Genetic diversity of Mycobacterium avium isolates recovered from clinical samples and from the environment: molecular characterization for diagnostic purposes

Isolation of Mycobacterium avium complex (MAC) organisms from clinical samples may occur in patients without clinical disease, making the interpretation of results difficult. The clinical relevance of MAC isolates from different types of clinical samples (n = 47) from 39 patients in different sections of a hospital was assessed by comparison with environmental isolates (n = 17) from the hospital. Various methods for identification and typing (commercial probes, phenotypic characteristics, PCR for detection of IS1245 and IS901, sequencing of the hsp65 gene, and pulsed-field gel electrophoresis) were evaluated. The same strain was found in all the environmental isolates, 21 out of 23 (91.3%) of the isolates cultured from urine samples, and 5 out of 19 (26.3%) isolates from respiratory specimens. This strain did not cause disease in the patients. Testing best characterized the strain as M. avium subsp. hominissuis, with the unusual feature that 81.4% of these isolates lacked the IS1245 element. Contamination of certain clinical samples with an environmental strain was the most likely event; therefore, characterization of the environmental mycobacteria present in health care facilities should be performed to discard false-positive isolations in nonsterile samples, mainly urine samples. Molecular techniques applied in this study demonstrated their usefulness for this purpose.

Bifidobacterium breve UCC2003 metabolises the human milk oligosaccharides lacto-N-tetraose and lacto-N-neo-tetraose through overlapping, yet distinct pathways

In this study, we demonstrate that the prototype B. breve strain UCC2003 possesses specific metabolic pathways for the utilisation of lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNnT), which represent the central moieties of Type I and Type II human milk oligosaccharides (HMOs), respectively. Using a combination of experimental approaches, the enzymatic machinery involved in the metabolism of LNT and LNnT was identified and characterised. Homologs of the key genetic loci involved in the utilisation of these HMO substrates were identified in B. breve, B. bifidum, B. longum subsp. infantis and B. longum subsp. longum using bioinformatic analyses, and were shown to be variably present among other members of the Bifidobacterium genus, with a distinct pattern of conservation among human-associated bifidobacterial species.

Développement de stratégies et d'outils analytiques novateurs pour la détection de vaches atteintes de paratuberculose

La paratuberculose bovine est une maladie causée par la mycobactérie Mycobacterium avium subsp. paratuberculosis (MAP). Elle est responsable d’énormes pertes économiques dans le monde. En effet, cette maladie provoque la diminution de la production laitière chez les vaches ainsi qu’un état de fatigue général en raison d’une entérite chronique chez les sujets atteints. Des indices mettent également en évidence le potentiel zoonotique de MAP et malheureusement aucun traitement n’est connu à ce jour. Ainsi, les stratégies actuelles pour contrer la maladie dans les troupeaux reposent plutôt sur des actions préventives. Actuellement, le diagnostic de la paratuberculose reste difficile et la prévalence de la maladie est probablement sous-estimée dans les troupeaux en raison de la faible sensibilité des tests diagnostiques. Dans l’optique de développer une nouvelle méthode diagnostique pour la paratuberculose, ce projet de recherche s’est établi en deux étapes : la mise en place d’un système de diagnostic robuste des animaux par les méthodes de dépistage traditionnelles, incluant une étude comparative de l’efficacité de trousses commerciales, et finalement l’étude de la prolifération cellulaire spécifique des lymphocytes comme d’une épreuve diagnostique pour la maladie. Ainsi, la comparaison des trousses commerciales a démontré un écart d’efficacité qui a permis d’établir de nouvelles recommandations pour l’analyse des animaux ainsi que l’amélioration du diagnostic de la paratuberculose dans les troupeaux. Concernant le développement d’une méthode de diagnostique basée sur la prolifération lymphocytaire, de nombreuses difficultés techniques ont entravé le bon déroulement du projet mais ces travaux montrent la possibilité de caractériser de manière plus complète les différents types lymphocytaires par cytométrie de flux chez le bovin laitier.

Descripción del análisis microbológico realizado mediante maldi-tof en muestras de la fundación santa fe de Bogotá.

