Melon. Communications in Soil Science and Plant Analysis, 36(11-12), 1557-1572. doi:10.1081/css-200059054Méndez, A., Paz-Ferreiro, J., Gil, E., & Gascó, G. (2015). The effect of paper sludge and biochar addition on brown peat and coir based growing media properties. Scientia Horticulturae, 193, 225-230. doi:10.1016/j.scienta.2015.07.032Nieto, A., Gascó, G., Paz-Ferreiro, J., Fernández, J. M., Plaza, C., & Méndez, A. (2016). The effect of pruning waste and biochar addition on brown peat based growing media properties. Scientia Horticulturae, 199, 142-148. doi:10.1016/j.scienta.2015.12.012Sáez, J. A., Belda, R. M., Bernal, M. P., & Fornes, F. (2016). Biochar improves agro-environmental aspects of pig slurry compost as a substrate for crops with energy and remediation uses. Industrial Crops and Products, 94, 97-106. doi:10.1016/j.indcrop.2016.08.035Smith, B. R., Fisher, P. R., & Argo, W. R. (2004). Growth and Pigment Content of Container-grown Impatiens and Petunia in Relation to Root Substrate pH and Applied Micronutrient Concentration. HortScience, 39(6), 1421-1425. doi:10.21273/hortsci.39.6.1421Solaiman, Z. M., Murphy, D. V., & Abbott, L. K. (2011). Biochars influence seed germination and early growth of seedlings. Plant and Soil, 353(1-2), 273-287. doi:10.1007/s11104-011-1031-4Steiner, C., & Harttung, T. (2014). Biochar as a growing media additive and peat substitute. Solid Earth, 5(2), 995-999. doi:10.5194/se-5-995-2014Tian, Y., Sun, X., Li, S., Wang, H., Wang, L., Cao, J., & Zhang, L. (2012). Biochar made from green waste as peat substitute in growth media for Calathea rotundifola cv. Fasciata. Scientia Horticulturae, 143, 15-18. doi:10.1016/j.scienta.2012.05.018Vaughn, S. F., Eller, F. J., Evangelista, R. L., Moser, B. R., Lee, E., Wagner, R. E., & Peterson, S. C. (2015). Evaluation of biochar-anaerobic potato digestate mixtures as renewable components of horticultural potting media. Industrial Crops and Products, 65, 467-471. doi:10.1016/j.indcrop.2014.10.04

Deep-sequencing reveals broad subtype-specific HCV resistance mutations associated with treatment failure

A percentage of hepatitis C virus (HCV)-infected patients fail direct acting antiviral (DAA)-based treatment regimens, often because of drug resistance-associated substitutions (RAS). The aim of this study was to characterize the resistance profile of a large cohort of patients failing DAA-based treatments, and investigate the relationship between HCV subtype and failure, as an aid to optimizing management of these patients. A new, standardized HCV-RAS testing protocol based on deep sequencing was designed and applied to 220 previously subtyped samples from patients failing DAA treatment, collected in 39 Spanish hospitals. The majority had received DAA-based interferon (IFN) a-free regimens; 79% had failed sofosbuvir-containing therapy. Genomic regions encoding the nonstructural protein (NS) 3, NS5A, and NS5B (DAA target regions) were analyzed using subtype-specific primers. Viral subtype distribution was as follows: genotype (G) 1, 62.7%; G3a, 21.4%; G4d, 12.3%; G2, 1.8%; and mixed infections 1.8%. Overall, 88.6% of patients carried at least 1 RAS, and 19% carried RAS at frequencies below 20% in the mutant spectrum. There were no differences in RAS selection between treatments with and without ribavirin. Regardless of the treatment received, each HCV subtype showed specific types of RAS. Of note, no RAS were detected in the target proteins of 18.6% of patients failing treatment, and 30.4% of patients had RAS in proteins that were not targets of the inhibitors they received. HCV patients failing DAA therapy showed a high diversity of RAS. Ribavirin use did not influence the type or number of RAS at failure. The subtype-specific pattern of RAS emergence underscores the importance of accurate HCV subtyping. The frequency of “extra-target” RAS suggests the need for RAS screening in all three DAA target regions

Gaia Focused Product Release: Radial velocity time series of long-period variables

The third Gaia Data Release (DR3) provided photometric time series of more than 2 million long-period variable (LPV) candidates. Anticipating the publication of full radial-velocity (RV) in DR4, this Focused Product Release (FPR) provides RV time series for a selection of LPVs with high-quality observations. We describe the production and content of the Gaia catalog of LPV RV time series, and the methods used to compute variability parameters published in the Gaia FPR. Starting from the DR3 LPVs catalog, we applied filters to construct a sample of sources with high-quality RV measurements. We modeled their RV and photometric time series to derive their periods and amplitudes, and further refined the sample by requiring compatibility between the RV period and at least one of the $G$, $G_{\rm BP}$, or $G_{\rm RP}$ photometric periods. The catalog includes RV time series and variability parameters for 9\,614 sources in the magnitude range $6\lesssim G/{\rm mag}\lesssim 14$, including a flagged top-quality subsample of 6\,093 stars whose RV periods are fully compatible with the values derived from the $G$, $G_{\rm BP}$, and $G_{\rm RP}$ photometric time series. The RV time series contain a mean of 24 measurements per source taken unevenly over a duration of about three years. We identify the great most sources (88%) as genuine LPVs, with about half of them showing a pulsation period and the other half displaying a long secondary period. The remaining 12% consists of candidate ellipsoidal binaries. Quality checks against RVs available in the literature show excellent agreement. We provide illustrative examples and cautionary remarks. The publication of RV time series for almost 10\,000 LPVs constitutes, by far, the largest such database available to date in the literature. The availability of simultaneous photometric measurements gives a unique added value to the Gaia catalog (abridged)Comment: 36 pages, 38 figure