Introducción: La rápida detección e identificación bacteriana es fundamental para el manejo de los pacientes críticos que presentan una patología infecciosa, esto requiere de métodos rápidos para el inicio de un correcto tratamiento. En Colombia se usan pruebas microbiología convencional. No hay estudios de espectrofotometría de masas en análisis de muestras de pacientes críticos en Colombia. Objetivo general: Describir la experiencia del análisis microbiológico mediante la tecnología MALDI-TOF MS en muestras tomadas en la Fundación Santa Fe de Bogotá. Materiales y Métodos: Entre junio y julio de 2013, se analizaron 147 aislamientos bacterianos de muestras clínicas, las cuales fueron procesadas previamente por medio del sistema VITEK II. Los aislamientos correspondieron a 88 hemocultivos (60%), 28 urocultivos (19%), y otros cultivos 31 (21%). Resultados: Se obtuvieron 147 aislamientos con identificación adecuada a nivel de género y/o especie así: en el 88.4% (130 muestras) a nivel de género y especie, con una concordancia del 100% comparado con el sistema VITEK II. El porcentaje de identificación fue de 66% en el grupo de bacilos gram negativos no fermentadores, 96% en enterobacterias, 100% en gérmenes fastidiosos, 92% en cocos gram positivos, 100% bacilos gram negativos móviles y 100% en levaduras. No se encontró ninguna concordancia en bacilos gram positivos y gérmenes del genero Aggregatibacter. Conclusiones: El MALDI-TOF es una prueba rápida para la identificación microbiológica de género y especie que concuerda con los resultados obtenidos de manera convencional. Faltan estudios para hacer del MALDI-TOF MS la prueba oro en identificación de gérmenes.

The flora and vegetation in an area of the Caatinga in Taperuaba, Sobral, Ceará state, Brazil

The Caatinga, covering about 800.000 km2, is the predominant vegetation type of the semi-arid region of Brazil. The Caatinga biome comprises several phytophysiognomies and floristic compositions, with many endemic species, especially in Fabaceae, Cactaceae, Euphorbiaceae, Bignoniaceae e Combretaceae. Despite considerable advances, the Brazilian semi-arid needs more studies and inventories of biodiversity, especially the Ceará state. On the basis of these considerations, the present study aims to identify the flora and vegetation, in order to characterize the phytophysiognomy in an area of the Caatinga, in locality of Taperuaba, municipality of Sobral, Ceará, Brazil. Field work was conducted in March 2015 and 2016 respectively, in three transects. The life-forms were established in accordance of Raunkiaer´s system. The floristic list is composed of 87 species, distributed in 66 genera and 36 families. The flora comprises 22 Brazilian endemic species. The most representative family was Fabaceae with 15 species, followed by Malvaceae (7) Convolvulaceae (6), Euphorbiaceae (5) and Poaceae (5). The biological spectrum had a high proportion of therophytes (29,9%), chamaephytes (29,9%) and phanerophytes (26,4%). In the area were identified two phytophysiognomies: outcrops communities highlighting succulent phanerophytes (Pilosocereus chrysostele (Vaupel) Byles & G.D. Rowley subsp. cearensis P.J. Braun & Esteves and P. gounellei (F.A.C. Weber) Byles & Rowley), chamaephytes (Encholirium spectabile Mart. ex Schult. & Schult. f. and Lepidaploa chalybaea (Mart. ex DC.) H. Rob.) and therophytes (Mitracarpus baturitensis Sucre), mixed with communities including small trees and shrubs on deeper soil, composed of Cereus jamacaru DC., a succulent phanerophyte, and many woody phanerophytes, such as Cordia oncocalyx Allemão, Crateva trapia L., Mimosa caesalpiniifolia Benth., M. tenuiflora (Willd.) Poir., Poincianella bracteosa (Tul.) L.P. Queiroz and P. pyramidalis (Tul.) L.P. Queiroz.

Effects of nitrogen level on purslane antioxidant activity.

The high antioxidant activity of purslane, Portulaca oleracea L., gives it a high nutritional and functional value. The commercial production of purslane has increased in Portugal, making it necessary to know the effects of inputs, mainly nitrogen, on the antioxidant activity. The main goal of this study was to evaluate the influence of nitrogen application on purslane antioxidant activity. The experiment was carried out with for treatments: 30, 60 and 90 kg/ha of nitrogen. Plants of golden-leaf purslane were grown in Styrofoam-boxes filled with substrate and fertigated two times per week, over four weeks with ammonium nitrate solution (16.9% NO3-N and 16.7 NH4+-N). The increase in the nitrogen level decreased the water-soluble proteins content. However the ascorbate, phenols content as well as antioxidant activity measured by FRAP method was not affected by nitrogen level. Plants shoot antioxidant activity, measured by DPPH method decreased significantly in the treatment with 90 kg N/ha (26.20 g/g gallic acid). On the other hand, plant shoot antioxidant activity mediated by peroxidases was higher in treatment 30 kg N/ha (0.459 µmol min-1/mg prot.). Application of 60 kg N/ha allowed a vigorous plant growth without disturb its antioxidants and conservation properties.

Antioxidant and anti-inflammatory potential of Lavandula spp.

Lavenders have been used in folk medicine as disinfectant, expectorant, analgesic, anti-spasmodic, laxative and stimulant. Some species are endemic of Iberian Peninsula and often found in the Portuguese montado, including Lavandula stoechas subsp. luisieri and Lavandula pedunculata. The investigation of the antioxidant and anti-inflammatory potential of the Portuguese montado flora is very poor and restricted to a few botanical families, and their biological activities are mainly attributed to the essential oils. So, it is crucial to know the properties of Lavandula EOs, contributing for animal health and the valorisation of Portuguese montado flora. The aim of this study was to evaluate chemical composition, antioxidant properties and screening anti-inflammatory potential of EOs and extracts of Lavandula stoechas L. subsps. luisieri Rozeira, Lavandula pedunculata (Mill.) Cav. subsp. pedunculata and Lavandula viridis L’Hér, wild grown in the south of Portugal.

Séries de vegetação prioritárias para a conservação no centro e sul de Portugal continental

Como corolário de vários estudos geobotânicos realizados, no sudoeste Ibérico, no âmbito do seminário internacional Gestão e Conservação da Biodiversidade VIII, apresentou-se uma conferência sobre as principais séries de vegetação prioritárias para a conservação no centro e sul de Portugal continental. Assim, neste trabalho, após uma breve introdução apresenta-se uma súmula da caracterização biofísica deste território e um conjunto de séries singulares destas superfícies. Assim, selecionaram-se as séries de vegetação potencial climatófilas, edafoxerófilas e edafo-higrófilas que possuem, do ponto de vista corológico ou florístico, maior originalidade. Dentro destas, com elevado valor conservacionista, destacam-se quatro séries de sobreirais de Quercus suber, seis carvalhais de folha marcescente (três de Quercus broteroi, uma de Quercus canariensis, uma de Quercus marianaica e uma de Quercus pyrenaica), seis de zimbrais (quatro de Juniperus turbinata, uma de Juniperus navicularis e uma de Juniperus oxycedrus subsp. lagunae), um carrascal arbóreo (Quercus rivasmartinezii), um zambujal (Olea europaea var. sylvestris), um salgueiral (Salix salviifolia subsp. australis) e duas comunidades arborescentes de cursos de água torrenciais (Nerium oleander e Flueggea tinctoria). Porém, algumas destas séries encerram o seu volar, particularmente nas suas etapas seriais, essencialmente devido à presença de plantas endémicas e/ou com estatuto de proteção legal. Neste sentido, salienta-se ainda ao nível da série, a sinecologia, a sincorologia e a sinestrutura. Contudo, a revisão da dinâmica serial e os trabalhos de campo efectuados recentemente, permitiram a identificação de uma nova associação vegetal descrita no presente trabalho, no âmbito das séries de Aro neglecti-Querco suberis sigmetum. Finalmente expõem-se alguns dados relativos ao estado de conservação das etapas seriais mais próximas do clímax, apresentando-se sugestões que visam a recuperação e valorização destes habitats boscosos, tendo em vista a criação e consolidação de uma estratégia nacional de conservação.

Análisis de la dimensión fractal del género Quercus en el sur de Italia

En estudios anteriores propusimos un nuevo método para el estudio del género Quercus (Musarella et al., 2013), baseado en la dimensión fractal (DF). En este trabajo analizamos la DF del género Quercus en el sur de Italia, para ello utilizamos hojas de árboles pertenecientes a Q. robur subsp. brutia, Q. cerris, Q. congesta, Q. crenata, Q. ilex, Q. suber, Q. virginiana. De cada árbol se toman hojas de cada uno de los puntos cardinales para complejiada de la estructura morfológica de las hojas. Este análisis extrae información sobre los caracteres fenotípicos de las hojas utilizadas, tales como el número y morfologia de los nervios, ángulos nervios secundarios con principal, contorno de hojas, aspecto reticulado de la hoja etc. En nuestro análisis, no se han detectado diferencias significativas entre la DF en cada una de la orientaciones y la DF global para cada una de las especies. En este trabajo corroboramos estudios anteriores realizados por los autores, en los que se proponía una DF < 1,6 para Quercus esclerófilos y DF entre dos especies sea cero o su cociente sea uno, el grado de parentesco entre las dos especies es del 100%; DFA - DFB = 0; DFA/DFB = 1, la especie Ay B son iguales; por ello cuanto menor es la diferencia o bien cuanto más se acerque el cociente a 1, mayor es la semejanza entre las especies. Si este cociente tiene un valor alejado de 1 como ocurre entre vfvi/vfsu>2, las especies Q. virginiana y Q. suber están muy distantes entre sí. Además, la realización del Test de Rango Múltiple, que es un procedimiento de comparación para determinar cuáles medias son significativamente diferentes unas de otras, confirma los resultados obtenidos de la forma anteriormente expuesta. Conto et al. (2007) ponen de manifiesto el origen hibridógeno de Q. crenata, y según el análisis molecular existe una mayor similitud genética entre Q. crenata y Q. cerris, que entre Q. crenata y Q. suber. Los DF de Q. crenata 1,868; Q. cerris 1,677 y Q. suber 0,932; siendo DFQsu 0,745 y DFQsu = 1,8, lo que significa que existe gran diferencia fenotípica (genética) entre los parentales, se presenta una mayor semejanza entre Q. crenata y Q. cerris que entre Q. crenata y Q. suber, ya que la diferencia DFQcr-DFQce = 0,191 y DFQcr/DFQce = 1,1, por lo que tienen un fuerte grado de semejanza, mientras que DFQcr-DFQsu = 0,936 y DFQcr/DFQsu > 2, lo que pone de manifiesto las fuertes diferencias fenotípicas entre el híbrido y el parental.

Phytosociology of the remaining xerophytic woodland associated to an environmental gradient at the banks of the São Francisco river - Petrolina, Pernambuco, Brazil1

Floristic and phytosociological surveys were carried out for 12 months in the Embrapa-SPSB, Petrolina, Pernambuco, Brazil. A transect was laid on starting at the river bank extending for 790 m away from the river and divided into 140 10 × 10 m contiguous plots. In each plot, all standing plants, alive or dead, with stem diameter at soil level ? 3 cm and total height ? 1 m were sampled. Along this transect, an elevation range of 9.40 m was registered and five topographical environments were identified: riverside (MR), dike (D), floodable depression (DI), boundary terrace (TL) - all of them belonging to the fluvial terrace with Fluvic Neosol and Haplic Cambisol both silty textured eutrophic soils - and the inlander tableland (TS), with medium sandy-textured Red-Yellow Argisols. Fourty-eight species/morphospecies, distributed into 39 genera and 21 families, were identified. Four phytogeoenvironments (MR, D + TL, DI + TL, and TS) were registered based on environmental variations and floristic similarities among plots using cluster analyses. The MR environment showed the largest total density, total basal area, maximum and medium heights and maximum diameter. Moreover, it had 8.1% of plants with heights above 8 m against 0.6% for D + TL, 0.2% for DI + TL, and 0% for TS. The species with the largest importance value were Inga vera subsp. affinis (DC.) T.D. Pennington in MR, Mimosa bimucronata Kunth in D + TL and DI + TL and M. tenuiflora (Willd.) Poir. in TS.

Extracción, identificación y prueba microbiológica del agar extraído de Gracilaria fortissima dawson (rhodophyta, gigartinales, gracilariaceae) (ING)

The red seaweed Gracilaria fortissima colected in the caribean coast of Costa Rica, was studied for the extraction, identification and microbiological performance of the agar contend of this plant, as well as the mineral contend. The research was done focused on the agar quality included pH, % extraction, geling point, fusion point and gel strength, as well as infrared analysis and the performance as a microbiological culture of bacteria and fungus and compared with commercial agar from BDH chemicals.

Essential oils and hydrolates as potential tools for integrated prevention of bacterial diseases in plants

The present work aims to investigate the potential use of natural substances against bacterial plant pathogens. Microdilution tests were therefore carried out in vitro to identify the minimum inhibitory and bactericidal concentrations (MIC and MBC) of several EOs and Hys against selected bacterial pathogens. Commercial products based on a mixture of EOs were in addition assayed with macrodilution experiments against Erwinia amylovora (Ea-causal agent of fire blight). Subsequently, using selected EOs, Hys, and commercial products, ex vivo tests on disease incidence and Ea population dynamics were carried out; the latter experiment was followed by SEM observations. In addition, in vivo resistance induction test was carried out against bacterial leaf of tomato, caused by Xanthomonas vesicatoria (Xv). EOs and Hys showed high bactericidal activity in vitro (MBC <0.1 and <10% for the most active EOs and Hys: Origanum compactum and Thymus vulgaris EOs and Citrus aurantium var. amara Hy, respectively), but they were not effective ex vivo, while resulted very active when used in vivo as resistance inducers in the tomato-Xv pathosystem (relative protection >40%). Differently, commercial products resulted active in all tests, but not as resistance inducers against Xv. An open field trial with commercial products was carried out on strawberry plants naturally infected with Xanthomonas fragariae; the results showed discrete relative protection, concerning that provided by the conventional products based on copper; mostly, the disease severity reduction on those plants treated with EOs commercial products was significant when disease severity resulted high. The papers already published described in the present work investigate (1)the activity of Hys in comparison to EOs with respect to their active volatile content; (2) the potential use of EOs and Hys in cultural heritage; for the restoration of paintings; (3) the induction of resistance caused by plasma-activated water-based root treatments.